https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&feedformat=atom&user=JenniferVendettiNCBO Wiki - User contributions [en]2026-06-05T12:13:18ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13152BioPortal Help2026-01-13T21:21:59Z<p>JenniferVendetti: /* BioPortal */</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
<br />
=== BioPortal ===<br />
Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Goncalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. ''Nucleic Acids Research'', Volume 53, Issue W1, 7 July 2025, Pages W84-W94, https://academic.oup.com/nar/article/53/W1/W84/8129374.<br />
<br />
=== Ontology Recommender ===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13151BioPortal Help2026-01-13T21:21:06Z<p>JenniferVendetti: /* How to cite NCBO and BioPortal */ Reorder sub-sections with most relevant at the top</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
<br />
=== BioPortal ===<br />
Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Goncalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. ''Nucleic Acids Research'', Volume 53, Issue W1, 7 July 2025, Pages W84-W94, https://academic.oup.com/nar/article/53/W1/W84/8129374<br />
<br />
=== Ontology Recommender ===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13150BioPortal Help2026-01-13T21:19:46Z<p>JenniferVendetti: /* BioPortal */ Update cite to new NAR paper</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
=== Ontology Recommender ===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
<br />
Jennifer Vendetti, Nomi L Harris, Michael V Dorf, Alex Skrenchuk, J Harry Caufield, Rafael S Goncalves, John B Graybeal, Harshad Hegde, Timothy Redmond, Christopher J Mungall, Mark A Musen. BioPortal: an open community resource for sharing, searching, and utilizing biomedical ontologies. ''Nucleic Acids Research'', Volume 53, Issue W1, 7 July 2025, Pages W84-W94, https://academic.oup.com/nar/article/53/W1/W84/8129374<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13149BioPortal Help2026-01-13T21:14:26Z<p>JenniferVendetti: /* NCBO Ontology Recommender */ Remove reference to "NCBO", which is now defunct</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
=== Ontology Recommender ===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13148Ontology Change Requests2025-06-13T23:38:17Z<p>JenniferVendetti: </p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is manually enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
* Editing a class definition<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== Enable change requests for your ontology ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.<br />
<br />
== Request a change ==<br />
You must be logged in to request changes in BioPortal. If you don't have an account, you can create one here: https://bioportal.bioontology.org/accounts/new.<br />
<br />
Once logged in, navigate to your ontology in BioPortal, and click on the Classes tab.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13146BioPortal Help2025-01-07T21:19:24Z<p>JenniferVendetti: /* Ontology visibility options */</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13145BioPortal Help2025-01-07T21:15:59Z<p>JenniferVendetti: /* Projects */ Fix button name to reflect current UI</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters can control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13144BioPortal Help2025-01-07T21:12:25Z<p>JenniferVendetti: /* Homepage */ Fix broken nav links</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Ontologies|browse the library]] of ontologies<br />
* [[#Search|search for a term]] across multiple ontologies<br />
* [[#Mappings|browse mappings]] between terms in different ontologies<br />
* [[#Recommender|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator|annotate text]] with terms from ontologies<br />
* [[#Projects|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal website is also available through the BioPortal REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters can control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13143BioPortal Help2025-01-07T21:10:25Z<p>JenniferVendetti: /* Ontologies */ Improve flow of sections and add headings for readability</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing biomedical ontologies ====<br />
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.<br />
<br />
==== Finding an ontology ====<br />
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.<br />
<br />
==== Ontology popularity ====<br />
<br />
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.<br />
<br />
==== Submitting an ontology ====<br />
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.<br />
<br />
==== Ontology visibility options ====<br />
Submitters can control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Programmatic access ====<br />
<br />
To access ontologies programmatically, see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Available Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13142BioPortal Help2025-01-07T20:18:47Z<p>JenniferVendetti: /* Browsing */ Remove outdated descriptions of how licensed and private ontologies are accessed</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing ====<br />
Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''quickly find a specific ontology''', type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can also narrow the results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by criteria such as category (domain), group, format, or other attributes.<br />
<br />
To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. When uploading an ontology to BioPortal, submitters can choose from three visibility designations:<br />
<br />
* '''Public:''' The ontology and its metadata are fully visible and accessible to all users.<br />
* '''Private:''' The ontology is restricted and only accessible to user accounts explicitly granted access by the submitter.<br />
* '''Summary-only''': Only metadata about the ontology is displayed, while the ontology’s terms are unavailable. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.<br />
<br />
==== Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13141BioPortal Help2025-01-07T20:04:41Z<p>JenniferVendetti: /* Browsing */</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing ====<br />
Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''quickly find a specific ontology''', type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can also narrow the results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by criteria such as category (domain), group, format, or other attributes.<br />
<br />
To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13140BioPortal Help2025-01-07T20:03:34Z<p>JenniferVendetti: /* Browsing */ Improve language describing faceted browsing</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing ====<br />
Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''quickly find a specific ontology''', type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can also narrow the results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by criteria such as “category” (domain), “group,” format, or other attributes.<br />
<br />
To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13139BioPortal Help2025-01-07T19:52:20Z<p>JenniferVendetti: /* Browsing */ Remove section about subscribing to updates, which we no longer have</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing ====<br />
Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the input field located at the top-center of the page with placeholder text of "Search...". You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13138BioPortal Help2025-01-07T19:48:51Z<p>JenniferVendetti: Drop the Tab designation for the navigation pages (no longer a tabbed interface)</p>
<hr />
<div>== UI primary navigation pages ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing ====<br />
Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the input field located at the top-center of the page with placeholder text of "Search...". You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13137BioPortal Help2025-01-07T19:41:55Z<p>JenniferVendetti: /* Browse Tab */ Change TOC items to better reflect the current UI. Use sentence case capitalization.</p>
<hr />
<div>== User Interface ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Ontologies ===<br />
<br />
==== Browsing ====<br />
Browse our library of biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the input field located at the top-center of the page with placeholder text of "Search...". You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13136BioPortal Help2025-01-07T19:34:04Z<p>JenniferVendetti: Use more modern spelling of homepage</p>
<hr />
<div>== User Interface ==<br />
=== Homepage ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the input field located at the top-center of the page with placeholder text of "Search...". You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Ontology Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic Access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13135BioPortal Help2025-01-07T19:23:46Z<p>JenniferVendetti: /* Browse Tab */ correct the name of the search field to reflect the current Browse page UI</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the input field located at the top-center of the page with placeholder text of "Search...". You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Ontology Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic Access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13134BioPortal Help2024-09-27T22:35:39Z<p>JenniferVendetti: /* Submitting an ontology */ add a minimum requirements section</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
==== Ontology Popularity ====<br />
<br />
Ontologies on the Browse tab are ordered based on their popularity, which is measured using the number of Google Analytics page views from the previous month. The more page views an ontology receives, the higher it appears on the list.<br />
<br />
==== Programmatic Access ====<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
<br />
==== Minimum requirements ====<br />
<br />
===== BioPortal account =====<br />
You need to create an account on BioPortal if you don’t already have one:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
This will allow you to manage submissions and updates to your ontology.<br />
<br />
===== Ontology formats =====<br />
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:<br />
<br />
* [https://www.w3.org/OWL/ OWL] (Web Ontology Language)<br />
* [https://obofoundry.org/ OBO] (Open Biomedical Ontologies)<br />
* [https://www.w3.org/2004/02/skos/ SKOS] (Simple Knowledge Organization System)<br />
<br />
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our [[SKOSSupport|SKOS Support]] page.<br />
<br />
===== File size =====<br />
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).<br />
<br />
===== Metadata =====<br />
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:<br />
<br />
* '''Name:''' the human-readable name of your ontology<br />
* '''Acronym:''' a unique identifier used to refer to your ontology in the system. The acronym is typically a short abbreviation of the ontology’s full name, often made up of capitalized initials or key terms. For example: '''SNOMEDCT''' (Systematized Nomenclature of Medicine – Clinical Terms). The acronym must be 17 characters or fewer.<br />
* '''Administrators:''' one or more BioPortal user accounts with administrative access to your ontology<br />
* '''Description:''' a short summary describing the purpose and scope of the ontology<br />
* '''Contact information:''' the names and email addresses of the ontology’s authors or maintainers<br />
* '''Format:''' the format of your ontology source file (OWL, OBO, or SKOS)<br />
* '''Status:''' alpha, beta, production, or retired<br />
* '''Release date:''' the release date of the ontology source file that you upload to BioPortal<br />
<br />
==== Creating an ontology entry ====<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13130Ontology Change Requests2024-06-01T00:29:12Z<p>JenniferVendetti: /* Request a change */</p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is manually enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== Enable change requests for your ontology ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.<br />
<br />
== Request a change ==<br />
You must be logged in to request changes in BioPortal. If you don't have an account, you can create one here: https://bioportal.bioontology.org/accounts/new.<br />
<br />
Once logged in, navigate to your ontology in BioPortal, and click on the Classes tab.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13129Ontology Change Requests2024-06-01T00:03:25Z<p>JenniferVendetti: </p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is manually enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== Enable change requests for your ontology ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.<br />
<br />
== Request a change ==</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13128Ontology Change Requests2024-06-01T00:02:18Z<p>JenniferVendetti: /* How to enable change requests for your ontology */</p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is manually enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== Enable change requests for your ontology ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13127Ontology Change Requests2024-06-01T00:01:49Z<p>JenniferVendetti: /* How to enable change requests */</p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is manually enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== How to enable change requests for your ontology ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13126Ontology Change Requests2024-05-23T18:00:31Z<p>JenniferVendetti: </p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is manually enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== How to enable change requests ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=User:NLHarris&diff=13125User:NLHarris2024-05-23T01:10:09Z<p>JenniferVendetti: Created blank page</p>
<hr />
<div></div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13124Ontology Change Requests2024-05-23T00:48:14Z<p>JenniferVendetti: add sections for supported change types and how to enable change requests for an ontology</p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology (ENVO)]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology (GO)]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology (MONDO)]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology (UBERON)]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. <br />
<br />
== Supported change types ==<br />
<br />
BioPortal supports several types of change requests including:<br />
<br />
* Adding a synonym to a class<br />
* Removing a synonym from a class<br />
* Marking a class as obsolete<br />
* Renaming a class<br />
<br />
Support for more types of changes are in the works including, adding and removing definitions, adding classes, and deleting classes to name a few.<br />
<br />
All of the change types that BioPortal supports are taken from the [https://incatools.github.io/kgcl/ Knowledge Graph Change Language], a formal model for describing ontology change operations.<br />
<br />
== How to enable change requests ==<br />
<br />
If you want to enable BioPortal's change request functionality for your ontology, please post a request on the [mailto:contact@bioportal.com BioPortal support] list. Include your ontology acronym in BioPortal, e.g., "MONDO", and the URL of the GitHub repository where your ontology is maintained, e.g., https://github.com/monarch-initiative/mondo.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13123Ontology Change Requests2024-05-23T00:25:35Z<p>JenniferVendetti: Add more introductory text</p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology]<br />
<br />
Change requests are mirrored as GitHub issues in the repository where the ontology is maintained. BioPortal supports several types of change requests including:<br />
<br />
* Adding synonyms<br />
* Removing synonyms<br />
* Marking a class obsolete<br />
* Renaming a class<br />
<br />
... with support for more types of changes to come.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13122Ontology Change Requests2024-05-23T00:11:06Z<p>JenniferVendetti: </p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is enabled on a per-ontology basis, and there are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology]</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13121Ontology Change Requests2024-05-23T00:07:22Z<p>JenniferVendetti: Add introductory text</p>
<hr />
<div>BioPortal allows users to request changes or extensions to an ontology when the ontology source file is maintained in [https://github.com/ GitHub]. The change request functionality is enabled on a per-ontology basis. There are currently four ontologies in our repository for which change requests are enabled:<br />
<br />
* [https://bioportal.bioontology.org/ontologies/ENVO Environment Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/GO Gene Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/MONDO Mondo Disease Ontology]<br />
* [https://bioportal.bioontology.org/ontologies/UBERON Uber Anatomy Ontology]</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Ontology_Change_Requests&diff=13120Ontology Change Requests2024-05-22T23:57:10Z<p>JenniferVendetti: Initial page creation</p>
<hr />
<div>= Requesting Changes to an Ontology in BioPortal =</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13118BioPortal Help2024-05-22T22:59:28Z<p>JenniferVendetti: /* Requesting ontology changes */ Add brief introductory sentence, and link to separate page</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
If you haven’t already signed up for an account at the BioPortal website, you’ll need to do that first:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology, e.g., name, acronym, etc. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our [[Ontology Change Requests]] page.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13117BioPortal Help2024-05-22T22:15:56Z<p>JenniferVendetti: /* Common Tasks */ Add section for documenting ontology change requests</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
If you haven’t already signed up for an account at the BioPortal website, you’ll need to do that first:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology, e.g., name, acronym, etc. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Requesting ontology changes ===<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SPARQL_BioPortal&diff=13110SPARQL BioPortal2024-01-05T01:16:32Z<p>JenniferVendetti: </p>
<hr />
<div><span style="color:red; font-weight:bold">PLEASE NOTE:</span><br />
<br />
The BioPortal open SPARQL endpoint is deprecated and shut down. This decision was made due to lack of resources to maintain the service. We understand the impact this may have on your workflows and apologize for any inconvenience caused.<br />
<br />
To continue accessing data in the BioPortal ontology repository, please use our actively maintained [https://data.bioontology.org/documentation REST API].<br />
<br />
If you have any questions or require assistance, please reach out [mailto:support@bioontology.org to support].<br /><br /><br />
<hr /><br /><br />
<br />
NCBO is releasing a free and open SPARQL endpoint to query ontologies hosted in the BioPortal ontology repository. This SPARQL service, that is in BETA status, is stable for testing by our community of users. If you encounter any errors or unexpected behavior please report it to us [mailto:support@bioontology.org support@bioontology.org]. <br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
Before using the BioPortal SPARQL service please read our [[SPARQL Release Notes And Usage Policy]]<br />
</div><br />
<br />
=== Web Interface and Query Examples ===<br />
<br />
There is a Web interface to test SPARQL queries at http://sparql.bioontology.org/<br />
<br />
Also, interactive examples can be tested here http://sparql.bioontology.org/examples<br />
<br />
=== Submitting SPARQL queries programmatically ===<br />
<br />
A github project contains examples to query our SPARQL service programmatically:<br />
<br />
https://github.com/ncbo/sparql-code-examples <br />
<br />
A tarball with these examples is for download here:<br />
<br />
https://github.com/ncbo/sparql-code-examples/tarball/master<br />
<br />
This project contains examples in Java, Python, JavaScript and Perl. Some of the examples use just language built-in capabilities and other need third-party libraries like Jena, Sesame or SPARQLWrapper. The github project and the tarball are self-contained, no need to download and install extra libraries.<br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
To run these examples or any other SPARQL queries programmatically an API key from BioPortal is required. If you do not have a BioPortal account go to [[http://bioportal.bioontology.org/accounts/new New Account]] and create one. Once you have the BioPortal account, login in BioPortal and go to your account details. You should see your API Key as part of your account profile.<br />
</div><br />
<br />
=== Database Named Graph Structure ===<br />
<br />
Each ontology is asserted into a single graph. The graph is named with an acronym based URI. For example, the graph:<br />
<br />
<pre><br />
http://bioportal.bioontology.org/ontologies/HP<br />
</pre><br />
<br />
contains the Human Phenotype Ontology ontology. And the graph:<br />
<br />
<pre><br />
http://bioportal.bioontology.org/ontologies/SNOMEDCT<br />
</pre><br />
<br />
contains the SNOMEDCT ontology.<br />
<br />
The following query would return all version IDs with the graph IDs where ontologies are located:<br />
<br />
<pre><br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/> <br />
<br />
SELECT DISTINCT ?version ?graph<br />
WHERE { <br />
?version meta:hasDataGraph ?graph<br />
}<br />
</pre><br />
<br />
=== BioPortal Preferred Label ===<br />
<br />
There are problematic cases of label definition. In order to provide a consistent mechanism to query by label across different ontologies we generate labels for the following cases. These label are attached to terms using the predicate '''http://bioportal.bioontology.org/metadata/def/prefLabel''' (bp:prefLabel)<br />
<br />
* '''Missing labels''': for every owl:Class that is missing a label we generate a label based on the latest fragment of URI. <br />
<br />
* '''Terms that use rdfs:label as preferred name''': BioPortal uses skos:prefLabel and skos:altLabel for preferred names and synonyms respectively. Both skos:prefLabel and skos:altLabel are subproperties of rdfs:label in the SKOS ontology. If someone uses rdfs:label to record preferred names, in the SKOS context, he would be saying that that name can be a preferred name or a synonym. To avoid this confusion we generate bp:prefLabel(s) for every rdfs:label used as preferred name.<br />
<br />
=== Preferred Label, Synonyms and other common predicates ===<br />
<br />
When ontologies are submitted to BioPortal the user can select which predicates that ontology uses for:<br />
<br />
* Preferred Names.<br />
* Synonyms or alternative names.<br />
* Author.<br />
* Description.<br />
<br />
The BioPortal SPARQL endpoint supports rdfs:subPropertyOf reasoning to enable cross querying across all these configurable predicates. In the triple store, the following URI:<br />
<br />
http://bioportal.bioontology.org/ontologies/globals<br />
<br />
is used as identifier for the named graph that contains all the sub-property of statements that have been configured by users when uploading their ontologies. The root properties to be used to trigger the reasoning are the following:<br />
<br />
* '''skos:prefLabel''' for Preferred name.<br />
* '''skos:altLabel''' for Synonyms or alternative names.<br />
* '''dc:author''' for Author.<br />
* '''skos:definition''' for Description.<br />
<br />
When using named graphs if you want to use this reasoning then you should include the globals graph that contains the subproperty statements, i.e:<br />
<br />
<pre><br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
PREFIX skos: <http://www.w3.org/2004/02/skos/core#><br />
SELECT DISTINCT ?termURI ?prefLabel<br />
FROM <http://bioportal.bioontology.org/ontologies/EHDA><br />
FROM <http://bioportal.bioontology.org/ontologies/globals> <br />
WHERE {<br />
?termURI a owl:Class;<br />
skos:prefLabel ?prefLabel .<br />
} <br />
</pre><br />
<br />
Otherwise the subproperty statements that take part in the query processor will not be taken into account.<br />
<br />
=== Mappings ===<br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
Notice that as of January 30th (2013) we are hosting the mappings in a separate endpoint. This eases our regular mapping updates. Programmatic queries that target mapping data need to use the following endpoint: http://sparql.bioontology.org/mappings/sparql<br />
</div><br />
<br />
The mapping data in the triple store is stored in the following graphs:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Graph Name!! Description<br />
|-<br />
| http://purl.bioontology.org/mapping/loom || Loom: lexical mappings.<br />
|-<br />
| http://purl.bioontology.org/mapping/rest || REST: User submitted by users via the REST API.<br />
|-<br />
| http://purl.bioontology.org/mapping/umls_cui || UMLS-CUI: CUI based mappings<br />
|-<br />
| http://purl.bioontology.org/mapping/cuinonumls || NOUMLS-CUI: Terms with same CUIs but for ontologies that are not part of UMLS.<br />
|-<br />
| http://purl.bioontology.org/mapping/obo_xref || OBO-XREF: Mappings for terms with same xref attribute.<br />
|-<br />
| http://purl.bioontology.org/mapping/uri_match || URI-MATCH: Mappings that for terms that in different ontologies are represented by the same URI.<br />
|}<br />
<br />
The following query returns the list of the graphs where mappings are located:<br />
<br />
<pre><br />
SELECT DISTINCT ?g WHERE { <br />
GRAPH ?g { <br />
?s a <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#One_To_One_Mapping> . }}<br />
</pre><br />
<br />
The following RDF/Turtle sample shows an example of a mapping instance:<br />
<pre><br />
@prefix maps: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> .<br />
<br />
<http://purl.bioontology.org/mapping/2767e8e0-001b-012e-749f-005056bd0010><br />
maps:has_process_info <.../procinfo/2008-04-23-38138> ;<br />
maps:comment "Manual mappings between Mouse anatomy and NCIT." ;<br />
maps:relation skos:closeMatch ;<br />
maps:target <http://purl.org/obo/owl/MA#MA_0001096> ;<br />
maps:source <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Olfactory_Nerve> ;<br />
maps:source_ontology_id <http://bioportal.bioontology.org/ontologies/1032> ;<br />
maps:target_ontology_id <http://bioportal.bioontology.org/ontologies/1000> ;<br />
a maps:One_To_One_Mapping .<br />
</pre><br />
<br />
The predicates we use to represent a mapping record both the target and source terms and target and source ontologies. A SPARQL query to return all the target terms for a giving source term would look like the following:<br />
<br />
<pre><br />
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#><br />
SELECT DISTINCT ?target WHERE {<br />
?s map:source <http://purl.obolibrary.org/obo/DOID_8545>;<br />
map:target ?target .<br />
}<br />
</pre><br />
<br />
If one wants to count at all the mappings for two given ontologies then the SPARQL would use the ''target_ontology'' and ''source_ontology'' predicates:<br />
<br />
<pre><br />
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#><br />
SELECT (count(?m) as ?c) WHERE {<br />
?m map:source_ontology <http://bioportal.bioontology.org/ontologies/1032> ;<br />
map:target_ontology <http://bioportal.bioontology.org/ontologies/1000> .<br />
}<br />
</pre><br />
<br />
In this case this query returns a count of 4393 solutions. <br />
It is important to notice that for mappings we use version based ontology URIs and not the ones that are based on acronyms.<br />
<br />
=== Federated SPARQL queries ===<br />
<br />
SPARQL Federation can be used with the Jena ARQ library. The Jena ARQ library handles the SERVICE SPARQL construct and directs sets of triple patterns to different endpoint and handles the joins. <br />
<br />
BioPortal offers two different SPARQL endpoints one for ontologies (metadata and terms) and a second one for mappings. There are use cases that require queries with joins from both endpoints. This can be achieved by using SPARQL federation and the SERVICE feature (SPARQL 1.1). The following example looks at the CSP term 'Neck' and retrieves the sources for all the mappings for that term (from the mapping endpoint). For each of those sources then gets the parents (from the ontologies endpoint). Notice the change in the SERVICE endpoints from 'mappings' in the first block to 'ontologies' in the second one.<br />
<br />
<pre><br />
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#><br />
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#><br />
PREFIX skos: <http://www.w3.org/2004/02/skos/core#><br />
SELECT DISTINCT ?mappedParent WHERE {<br />
SERVICE <http://sparql.bioontology.org/mappings/sparql/?apikey=YOUR API KEY HERE> {<br />
?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .<br />
?mapping map:source ?source .<br />
}<br />
SERVICE <http://sparql.bioontology.org/ontologies/sparql/?apikey=YOUR API KEY HERE> {<br />
?source rdfs:subClassOf ?mappedParent .<br />
}<br />
}<br />
</pre><br />
<br />
Full example: https://github.com/ncbo/sparql-code-examples/blob/master/java/src/org/ncbo/stanford/sparql/examples/JenaARQFederationExample.java<br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
<b>Note</b> SPARQL Federation can be used programmatically only. Our web front-end at http://sparql.bioontology.org/ does not support mediation for the SERVICE clause. Our tests for SPARQL federation use Jena ARQ 2.9.4, this version is able to correctly submit the BioPortal API keys.<br />
</div><br />
<br />
=== Partial or Incomplete Results ===<br />
<br />
sparql.bioontology.org uses 4store's soft-limit internal mechanism to limit resources for expensive queries. Our setup is configured to bind 8K elements per triple pattern. If you hit these limits a warning message will be appended to the query response. This message says something like: "hit complexity limit 8 times". If you see this warning it means that the results are incomplete, and probably there is a more efficient way to write that query. <br />
<br />
Contact our support mail list if you need help to rewrite your query in a more efficient way and avoid incomplete results.<br />
<br />
=== Slides ===<br />
* '''''BioPortal SPARQL presentation at ISWC 2012''''' http://www.slideshare.net/manuelso/using-sparql-to-query-bioportal-ontologies-and-metadata<br />
* '''''BioPortal SPARQL tutorial from SWAT4LS 2011''''' http://www.bioontology.org/wiki/index.php/File:Whetzel_SPARQL.pdf<br />
* '''''NCBO Hackathon slides for the SPARQL tutorial''''' http://www.stanford.edu/~manuelso/ncbohack/index.html</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SPARQL_BioPortal&diff=13109SPARQL BioPortal2024-01-05T01:13:25Z<p>JenniferVendetti: Add a deprecation and shut down notification for the open SPARQL endpoint</p>
<hr />
<div><span style="color:red; font-weight:bold">PLEASE NOTE:</span><br />
<br />
The BioPortal open SPARQL endpoint is deprecated and shut down. This decision was made due to lack of resources to maintain the service. We understand the impact this may have on your workflows and apologize for any inconvenience caused.<br />
<br />
To continue accessing data in the BioPortal ontology repository, please use our actively maintained [https://data.bioontology.org/documentation REST API].<br /><br /><br />
<hr /><br /><br />
<br />
NCBO is releasing a free and open SPARQL endpoint to query ontologies hosted in the BioPortal ontology repository. This SPARQL service, that is in BETA status, is stable for testing by our community of users. If you encounter any errors or unexpected behavior please report it to us [mailto:support@bioontology.org support@bioontology.org]. <br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
Before using the BioPortal SPARQL service please read our [[SPARQL Release Notes And Usage Policy]]<br />
</div><br />
<br />
=== Web Interface and Query Examples ===<br />
<br />
There is a Web interface to test SPARQL queries at http://sparql.bioontology.org/<br />
<br />
Also, interactive examples can be tested here http://sparql.bioontology.org/examples<br />
<br />
=== Submitting SPARQL queries programmatically ===<br />
<br />
A github project contains examples to query our SPARQL service programmatically:<br />
<br />
https://github.com/ncbo/sparql-code-examples <br />
<br />
A tarball with these examples is for download here:<br />
<br />
https://github.com/ncbo/sparql-code-examples/tarball/master<br />
<br />
This project contains examples in Java, Python, JavaScript and Perl. Some of the examples use just language built-in capabilities and other need third-party libraries like Jena, Sesame or SPARQLWrapper. The github project and the tarball are self-contained, no need to download and install extra libraries.<br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
To run these examples or any other SPARQL queries programmatically an API key from BioPortal is required. If you do not have a BioPortal account go to [[http://bioportal.bioontology.org/accounts/new New Account]] and create one. Once you have the BioPortal account, login in BioPortal and go to your account details. You should see your API Key as part of your account profile.<br />
</div><br />
<br />
=== Database Named Graph Structure ===<br />
<br />
Each ontology is asserted into a single graph. The graph is named with an acronym based URI. For example, the graph:<br />
<br />
<pre><br />
http://bioportal.bioontology.org/ontologies/HP<br />
</pre><br />
<br />
contains the Human Phenotype Ontology ontology. And the graph:<br />
<br />
<pre><br />
http://bioportal.bioontology.org/ontologies/SNOMEDCT<br />
</pre><br />
<br />
contains the SNOMEDCT ontology.<br />
<br />
The following query would return all version IDs with the graph IDs where ontologies are located:<br />
<br />
<pre><br />
PREFIX meta: <http://bioportal.bioontology.org/metadata/def/> <br />
<br />
SELECT DISTINCT ?version ?graph<br />
WHERE { <br />
?version meta:hasDataGraph ?graph<br />
}<br />
</pre><br />
<br />
=== BioPortal Preferred Label ===<br />
<br />
There are problematic cases of label definition. In order to provide a consistent mechanism to query by label across different ontologies we generate labels for the following cases. These label are attached to terms using the predicate '''http://bioportal.bioontology.org/metadata/def/prefLabel''' (bp:prefLabel)<br />
<br />
* '''Missing labels''': for every owl:Class that is missing a label we generate a label based on the latest fragment of URI. <br />
<br />
* '''Terms that use rdfs:label as preferred name''': BioPortal uses skos:prefLabel and skos:altLabel for preferred names and synonyms respectively. Both skos:prefLabel and skos:altLabel are subproperties of rdfs:label in the SKOS ontology. If someone uses rdfs:label to record preferred names, in the SKOS context, he would be saying that that name can be a preferred name or a synonym. To avoid this confusion we generate bp:prefLabel(s) for every rdfs:label used as preferred name.<br />
<br />
=== Preferred Label, Synonyms and other common predicates ===<br />
<br />
When ontologies are submitted to BioPortal the user can select which predicates that ontology uses for:<br />
<br />
* Preferred Names.<br />
* Synonyms or alternative names.<br />
* Author.<br />
* Description.<br />
<br />
The BioPortal SPARQL endpoint supports rdfs:subPropertyOf reasoning to enable cross querying across all these configurable predicates. In the triple store, the following URI:<br />
<br />
http://bioportal.bioontology.org/ontologies/globals<br />
<br />
is used as identifier for the named graph that contains all the sub-property of statements that have been configured by users when uploading their ontologies. The root properties to be used to trigger the reasoning are the following:<br />
<br />
* '''skos:prefLabel''' for Preferred name.<br />
* '''skos:altLabel''' for Synonyms or alternative names.<br />
* '''dc:author''' for Author.<br />
* '''skos:definition''' for Description.<br />
<br />
When using named graphs if you want to use this reasoning then you should include the globals graph that contains the subproperty statements, i.e:<br />
<br />
<pre><br />
PREFIX owl: <http://www.w3.org/2002/07/owl#><br />
PREFIX skos: <http://www.w3.org/2004/02/skos/core#><br />
SELECT DISTINCT ?termURI ?prefLabel<br />
FROM <http://bioportal.bioontology.org/ontologies/EHDA><br />
FROM <http://bioportal.bioontology.org/ontologies/globals> <br />
WHERE {<br />
?termURI a owl:Class;<br />
skos:prefLabel ?prefLabel .<br />
} <br />
</pre><br />
<br />
Otherwise the subproperty statements that take part in the query processor will not be taken into account.<br />
<br />
=== Mappings ===<br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
Notice that as of January 30th (2013) we are hosting the mappings in a separate endpoint. This eases our regular mapping updates. Programmatic queries that target mapping data need to use the following endpoint: http://sparql.bioontology.org/mappings/sparql<br />
</div><br />
<br />
The mapping data in the triple store is stored in the following graphs:<br />
<br />
{| class="wikitable"<br />
|-<br />
! Graph Name!! Description<br />
|-<br />
| http://purl.bioontology.org/mapping/loom || Loom: lexical mappings.<br />
|-<br />
| http://purl.bioontology.org/mapping/rest || REST: User submitted by users via the REST API.<br />
|-<br />
| http://purl.bioontology.org/mapping/umls_cui || UMLS-CUI: CUI based mappings<br />
|-<br />
| http://purl.bioontology.org/mapping/cuinonumls || NOUMLS-CUI: Terms with same CUIs but for ontologies that are not part of UMLS.<br />
|-<br />
| http://purl.bioontology.org/mapping/obo_xref || OBO-XREF: Mappings for terms with same xref attribute.<br />
|-<br />
| http://purl.bioontology.org/mapping/uri_match || URI-MATCH: Mappings that for terms that in different ontologies are represented by the same URI.<br />
|}<br />
<br />
The following query returns the list of the graphs where mappings are located:<br />
<br />
<pre><br />
SELECT DISTINCT ?g WHERE { <br />
GRAPH ?g { <br />
?s a <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#One_To_One_Mapping> . }}<br />
</pre><br />
<br />
The following RDF/Turtle sample shows an example of a mapping instance:<br />
<pre><br />
@prefix maps: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#> .<br />
<br />
<http://purl.bioontology.org/mapping/2767e8e0-001b-012e-749f-005056bd0010><br />
maps:has_process_info <.../procinfo/2008-04-23-38138> ;<br />
maps:comment "Manual mappings between Mouse anatomy and NCIT." ;<br />
maps:relation skos:closeMatch ;<br />
maps:target <http://purl.org/obo/owl/MA#MA_0001096> ;<br />
maps:source <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Olfactory_Nerve> ;<br />
maps:source_ontology_id <http://bioportal.bioontology.org/ontologies/1032> ;<br />
maps:target_ontology_id <http://bioportal.bioontology.org/ontologies/1000> ;<br />
a maps:One_To_One_Mapping .<br />
</pre><br />
<br />
The predicates we use to represent a mapping record both the target and source terms and target and source ontologies. A SPARQL query to return all the target terms for a giving source term would look like the following:<br />
<br />
<pre><br />
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#><br />
SELECT DISTINCT ?target WHERE {<br />
?s map:source <http://purl.obolibrary.org/obo/DOID_8545>;<br />
map:target ?target .<br />
}<br />
</pre><br />
<br />
If one wants to count at all the mappings for two given ontologies then the SPARQL would use the ''target_ontology'' and ''source_ontology'' predicates:<br />
<br />
<pre><br />
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#><br />
SELECT (count(?m) as ?c) WHERE {<br />
?m map:source_ontology <http://bioportal.bioontology.org/ontologies/1032> ;<br />
map:target_ontology <http://bioportal.bioontology.org/ontologies/1000> .<br />
}<br />
</pre><br />
<br />
In this case this query returns a count of 4393 solutions. <br />
It is important to notice that for mappings we use version based ontology URIs and not the ones that are based on acronyms.<br />
<br />
=== Federated SPARQL queries ===<br />
<br />
SPARQL Federation can be used with the Jena ARQ library. The Jena ARQ library handles the SERVICE SPARQL construct and directs sets of triple patterns to different endpoint and handles the joins. <br />
<br />
BioPortal offers two different SPARQL endpoints one for ontologies (metadata and terms) and a second one for mappings. There are use cases that require queries with joins from both endpoints. This can be achieved by using SPARQL federation and the SERVICE feature (SPARQL 1.1). The following example looks at the CSP term 'Neck' and retrieves the sources for all the mappings for that term (from the mapping endpoint). For each of those sources then gets the parents (from the ontologies endpoint). Notice the change in the SERVICE endpoints from 'mappings' in the first block to 'ontologies' in the second one.<br />
<br />
<pre><br />
PREFIX map: <http://protege.stanford.edu/ontologies/mappings/mappings.rdfs#><br />
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#><br />
PREFIX skos: <http://www.w3.org/2004/02/skos/core#><br />
SELECT DISTINCT ?mappedParent WHERE {<br />
SERVICE <http://sparql.bioontology.org/mappings/sparql/?apikey=YOUR API KEY HERE> {<br />
?mapping map:target <http://purl.bioontology.org/ontology/CSP/0468-5952> .<br />
?mapping map:source ?source .<br />
}<br />
SERVICE <http://sparql.bioontology.org/ontologies/sparql/?apikey=YOUR API KEY HERE> {<br />
?source rdfs:subClassOf ?mappedParent .<br />
}<br />
}<br />
</pre><br />
<br />
Full example: https://github.com/ncbo/sparql-code-examples/blob/master/java/src/org/ncbo/stanford/sparql/examples/JenaARQFederationExample.java<br />
<br />
<div style="margin-top: 10px; background: #F6F9ED; padding: 6px; border: 1px solid #aaaaaa; margin-bottom: 20px;"><br />
<b>Note</b> SPARQL Federation can be used programmatically only. Our web front-end at http://sparql.bioontology.org/ does not support mediation for the SERVICE clause. Our tests for SPARQL federation use Jena ARQ 2.9.4, this version is able to correctly submit the BioPortal API keys.<br />
</div><br />
<br />
=== Partial or Incomplete Results ===<br />
<br />
sparql.bioontology.org uses 4store's soft-limit internal mechanism to limit resources for expensive queries. Our setup is configured to bind 8K elements per triple pattern. If you hit these limits a warning message will be appended to the query response. This message says something like: "hit complexity limit 8 times". If you see this warning it means that the results are incomplete, and probably there is a more efficient way to write that query. <br />
<br />
Contact our support mail list if you need help to rewrite your query in a more efficient way and avoid incomplete results.<br />
<br />
=== Slides ===<br />
* '''''BioPortal SPARQL presentation at ISWC 2012''''' http://www.slideshare.net/manuelso/using-sparql-to-query-bioportal-ontologies-and-metadata<br />
* '''''BioPortal SPARQL tutorial from SWAT4LS 2011''''' http://www.bioontology.org/wiki/index.php/File:Whetzel_SPARQL.pdf<br />
* '''''NCBO Hackathon slides for the SPARQL tutorial''''' http://www.stanford.edu/~manuelso/ncbohack/index.html</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=13073BioPortal Help2023-09-13T23:04:35Z<p>JenniferVendetti: /* Glossary */ Change "slice_definition" span to div. Testing anchors for incoming links.</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Resource Index Tab|search biomedical resources]] for a term<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Resource Index Tab ===<br />
<br />
The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button. <br />
<br />
To '''access annotations for resources programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide Resource Index REST API documentation].<br />
<br />
Further information on ontology-based search and mining of biomedical resources is available in [http://www.ncbi.nlm.nih.gov/pubmed/21918645 Jonquet et al Web Semant. 2011 Sep 1;9(3):316-324], [http://www.ncbi.nlm.nih.gov/pubmed/21550421 LePendu et al J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8] and [http://www.ncbi.nlm.nih.gov/pubmed/22494789 Liu et al J Am Med Inform Assoc. 2012 Apr 11]<br />
<br />
If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
If you haven’t already signed up for an account at the BioPortal website, you’ll need to do that first:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology, e.g., name, acronym, etc. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
==== Updating an existing ontology submission ==== <br />
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology. <br />
<br />
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.<br />
<br />
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).<br />
<br />
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).<br />
<br />
==== Updating metadata for your submission ====<br />
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.<br />
<br />
==== Update ontology settings ====<br />
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page). <br />
<br />
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <div id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== BioPortal Frequently Asked Questions (FAQ) ==<br />
<br />
Many specific questions are addressed at our [https://www.bioontology.org/wiki/BioPortal_FAQ FAQ for the BioPortal system].<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=LOOM&diff=13072LOOM2023-07-10T18:04:46Z<p>JenniferVendetti: </p>
<hr />
<div>== About LOOM ==<br />
<br />
Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. It identifies two concepts from different ontologies as similar, if and only if their preferred names or synonyms are equivalent based on a modified string-comparison function. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). It then uses an approximate matching technique to compare the strings, allowing for a mismatch of at most one character in strings with length greater than four and no mismatches for shorter strings.<br />
<br />
More information about LOOM can be found in the [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474/ technical report]<br />
<br />
== Obtaining LOOM ==<br />
<br />
LOOM can currently be obtained [https://github.com/ncbo/bioportal_mappings here]<br />
<!-- Old, broken link to the LOOM JAR file --><br />
<!-- LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here] --><br />
<br />
== Using LOOM ==<br />
<br />
LOOM can be executed with a command of the following form: <br><br />
% java -jar [-Xmx1500m] Loom.jar source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI<br />
<br />
In this command, source.pprj is the protege project file for the OWL source ontology to be mapped. target.pprj is the protege project file for the target ontology. SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names. TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology. These URIs are quite often annotation properties in the ontologies.<br />
<br />
NOTE: The [] designates an optional flag for allocating additional virtual memory to LOOM. <br />
For example, if you were to try to use LOOM to map Mouse Adult Gross Anatomy to Zebrafish Anatomy and Development, you would use the following command:<br><br />
% java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym<br />
<br />
NOTE: LOOM can be used with ontologies in OBO format by loading the file into Protege 4 (http://protege.stanford.edu). <br />
<br />
A few additional important tips:<br />
# You should keep the .owl and .pprj files in the same folder as LOOM.<br />
# Your project should be configured so that the preferred name of the concepts and synonyms are set as the browser text (instructions on how to do this are below).<br />
# LOOM makes use of thread synchronization and so its speed is significantly improved with additional memory allocation. We strongly advise allocating additional virtual memory with the command -Xmx1500m (or however memory you choose to allocate).<br />
<br />
== Notes ==<br />
<br />
How to configure your protege project so concepts have preferred name as browser text:<br />
# Go to OWL -> Preferences. Under the visibility tab, put a check by owl:Class. Close preferences.<br />
# In the main screen, go to the individuals tab. Select owl:Class from the class hierarchy browser. Now, in the individual browser, select the downward-pointing arrow (menu button) near the top. Then choose Set Display Slot and select the slot that you want to display as browser text (in most cases this will be rdfs:label).<br />
# You should repeat this process to ensure that your synonym slot also displays the preferred name.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=LOOM&diff=13071LOOM2023-07-10T18:04:27Z<p>JenniferVendetti: /* Obtaining LOOM */ Fixed broken link. LOOM JAR file is no longer accessible. Pointed to the archived version of the code in GitHub.</p>
<hr />
<div>== About LOOM ==<br />
<br />
Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. It identifies two concepts from different ontologies as similar, if and only if their preferred names or synonyms are equivalent based on a modified string-comparison function. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). It then uses an approximate matching technique to compare the strings, allowing for a mismatch of at most one character in strings with length greater than four and no mismatches for shorter strings.<br />
<br />
More information about LOOM can be found in the [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474/ technical report]<br />
<br />
== Obtaining LOOM ==<br />
<br />
LOOM can currently be obtained [https://github.com/ncbo/bioportal_mappings here]<br />
<br />
<!-- Old, broken link to the LOOM JAR file --><br />
<!-- LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here] --><br />
<br />
== Using LOOM ==<br />
<br />
LOOM can be executed with a command of the following form: <br><br />
% java -jar [-Xmx1500m] Loom.jar source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI<br />
<br />
In this command, source.pprj is the protege project file for the OWL source ontology to be mapped. target.pprj is the protege project file for the target ontology. SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names. TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology. These URIs are quite often annotation properties in the ontologies.<br />
<br />
NOTE: The [] designates an optional flag for allocating additional virtual memory to LOOM. <br />
For example, if you were to try to use LOOM to map Mouse Adult Gross Anatomy to Zebrafish Anatomy and Development, you would use the following command:<br><br />
% java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym<br />
<br />
NOTE: LOOM can be used with ontologies in OBO format by loading the file into Protege 4 (http://protege.stanford.edu). <br />
<br />
A few additional important tips:<br />
# You should keep the .owl and .pprj files in the same folder as LOOM.<br />
# Your project should be configured so that the preferred name of the concepts and synonyms are set as the browser text (instructions on how to do this are below).<br />
# LOOM makes use of thread synchronization and so its speed is significantly improved with additional memory allocation. We strongly advise allocating additional virtual memory with the command -Xmx1500m (or however memory you choose to allocate).<br />
<br />
== Notes ==<br />
<br />
How to configure your protege project so concepts have preferred name as browser text:<br />
# Go to OWL -> Preferences. Under the visibility tab, put a check by owl:Class. Close preferences.<br />
# In the main screen, go to the individuals tab. Select owl:Class from the class hierarchy browser. Now, in the individual browser, select the downward-pointing arrow (menu button) near the top. Then choose Set Display Slot and select the slot that you want to display as browser text (in most cases this will be rdfs:label).<br />
# You should repeat this process to ensure that your synonym slot also displays the preferred name.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=LOOM&diff=13070LOOM2023-07-10T17:58:02Z<p>JenniferVendetti: /* About LOOM */ Fixed broken link to the LOOM technical report</p>
<hr />
<div>== About LOOM ==<br />
<br />
Lexical OWL Ontology Matcher (LOOM) is a freely available tool for ontology alignment. LOOM takes two ontologies represented in OWL and produces pairs of related concepts from the ontologies. In order to identify the corresponding concepts, LOOM compares the preferred names and synonyms of the concepts in both ontologies. It identifies two concepts from different ontologies as similar, if and only if their preferred names or synonyms are equivalent based on a modified string-comparison function. Our string-comparison function first removes all delimiters from both strings (e.g., spaces, underscores, parentheses, etc.). It then uses an approximate matching technique to compare the strings, allowing for a mismatch of at most one character in strings with length greater than four and no mismatches for shorter strings.<br />
<br />
More information about LOOM can be found in the [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815474/ technical report]<br />
<br />
== Obtaining LOOM ==<br />
<br />
LOOM can currently be obtained [http://www.stanford.edu/~amirg/Loom.jar.zip here]<br />
<br />
== Using LOOM ==<br />
<br />
LOOM can be executed with a command of the following form: <br><br />
% java -jar [-Xmx1500m] Loom.jar source.pprj target.pprj SourceSynonymSlotURI TargetSynonymSlotURI<br />
<br />
In this command, source.pprj is the protege project file for the OWL source ontology to be mapped. target.pprj is the protege project file for the target ontology. SourceSynonymSlotURI is the full URI for the slot in which the source ontology stores synonym names. TargetSynonymSlotURI is the full URI for the slot containing synonyms in the target ontology. These URIs are quite often annotation properties in the ontologies.<br />
<br />
NOTE: The [] designates an optional flag for allocating additional virtual memory to LOOM. <br />
For example, if you were to try to use LOOM to map Mouse Adult Gross Anatomy to Zebrafish Anatomy and Development, you would use the following command:<br><br />
% java -jar -Xmx1500m Loom.jar mouse.pprj zebrafish.pprj http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym http://www.geneontology.org/formats/oboInOwl#hasExactSynonym<br />
<br />
NOTE: LOOM can be used with ontologies in OBO format by loading the file into Protege 4 (http://protege.stanford.edu). <br />
<br />
A few additional important tips:<br />
# You should keep the .owl and .pprj files in the same folder as LOOM.<br />
# Your project should be configured so that the preferred name of the concepts and synonyms are set as the browser text (instructions on how to do this are below).<br />
# LOOM makes use of thread synchronization and so its speed is significantly improved with additional memory allocation. We strongly advise allocating additional virtual memory with the command -Xmx1500m (or however memory you choose to allocate).<br />
<br />
== Notes ==<br />
<br />
How to configure your protege project so concepts have preferred name as browser text:<br />
# Go to OWL -> Preferences. Under the visibility tab, put a check by owl:Class. Close preferences.<br />
# In the main screen, go to the individuals tab. Select owl:Class from the class hierarchy browser. Now, in the individual browser, select the downward-pointing arrow (menu button) near the top. Then choose Set Display Slot and select the slot that you want to display as browser text (in most cases this will be rdfs:label).<br />
# You should repeat this process to ensure that your synonym slot also displays the preferred name.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=13048BioPortal Release Notes2022-02-04T20:56:22Z<p>JenniferVendetti: Noted that this page is no longer used, in favor of GitHub releases. Added links to release notes pages for API and UI.</p>
<hr />
<div>'''<span style="color:red;">Please note: this page is deprecated and no longer updated. To view current release notes for BioPortal, please refer to one of the following pages:</span>'''<br />
<br />
BioPortal REST API release notes: https://github.com/ncbo/ontologies_api/releases<br><br />
BioPortal web application release notes: https://github.com/ncbo/bioportal_web_ui/releases<br />
<br />
<br />
''This page contains software release notes for the 5.x series of [http://bioportal.bioontology.org/ BioPortal].'' <br />
<br />
Use the following links to access release notes for the BioPortal Virtual Appliance, and older versions of BioPortal:<br />
<br />
* [[BioPortal_Virtual_Appliance_Release_Notes|BioPortal Virtual Appliance release notes]]<br />
* [[BioPortal_4_Release_Notes|BioPortal 4.x release notes]]<br />
* [[BioPortal_Release_3_Release_Notes|BioPortal 3.x release notes]]<br />
* [[BioPortal_Release_2_Release_Notes|BioPortal 2.x release notes]]<br />
<br />
<br />
__TOC__<br />
<br />
<br />
== BioPortal 5.22.1 (2021-July-08, 2021-August-10) ==<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a bug that caused Mapping Submission IDs query to fail in AllegroGraph ([https://github.com/ncbo/ontologies_linked_data/issues/120 ncbo/ontologies_linked_data#120])<br />
* Fixed a bug that prevented UMLS ontologies from being processed in AllegroGraph ([https://github.com/ncbo/bioportal-project/issues/215 ncbo/bioportal-project#215])<br />
* Fixed a security vulnerability<br />
<br />
<br />
== BioPortal 5.21.0 (2021-May-18) ==<br />
<br />
'''New Features'''<br />
<br />
* Further optimize the mapping counts generation job, including periodic 4store health checks ([https://github.com/ncbo/ncbo_cron/issues/40 ncbo/ncbo_cron#40])<br />
* Added incremental progress logging to the Annotator dictionary generation job ([https://github.com/ncbo/ncbo_annotator/issues/16 ncbo/ncbo_annotator#16])<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed the 4store health status check API ([https://github.com/ncbo/goo/issues/112 ncbo/goo#112])<br />
<br />
<br />
== BioPortal 5.20.0 (2021-April-02) ==<br />
<br />
'''New Features'''<br />
<br />
* A new CRON job that allows regenerating total mapping count and mapping count pairs on demand ([https://github.com/ncbo/ncbo_cron/issues/37 ncbo/ncbo_cron#37])<br />
* An enhancement to the ontology pull process to allow clearing caches after the full run ([https://github.com/ncbo/ncbo_cron/issues/38 ncbo/ncbo_cron#38])<br />
<br />
'''Bug Fixes'''<br />
<br />
* The mapping counts generation script failed to properly count mappings between ontoloigies ([https://github.com/ncbo/ontologies_linked_data/issues/88 ncbo/ontologies_linked_data#88])<br />
* Reported mapping counts between ontologies are always higher than the actual counts ([https://github.com/ncbo/ontologies_linked_data/issues/115 ncbo/ontologies_linked_data#115])<br />
* Incorrect mapping count statistics generated for some ontologies ([https://github.com/ncbo/ontologies_linked_data/issues/94 ncbo/ontologies_linked_data#94])<br />
* Empty pages in paged result sets ([https://github.com/ncbo/ontologies_linked_data/issues/66 ncbo/ontologies_linked_data#66])<br />
<br />
<br />
== BioPortal 5.19.0 (2020-September-04) ==<br />
<br />
'''New Features'''<br />
<br />
* A new CRON job that synchronizes the search index with the master data stored in the triple store ([https://github.com/ncbo/ncbo_cron/issues/34 ncbo/ncbo_cron#34])<br />
* An enhancement to the test runner script that uses a Dockerized instance of Redis for the tests run against<br />
<br />
'''Bug Fixes'''<br />
<br />
* A fix to the test runner script that detects when a test fails instead of always reporting SUCCESS ([https://github.com/ncbo/ontologies_linked_data/issues/111 ncbo/ontologies_linked_data#111])<br />
* Fixed a bug that prevented the ontologies report refresh from completing successfully ([https://github.com/ncbo/ncbo_cron/issues/35 ncbo/ncbo_cron#35])<br />
<br />
<br />
== BioPortal 5.18.0 (2020-July-14) ==<br />
<br />
'''New Features'''<br />
<br />
* Upgraded OWL API to version 4.5.17; updated the OWL API Wrapper to reflect this upgrade ([https://github.com/ncbo/owlapi_wrapper/releases/tag/v1.3.6 owlapi_wrapper/releases/tag/v1.3.6])<br />
* In OWL API Wrapper, expanded the list of allowed suffixes for ontology files to include .n3, .nt, .nq, .skos, .rdf, and .rdfs ([https://github.com/ncbo/owlapi_wrapper/releases/tag/v1.3.6 owlapi_wrapper/releases/tag/v1.3.6])<br />
* Implemented a script to allow an on-demand regenerating of the ontology admin report ([https://github.com/ncbo/ncbo_cron/issues/32 ncbo/ncbo_cron#32])<br />
* Implemented a script to allow an on-demand regenerating of the ontology analytics data ([https://github.com/ncbo/ncbo_cron/issues/19 ncbo/ncbo_cron#19])<br />
* Implemented a script to allow an on-demand regenerating of the ontology rank data ([https://github.com/ncbo/ncbo_cron/issues/31 ncbo/ncbo_cron#31])<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a deprecation warning `Redis#exists(key)` will return an Integer in redis-rb 4.3 ([https://github.com/ncbo/sparql-client/issues/3 ncbo/sparql-client#3], [https://github.com/ncbo/ncbo_annotator/issues/12 ncbo/ncbo_annotator#12])<br />
<br />
<br />
== BioPortal 5.17.0 (2020-June-22) ==<br />
<br />
'''New Features'''<br />
<br />
* Implemented the ability to retrieve sorted ontology classes via the search endpoint ([https://github.com/ncbo/bioportal_project/issues/165 ncbo/bioportal_project#165]). The API signature is as follows:<br/>http://data.bioontology.org/search?ontologies=NCIT&sort=prefLabel<br />
* Implemented the ability to retrieve sorted descendant classes via the subtree search endpoint ([https://github.com/ncbo/bioportal_project/issues/165 ncbo/bioportal_project#165]). The API signature is as follows:<br/>http://localhost:9393/search?subtree_ontology=NCIT&subtree_root_id=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C16275&sort=prefLabel<br />
* Implemented a test runner script that uses Dockerized versions of 4store and AllegroGraph to run the test suite. The triple store backends and their versions can now be switched seamlessly when running unit tests ([https://github.com/ncbo/ontologies_linked_data/issues/105 ncbo/ontologies_linked_data#105])<br />
<pre><br />
Usage: bundle exec ruby run_tests.rb [options]<br />
<br />
-b, --backend [4store|ag] An optional backend name. Default: 4store<br />
-v, --version VERSION An optional version of the server to test against. Default: 'latest'<br />
Must be a valid image tag published on repositories:<br />
https://hub.docker.com/r/bde2020/4store/tags for 4store<br />
https://hub.docker.com/r/franzinc/agraph/tags for ag<br />
-p, --port PORT An optional port number of the server to test against. Default: 9000 for 4store, 10035 for ag<br />
Must be a valid integer value<br />
-f, --file TEST_FILE_PATH An optional path to a test file to be run. Default: all test files<br />
-t, --test TEST_NAME An optional name of the test to be run. Default: all tests<br />
-h, --help Display this screen<br />
</pre><br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed an issue running against AllegroGraph v7+ that prevented paged calls from completing properly ([https://github.com/ncbo/goo/issues/106 ncbo/goo#106])<br />
* Fixed an issue running against AllegroGraph v7+, where a test for ontology properties failed ([https://github.com/ncbo/ontologies_linked_data/issues/106 ncbo/ontologies_linked_data#106])<br />
* Fixed an issue that caused Zlib::GzipWriter runtime errors during ontology processing ([https://github.com/ncbo/ontologies_linked_data/issues/107 ncbo/ontologies_linked_data#107])<br />
* Removed a workaround that was implemented to address a bug in AllegroGraph v6+, which caused certain SPARQL queries to fail. AllegroGraph v7.0.1 release has addressed the issue ([https://github.com/ncbo/goo/issues/104 ncbo/goo#104])<br />
* Fixed an issue that caused runtime errors when running the code against Ruby 2.7.0 and Ruby 2.7.1 ([https://github.com/ncbo/ontologies_api/issues/69 ncbo/ontologies_api#69])<br />
* Fixed an issue, where a search on term id with exact match returns irrelevant results ([https://github.com/ncbo/ontologies_api/issues/57 ncbo/ontologies_api#57])<br />
* Fixed an issue, where a call to the class descendants endpoint fails if properties are included ([https://github.com/ncbo/ontologies_api/issues/54 ncbo/ontologies_api#54])<br />
<br />
<br />
== BioPortal 5.16.0 (2020-April-16) ==<br />
<br />
'''New Features'''<br />
<br />
* Full integration with the AllegroGraph Semantic Graph Database; 4store backwards compatibility assured ([https://github.com/ncbo/bioportal_project/issues/122 ncbo/bioportal_project#122], [https://github.com/ncbo/goo/issues/100 ncbo/goo#100])<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed an issue with AllegroGraph request chain breaking with existing Goo code ([https://github.com/ncbo/goo/issues/101 ncbo/goo#101])<br />
* Fixed an issue, where no parsed ontology records appeared in AllegroGraph after ontology has been parsed ([https://github.com/ncbo/goo/issues/102 ncbo/goo#102])<br />
* Fixed an issue with the paging calls returning wrong results in AllegroGraph ([https://github.com/ncbo/goo/issues/103 ncbo/goo#103])<br />
<br />
<br />
== BioPortal 5.14.0 (2019-December-09) ==<br />
<br />
* Implemented a number of enhancements that drastically improved performance of the class descendants call ([https://github.com/metadatacenter/cedar-project/issues/980 metadatacenter/cedar-project/issues/#980])<br />
* Introduced a new version of owlapi-wrapper (OWL API v4.5.13)<br />
* Updated Solr to version 8.2.0; introduced changes to the config files to conform to the latest version of Solr<br />
* Updated code to use secure protocol for password reset URLs ([https://github.com/ncbo/ontologies_linked_data/issues/98 ncbo/ontologies_linked_data#98])<br />
<br />
<br />
== BioPortal 5.11.0 (2019-February-13) ==<br />
<br />
* Implemented the ability to index and efficiently search ontology branches ([https://github.com/ncbo/ontologies_linked_data/issues/90 ncbo/ontologies_linked_data#90])<br />
* Added path_to_root functionality to provisional classes<br />
* Migrated code to Google Analytics API v0.10; updated the library and the method calls to the new signatures<br />
* Added the ability to query properties on class descendants endpoint<br />
<br />
<br />
== BioPortal 5.8.0 (2018-April-26) ==<br />
<br />
* Implemented a configurable number of retries for 4store failures ([https://github.com/ncbo/ontologies_linked_data/issues/84 ncbo/ontologies_linked_data#84])<br />
* Added a script for running SPAM deletion form the command line, added provisional classes to SPAM deletion artifacts ([https://github.com/ncbo/ncbo_cron/issues/13 ncbo/ncbo_cron#13])<br />
* Bug Fix: Recommender fails when input includes the word "concept" ([https://github.com/ncbo/ncbo_ontology_recommender/issues/7 ncbo/ncbo_ontology_recommender#7])<br />
* Fixed the pull process to ignore submission candidates that do not pass the OWLAPI parser ([https://github.com/ncbo/ncbo_cron/issues/10 ncbo/ncbo_cron#10])<br />
<br />
<br />
== BioPortal 5.6.0 (2017-December-19) ==<br />
<br />
* Added ontologyId field to the schema in preparation for Solr upgrade<br />
* Implemented the ability to browse flat ontologies in tree view ([https://github.com/metadatacenter/cedar-project/issues/407 metadatacenter/cedar-project/issues/#407])<br />
* Developed an endpoint to retrieve all ontologies with extended metadata ([https://github.com/metadatacenter/cedar-project/issues/660 metadatacenter/cedar-project/issues/#660])<br />
* Added the ability to sort terms in "/roots" and "/tree" endpoints ([https://github.com/metadatacenter/cedar-project/issues/409 metadatacenter/cedar-project/issues/#409])<br />
<br />
<br />
== BioPortal 5.3.1 (2017-May-22) ==<br />
<br />
* Fixed an issue that prevented the [http://bioportal.bioontology.org/ontologies/HIV HIV ontology] from parsing.<br />
* Fixed an issue that caused a 404 error in the BioPortal user interface when attempting to view the class tree of the HIV ontology.<br />
* Fixed an issue that prevented proper calculation of the set of root classes for the [http://bioportal.bioontology.org/ontologies/HP HP ontology].<br />
<br />
<br />
== BioPortal 5.3.0 (2017-May-02) ==<br />
<br />
This API-only release adds a suite of REST endpoints for retrieving ontology properties. It also addresses limitations with our auto-generated API documentation.<br />
<br />
'''New Features'''<br />
<br />
* Implemented an endpoint for retrieving property trees ([https://github.com/ncbo/ontologies_api/issues/27 ontologies_api/issues/27]). [http://data.bioontology.org/documentation#ObjectProperty Documentation]. [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002210/tree Example link].<br />
* Implemented an endpoint for retrieving property roots ([https://github.com/ncbo/ontologies_api/issues/28 ontologies_api/issues/28]). [http://data.bioontology.org/ontologies/UBERON/properties/roots Example link].<br />
* Implemented an endpoint for retrieving property parents ([https://github.com/ncbo/ontologies_api/issues/29 ontologies_api/issues/29]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002210/parents Example link].<br />
* Implemented an endpoint for retrieving property children ([https://github.com/ncbo/ontologies_api/issues/30 ontologies_api/issues/30]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002203/children Example link].<br />
* Implemented an endpoint for retrieving property ancestors ([https://github.com/ncbo/ontologies_api/issues/31 ontologies_api/issues/31]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002210/ancestors Example link].<br />
* Implemented an endpoint for retrieving property descendants ([https://github.com/ncbo/ontologies_api/issues/32 ontologies_api/issues/32]). [http://data.bioontology.org/ontologies/UBERON/properties/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002286/descendants Example link].<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a bug that prevented the API documentation from being auto-generated for ontology properties endpoints ([https://github.com/ncbo/ontologies_api/issues/33 ontologies_api/issues/33]).<br />
<br />
<br />
== BioPortal 5.1.0 (2017-Apr-05) ==<br />
<br />
This is an API release, which adds two new REST endpoints as well as a number of fixes and enhancements, designed to improve the asynchronous processing of ontology data.<br />
<br />
'''New Features'''<br />
<br />
* Implemented an endpoint for searching ontology properties ([https://github.com/ncbo/ontologies_api/issues/21 ontologies_api/issues/21]). [http://data.bioontology.org/documentation#nav_prop_search Documentation]. [http://data.bioontology.org/property_search?q=pref+label Example link].<br />
* Implemented an endpoint for retrieving a specific ontology property by its ID ([https://github.com/ncbo/ontologies_api/issues/22 ontologies_api/issues/22]). [http://data.bioontology.org/ontologies/BIBFRAME/properties/http%3A%2F%2Fid.loc.gov%2Fontologies%2Fbibframe%2FvoiceType Example link].<br />
<br />
'''Enhancements'''<br />
<br />
* Improved logging of the CRON job processing<br />
* A more robust error handling of the CRON batch operations<br />
* A new CRON task that allows indexing ontology properties<br />
* An enhanced ontology processing script that now accepts a list of tasks to be performed<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a bug that prevented mappings from being saved in a file correctly during processing ([https://github.com/ncbo/ontologies_linked_data/issues/70 ontologies_linked_data/issues/70]).<br />
<br />
<br />
== BioPortal 5.0.0 (2017-Feb-06) ==<br />
<br />
This release represents an overhaul of our user interface, using bootstrap as the front-end framework to enable immediate and longer-term improvements. (Since the October 2016 release, we have also made a number of minor changes, mostly under the hood, and recently added a few significant features to the Recommender; Release Notes will be added shortly for those changes.)<br />
<br />
Please Note: Although we are aware of some bugs that have surfaced since the transition, so far they have been relatively minor and most can be worked around by re-sizing the page or changing tabs. We will be working to squash those bugs in the next few days, so please bear with us for this brief period.<br />
<br />
'''Enhancements'''<br />
<br />
* Released new BioPortal user interface, including the features described below.<br />
* Implemented new UI framework based on boostrap, enabling cleaner management of all UI elements.<br />
* Redesigned the front page to provide cleaner and more informative look and feel, and put key features front and center.<br />
* Added graph to show top ontology access counts, replacing table with similar information.<br />
* Redesigned header to move most links to the menu bar, simplifying header and unifying it across all pages.<br />
* Redesigned footer to include appropriate and cleanly presented content, including social links, unified across all pages.<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed an issue with the prompt for the ontology search on the front page, which would not produce desired results.<br />
* Fixed layout issues in front page header.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=12970BioPortal Help2018-03-06T01:02:13Z<p>JenniferVendetti: Add citation instructions for Recommender</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Resource Index Tab|search biomedical resources]] for a term<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
To '''cite the NCBO Ontology Recommender''', please use:<br />
<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Resource Index Tab ===<br />
<br />
The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button. <br />
<br />
To '''access annotations for resources programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide Resource Index REST API documentation].<br />
<br />
Further information on ontology-based search and mining of biomedical resources is available in [http://www.ncbi.nlm.nih.gov/pubmed/21918645 Jonquet et al Web Semant. 2011 Sep 1;9(3):316-324], [http://www.ncbi.nlm.nih.gov/pubmed/21550421 LePendu et al J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8] and [http://www.ncbi.nlm.nih.gov/pubmed/22494789 Liu et al J Am Med Inform Assoc. 2012 Apr 11]<br />
<br />
If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
If you haven’t already signed up for an account at the BioPortal website, you’ll need to do that first:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology, e.g., name, acronym, etc. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <span id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Help&diff=12969BioPortal Help2018-03-06T00:56:39Z<p>JenniferVendetti: Add citation instructions for Recommender</p>
<hr />
<div>== User Interface ==<br />
=== Home Page ===<br />
<br />
BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to <br />
* [[#Browse Tab|browse the library]] of ontologies<br />
* [[#Search Tab|search for a term]] across multiple ontologies<br />
* [[#Mappings Tab|browse mappings]] between terms in different ontologies<br />
* [[#Recommender Tab|receive recommendations]] on which ontologies are most relevant for a corpus<br />
* [[#Annotator Tab|annotate text]] with terms from ontologies<br />
* [[#Resource Index Tab|search biomedical resources]] for a term<br />
* [[#Projects Tab|browse a selection of projects]] that use BioPortal resources<br />
<br />
All information available through the BioPortal Web site is also available through the NCBO Web service REST API. Please see [http://data.bioontology.org/documentation REST API documentation] for more information.<br />
<br />
=== Browse Tab ===<br />
<br />
Browse our library of Biomedical ontologies and submit your own ontology. This page displays some summary information about each ontology. More detailed summary information is available on the ontology summary page for each ontology. You can reach this page by clicking on the ontology name link.<br />
<br />
To '''find a particular ontology quickly''', begin typing the ontology name or abbreviation in the “Filter by Text” field. You can also narrow the list of ontologies shown by selecting a specific “category” (a domain) or a “group” to which the ontology belongs. To '''submit an ontology''' press the “Submit New Ontology” button. You must be logged in to BioPortal to submit an ontology. You can subscribe to '''receive RSS updates''' when any ontology in the system changes by clicking the subscribe link. You can subscribe to updates for a particular ontology from the summary page for that ontology. To go to the summary page click on the ontology name link.<br />
<br />
Some submitters want to control who can browse the terms in their ontology. These ontologies are marked with visibility “Private” or “Licensed”. To browse the terms in these ontologies you must be both <br />
* logged in to BioPortal<br />
* granted access to the ontology<br />
For '''private ontologies''', the ontology submitter directly controls access to the ontology. Please contact the submitter to gain access to a private ontology. Contact information for the ontology is available on the ontology summary page. For '''licensed ontologies''', the submitter indirectly controls access to the ontology. When you attempt to access a licensed ontology, the system will prompt you to enter the license information required by the submitter. When you have entered the required information, the system will allow you to access the ontology. In addition, there are '''"summary only" ontologies'''. The terms for these ontologies are not available in BioPortal at all. Please contact the ontology submitter for more information about these ontologies.<br />
<br />
To '''access ontologies programmatically''', see our [http://data.bioontology.org/documentation#nav_resource_endpoints Resources REST API documentation] (then look under Media Types).<br />
<br />
=== Search Tab ===<br />
<br />
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.<br />
<br />
To '''find a term in any ontology''' enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to '''search only in a subset of ontologies''' you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link. <br />
<br />
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned. <br />
<br />
To '''search programmatically''' see our [http://data.bioontology.org/documentation#nav_search Search REST API documentation].<br />
<br />
=== Mappings Tab ===<br />
<br />
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings Mapping Documentation]).<br />
<br />
To '''browse mappings''' for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.<br />
<br />
To '''access mappings programmatically''', please see our [http://data.bioontology.org/documentation#Mapping Mappings REST API documentation].<br />
<br />
=== Recommender Tab ===<br />
<br />
The Recommender takes as input a text or a list of keywords and '''suggests appropriate ontologies''' for it.<br />
<br />
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:<br />
* '''Coverage''': At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology.<br />
* '''Acceptance''': How well-known and trusted is the ontology by the biomedical community? The number of visits to the ontology page in BioPortal and the presence or absence of the ontology in UMLS are used to compute an acceptance score for each ontology.<br />
* '''Detail of knowledge''': What is the level of detail provided by the ontology for the input data? It is computed using the number of definitions, synonyms and properties of the ontology classes that cover the input data.<br />
* '''Specialization''': How specialized is the ontology to the input data’s domain? It is calculated using the number and type of the annotations done with the ontology and the position of each annotated class in the ontology hierarchy. The result is normalized by the size of the ontology, in order to identify small ontologies that are specialized to the input data.<br />
<br />
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.<br />
<br />
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.<br />
<br />
To '''retrieve ontology recommendations programmatically''', please see our [http://data.bioontology.org/documentation#nav_recommender Ontology Recommender REST API documentation].<br />
<br />
=== Annotator Tab ===<br />
<br />
To '''generate annotations for text''', simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids. <br />
<br />
In addition to the direct matches, the user may '''expand the set of matches''' by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.<br />
<br />
<br />
To '''generate annotations programmatically''' see the [http://www.bioontology.org/wiki/index.php/Annotator_User_Guide REST API documentation].<br />
<br />
Further information about the workings of the Annotator is available at [http://www.ncbi.nlm.nih.gov/pubmed/19761568 Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14]<br />
<br />
=== Resource Index Tab ===<br />
<br />
The resource index is a pre-calculated set of annotations of selected biomedical resources. We have used the Annotator web service to annotate these resources with all terms in all ontologies in BioPortal. To retrieve records annotated with a specific ontology term, select the term in the search box and press the "Search" button. <br />
<br />
To '''access annotations for resources programmatically''', please see our [http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide Resource Index REST API documentation].<br />
<br />
Further information on ontology-based search and mining of biomedical resources is available in [http://www.ncbi.nlm.nih.gov/pubmed/21918645 Jonquet et al Web Semant. 2011 Sep 1;9(3):316-324], [http://www.ncbi.nlm.nih.gov/pubmed/21550421 LePendu et al J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8] and [http://www.ncbi.nlm.nih.gov/pubmed/22494789 Liu et al J Am Med Inform Assoc. 2012 Apr 11]<br />
<br />
If you know of a publicly available biomedical resource that you would like to see in the Resource Index please send a request to include it to support@bioontology.org.<br />
<br />
=== Projects Tab ===<br />
<br />
This page shows selected projects which make use of BioPortal technology. To '''add your project''' to this list press the "Create New Project" button. You must be logged in to BioPortal to create a new project.<br />
<br />
== Common Tasks ==<br />
<br />
=== Submitting an ontology ===<br />
If you haven’t already signed up for an account at the BioPortal website, you’ll need to do that first:<br />
<br />
http://bioportal.bioontology.org/accounts/new<br />
<br />
Once you have an account and are logged in, navigate to the Browse page:<br />
<br />
http://bioportal.bioontology.org/ontologies<br />
<br />
… and click the "Submit New Ontology" button.<br />
<br />
In the resulting form, you’ll be asked to fill out some metadata about your ontology, e.g., name, acronym, etc. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it. <br />
<br />
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file. <br />
<br />
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on. <br />
<br />
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.<br />
<br />
=== Viewing and editing mappings ===<br />
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.<br />
<br />
=== Viewing and editing notes ===<br />
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.<br />
<br />
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.<br />
<br />
=== Viewing and editing reviews ===<br />
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.<br />
<br />
=== Visualizing concepts and mappings ===<br />
With the BioPortal user interface, you can [http://www.bioontology.org/wiki/index.php/Visualizing_Concepts_and_Mappings visualize ontology concepts and their mappings with other ontologies].<br />
<br />
== Programming with the BioPortal API ==<br />
Documentation about how to use the BioPortal REST API to access information is available here:<br />
<br />
http://data.bioontology.org/documentation<br />
<br />
=== Getting an API key ===<br />
Use of the BioPortal REST API requires an API key. <br />
<br />
To retrieve your API key, log into your account on the [http://bioportal.bioontology.org BioPortal website]. If you don't have an account, you'll need to [http://bioportal.bioontology.org/accounts/new create one].<br />
<br />
Your API key will be listed in plain text on your account page.<br />
<br />
== Glossary ==<br />
; <span id="glossary_class">class</span>: A concept in the domain of the ontology. Used within BioPortal, class is a synonym for term or concept. Term is the preferred BioPortal label.<br />
; concept: (from SKOS documentation) A concept is an idea or notion; a unit of thought. <br />
; CUI: Abbreviation for "Concept Unique Identifier". These values that are assigned by UMLS for all terms in its ontologies. A CUI represents a "UMLS concept". An ontology term may be assigned to more than one CUI. The assignment of terms to CUI is intended to allow the creation of maps between terms in different ontologies. <br />
; deprecated term: synonym for "obsolete term" in some ontologies.<br />
; group: a collection of ontologies that are typically associated with some outside group or organization. <br />
; <span id="glossary_obsolete_term">obsolete term</span>: A term that the authors of the ontology have flagged as being "obsolete" and which they recommend that people not use. These terms are often left in ontologies (rather than removing them entirely) so that existing systems that depend on them will continue to function.<br />
; mapping: Asserted relationship between two terms in different ontologies. The nature of the exact relationship is left to the mapping author. The most common relationship for mappings between terms is "same as".<br />
; preferred name : Human readable label for a term that the authors of the ontology suggest be used when referring to the term. Alternate, non-preferred, names are synonyms.<br />
; <span id="glossary_property">property</span>: Named association between two entities. Examples are "definition" (a relation between a term and some text) and "part-of" (a relation between two terms). <br />
; resource: Biomedical resource (publication, database) that has been indexed with the ontologies in BioPortal.<br />
; <span id="slice_definition">slice</span>: An alternate entry point into BioPortal which has been configured to display and use a subset of the available ontologies. The slice is accessed via URL of the form http://<slice-name>.bioportal.bioontology.org . There is currently no way for an end user to create or configure slice. However, you may send a request to support@bioontology.org and request that a new slice be created for you.<br />
; synonym: Alternate name for a term. Every term has a single "preferred" name and may have any number of synonyms.<br />
; term: Concept in the domain of the ontology. Within BioPortal, term is a synonym for class or concept. Term is the preferred label.<br />
; term mappings: Set of mappings for a given term to terms other ontologies. <br />
; term resources: Set of resources that contain annotations for a given term.<br />
<br />
== How to cite NCBO and BioPortal ==<br />
=== NCBO ===<br />
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.<br />
<br />
===NCBO Ontology Recommender===<br />
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).<br />
<br />
=== BioPortal ===<br />
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.<br />
<br />
=== SPARQL Endpoint ===<br />
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=12955Main Page2017-12-07T00:44:45Z<p>JenniferVendetti: Add link to documentation of SKOS support</p>
<hr />
<div>Welcome to the '''National Center for Biomedical Ontology (NCBO) public wiki'''. This wiki provides information about collaborative ontology development efforts, as well as user guides and technical documentation for software developed by NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
To follow is a list of software developed and maintained by NCBO:<br />
<br />
* [https://bioportal.bioontology.org BioPortal] - A web-based application for accessing and sharing biomedical ontologies<br />
* [https://data.bioontology.org/ BioPortal REST API] - A RESTful API to access BioPortal content<br />
* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - Contains BioPortal and the BioPortal REST API, runs on Linux<br />
* [http://sparql.bioontology.org/ BioPortal SPARQL Endpoint] - Access BioPortal content via SPARQL queries ''(obsolete)''<br />
<br />
Please refer to our [[BioPortal_Release_Notes|release notes]] page for change logs.<br />
<br />
<br />
== Documentation ==<br />
<br />
*[[BioPortal Help|BioPortal]] - get help with the user interface and instructions for commonly performed tasks<br />
* [http://data.bioontology.org/documentation BioPortal REST API] - see a list of available endpoints with usage instructions<br />
* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - read a getting started guide and installation instructions<br />
* [[Using_NCBO_Technology_In_Your_Project|Using NCBO technologies in your project]] - get ideas for how to employ NCBO technologies in your website or application<br />
* [[SKOSSupport|SKOS support]] - view the specifics of BioPortal's support for SKOS vocabularies<br />
* [[SPARQL_BioPortal|BioPortal SPARQL Endpoint]] - read about programmatic submission of SPARQL queries and the named graph structure<br />
* [[NCBO_Developer_Documentation|Developer documentation]]<br />
<br />
<br />
<br />
== Ontology Development Projects ==<br />
<br />
These are some of the ontology development projects that NCBO has participated in:<br />
<br />
* [http://bioportal.bioontology.org/ontologies/BRO Biomedical Resource Ontology]<br />
* [http://bioportal.bioontology.org/ontologies/TMO Translational Medicine Ontology] <br />
* [[NPO:Main_Page|NanoParticle Ontology]] <br />
* [http://bioportal.bioontology.org/ontologies/PATO Phenotypic Quality Ontology]<br />
* [[RO:Main_Page|OBO Relations Ontology]]<br />
* [[CARO:Main_Page|Common Anatomy Reference Ontology]]<br />
* [[CL:Main_Page|Cell Ontology]]<br />
* [[SO:Main_Page|Sequence Types and Features Ontology]]<br />
* [[Disease:Main_Page|Disease Ontology]], and other ontologies pertaining to diseases and disorders<br />
* [[OCI:Main_Page|Ontology of Clinical Investigation]]</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12954SKOSSupport2017-12-04T22:30:47Z<p>JenniferVendetti: Separate out skos:broader into it's own section</p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
<br />
==== Hierarchy in SKOS vocabularies ====<br />
<br />
The only semantic relationship in SKOS vocabularies that BioPortal uses to construct and display concept hierarchies is the skos:broader property.<br />
<br />
ex:mammals rdf:type skos:Concept;<br />
skos:prefLabel "mammals"@en;<br />
skos:broader ex:animals.<br />
<br />
Other properties used to denote hierarchical relationships like skos:narrower, skos:broaderTransitive, and skos:narrowerTranstive, are ignored.<br />
<br />
<br />
==== Metrics data for SKOS vocabularies ====<br />
<br />
BioPortal uses the [https://owlcs.github.io/owlapi/ OWL API] for parsing all ontology and vocabulary submissions, as well as for the calculation of metrics data. The OWL API treats SKOS vocabularies as RDF files containing classes and instances. According to the SKOS Reference, concepts are [https://www.w3.org/TR/skos-reference/#L842 instances of owl:Class], and thus are counted as instances (a.k.a. "individuals").<br />
<br />
When viewing metrics tables in the BioPortal user interface, the value for the "NUMBER OF INDIVIDUALS" corresponds to the number of concepts in any given SKOS vocabulary.<br />
<br />
<br />
[[File:Metrics.png|none|frame|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
<br />
==== SKOS-XL ====<br />
<br />
Currently BioPortal offers no support for the [https://www.w3.org/TR/skos-reference/#xl SKOS eXtension for Labels (SKOS-XL)]. A suggested workaround for SKOS vocabularies that make use of SKOS-XL, is to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
<br />
==== SKOS mapping properties ====<br />
<br />
At this time, BioPortal doesn't use SKOS mapping properties, i.e., skos:*Match, to populate the mapping repository. One-to-one mappings between SKOS concepts need to be uploaded separately via the [http://data.bioontology.org/documentation BioPortal REST API].</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12953SKOSSupport2017-12-04T20:27:36Z<p>JenniferVendetti: </p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
<br />
==== Metrics data for SKOS vocabularies ====<br />
<br />
BioPortal uses the [https://owlcs.github.io/owlapi/ OWL API] for parsing all ontology and vocabulary submissions, as well as for the calculation of metrics data. The OWL API treats SKOS vocabularies as RDF files containing classes and instances. According to the SKOS Reference, concepts are [https://www.w3.org/TR/skos-reference/#L842 instances of owl:Class], and thus are counted as instances (a.k.a. "individuals").<br />
<br />
When viewing metrics tables in the BioPortal user interface, the value for the "NUMBER OF INDIVIDUALS" corresponds to the number of concepts in any given SKOS vocabulary.<br />
<br />
<br />
[[File:Metrics.png|none|frame|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
<br />
==== SKOS-XL ====<br />
<br />
Currently BioPortal offers no support for the [https://www.w3.org/TR/skos-reference/#xl SKOS eXtension for Labels (SKOS-XL)]. A suggested workaround for SKOS vocabularies that make use of SKOS-XL, is to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
<br />
==== SKOS mapping properties ====<br />
<br />
At this time, BioPortal doesn't use SKOS mapping properties, i.e., skos:*Match, to populate the mapping repository. One-to-one mappings between SKOS concepts need to be uploaded separately via the [http://data.bioontology.org/documentation BioPortal REST API].</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12952SKOSSupport2017-12-04T20:19:51Z<p>JenniferVendetti: </p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
<br />
==== Metrics data for SKOS vocabularies ====<br />
<br />
BioPortal uses the [https://owlcs.github.io/owlapi/ OWL API] for parsing all ontology and vocabulary submissions, as well as for the calculation of metrics data. The OWL API treats SKOS vocabularies as RDF files containing classes and instances. According to the SKOS Reference, concepts are [https://www.w3.org/TR/skos-reference/#L842 instances of owl:Class], and thus are counted as instances (a.k.a. "individuals").<br />
<br />
When viewing metrics tables in the BioPortal user interface, the value for the "NUMBER OF INDIVIDUALS" corresponds to the number of concepts in any given SKOS vocabulary.<br />
<br />
<br />
[[File:Metrics.png|none|frame|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
<br />
==== SKOS-XL ====<br />
<br />
Currently BioPortal offers no support for the [https://www.w3.org/TR/skos-reference/#xl SKOS eXtension for Labels (SKOS-XL)]. A suggested workaround for SKOS vocabularies that make use of SKOS-XL, is to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
<br />
==== Note on mapping properties ====<br />
<br />
As of now, skos:*Match properties are parsed as any properties, but will not be used to populated BioPortal's mapping repository. <br />
One-to-one mappings between concepts need to be uploaded aside using the REST API.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12951SKOSSupport2017-12-04T20:16:45Z<p>JenniferVendetti: Rewrite Metrics section</p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
<br />
==== Metrics data for SKOS vocabularies ====<br />
<br />
BioPortal uses the [https://owlcs.github.io/owlapi/ OWL API] for parsing all ontology and vocabulary submissions, as well as for the calculation of metrics data. The OWL API treats SKOS vocabularies as RDF files containing classes and instances. According to the SKOS Reference, concepts are [https://www.w3.org/TR/skos-reference/#L842 instances of owl:Class], and thus are counted as instances (a.k.a. "individuals").<br />
<br />
When viewing metrics tables in the BioPortal user interface, the value for the "NUMBER OF INDIVIDUALS" corresponds to the number of concepts in any given SKOS vocabulary.<br />
<br />
<br />
[[File:Metrics.png|none|frame|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
<br />
==== SKOS-XL ====<br />
<br />
Currently BioPortal offers no support for the SKOS eXtension for Labels (SKOS-XL). A suggested workaround for SKOS vocabularies that make use of SKOS-XL, is to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
<br />
==== Note on mapping properties ====<br />
<br />
As of now, skos:*Match properties are parsed as any properties, but will not be used to populated BioPortal's mapping repository. <br />
One-to-one mappings between concepts need to be uploaded aside using the REST API.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12950SKOSSupport2017-12-04T19:43:57Z<p>JenniferVendetti: </p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
<br />
==== Note on metrics ====<br />
<br />
[[File:Metrics.png|thumb|400px|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
Because BioPortal's metrics are mostly being computed by the OWL-API, a SKOS vocabulary will be then treated like any RDF file with classes and instances. According to the SKOS specification, because skos:Concept are instances, they will be counted as "individuals" (not class). <br />
Therefore, when looking a the metrics, one shall consider that the number of individuals reports the number of concepts in the vocabulary and not the number of classes like this is the case with OWL format ontologies.<br />
<br />
<br />
==== SKOS-XL ====<br />
<br />
Currently BioPortal offers no support for the SKOS eXtension for Labels (SKOS-XL). A suggested workaround for SKOS vocabularies that make use of SKOS-XL, is to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
<br />
==== Note on mapping properties ====<br />
<br />
As of now, skos:*Match properties are parsed as any properties, but will not be used to populated BioPortal's mapping repository. <br />
One-to-one mappings between concepts need to be uploaded aside using the REST API.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12949SKOSSupport2017-12-04T19:31:43Z<p>JenniferVendetti: </p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
==== Note on metrics ====<br />
<br />
[[File:Metrics.png|thumb|400px|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
Because BioPortal's metrics are mostly being computed by the OWL-API, a SKOS vocabulary will be then treated like any RDF file with classes and instances. According to the SKOS specification, because skos:Concept are instances, they will be counted as "individuals" (not class). <br />
Therefore, when looking a the metrics, one shall consider that the number of individuals reports the number of concepts in the vocabulary and not the number of classes like this is the case with OWL format ontologies.<br />
<br />
==== Note on SKOS-XL ====<br />
<br />
SKOS-XL extension of the SKOS format is currently not supported by BioPortal.<br />
It is advised to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
==== Note on mapping properties ====<br />
<br />
As of now, skos:*Match properties are parsed as any properties, but will not be used to populated BioPortal's mapping repository. <br />
One-to-one mappings between concepts need to be uploaded aside using the REST API.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12948SKOSSupport2017-12-04T19:28:58Z<p>JenniferVendetti: /* skos:Concept */</p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. <br />
<br />
See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
'''Note:''' Some OWL ontologies declare the SKOS namespace to facilitate minimal use of SKOS constructs for things like labels (e.g., skos:prefLabel, skos:altLabel) or mappings (e.g., skos:exactMatch, skos:broaderMatch). In these cases, the proper format for new ontology submissions is OWL, not SKOS.<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
==== Note on metrics ====<br />
<br />
[[File:Metrics.png|thumb|400px|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
Because BioPortal's metrics are mostly being computed by the OWL-API, a SKOS vocabulary will be then treated like any RDF file with classes and instances. According to the SKOS specification, because skos:Concept are instances, they will be counted as "individuals" (not class). <br />
Therefore, when looking a the metrics, one shall consider that the number of individuals reports the number of concepts in the vocabulary and not the number of classes like this is the case with OWL format ontologies.<br />
<br />
==== Note on SKOS-XL ====<br />
<br />
SKOS-XL extension of the SKOS format is currently not supported by BioPortal.<br />
It is advised to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
==== Note on mapping properties ====<br />
<br />
As of now, skos:*Match properties are parsed as any properties, but will not be used to populated BioPortal's mapping repository. <br />
One-to-one mappings between concepts need to be uploaded aside using the REST API.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12947SKOSSupport2017-12-04T19:11:57Z<p>JenniferVendetti: /* skos:ConceptScheme & skos:hasTopConcept */</p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
__TOC__<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
If you declare the skos name space only for the purpose of using SKOS properties for label or mapping, it is not needed to select the SKOS format when uploading your ontology. Use the normal OWL format instead.<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes<br />
<br />
If your vocabulary declares more than one concept scheme, all of the top concepts will be aggregated and displayed as root level concepts. BioPortal's user interface doesn't provide support for grouping top level concepts by concept scheme. It is recommended to declare a owl:Ontology, especially for metadata annotations.<br />
<br />
===== skos:broader hierachy =====<br />
<br />
For the hierarchy to be handle and display properly by BioPortal, hierarchical relations between skos:Concept need to defined by the skos:broader. <br />
If another property is used (narrower, transitive), it is not an issue, but BioPortal will display hierarchies on based on skos:broader properties. <br />
<br />
ex:zebra rdf:type skos:Concept;<br />
skos:inScheme ex:animalThesaurus;<br />
skos:prefLabel "Plains zebra";<br />
skos:altLabel "Equus quagga";<br />
skos:broader ex:mammals.<br />
<br />
==== Note on metrics ====<br />
<br />
[[File:Metrics.png|thumb|400px|PLOS Thesaurus metrics in BioPortal]]<br />
<br />
Because BioPortal's metrics are mostly being computed by the OWL-API, a SKOS vocabulary will be then treated like any RDF file with classes and instances. According to the SKOS specification, because skos:Concept are instances, they will be counted as "individuals" (not class). <br />
Therefore, when looking a the metrics, one shall consider that the number of individuals reports the number of concepts in the vocabulary and not the number of classes like this is the case with OWL format ontologies.<br />
<br />
==== Note on SKOS-XL ====<br />
<br />
SKOS-XL extension of the SKOS format is currently not supported by BioPortal.<br />
It is advised to dump the value of labels (i.e., skosxl:literalForm of skosxl:*Label instances) into the corresponding skos:*Label property.<br />
<br />
==== Note on mapping properties ====<br />
<br />
As of now, skos:*Match properties are parsed as any properties, but will not be used to populated BioPortal's mapping repository. <br />
One-to-one mappings between concepts need to be uploaded aside using the REST API.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12938SKOSSupport2017-12-01T18:48:16Z<p>JenniferVendetti: </p>
<hr />
<div>[[File:Plos_thesaurus_class_tree.png|thumb|400px|PLOS Thesaurus concept tree in BioPortal]]<br />
<br />
<br />
<br />
__TOC__<br />
<br />
<br />
=== Support for SKOS vocabularies in BioPortal ===<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.<br />
<br />
Please note that the SKOS constructs described here are handled only for vocabularies that are identified as SKOS when they are submitted to BioPortal. Vocabularies submitted as OWL or OBO formats are not examined for SKOS constructs.<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
<br />
===== skos:Concept =====<br />
<br />
''Concepts'' are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:<br />
<br />
<nowiki><http://www.example.com/animals></nowiki> rdf:type skos:Concept<br />
<br />
In SKOS vocabularies, BioPortal only treats the SKOS concept assertions as concepts to be displayed. If the vocabulary contains other assertions about other types of concepts, BioPortal will not treat these as concepts in any of its displays or features. See the W3C's SKOS System Primer and SKOS Reference for concept documentation and examples:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secconcept<br />
<br />
https://www.w3.org/TR/skos-reference/#concepts<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====<br />
<br />
For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes. <br />
<br />
In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).<br />
<br />
The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:<br />
<br />
@prefix skos: <nowiki><http://www.w3.org/2004/02/skos/core#></nowiki> .<br />
@prefix rdf: <nowiki><http://www.w3.org/1999/02/22-rdf-syntax-ns#></nowiki> .<br />
@prefix ex: <nowiki><http://www.example.com/></nowiki> .<br />
<br />
ex:animalThesaurus rdf:type skos:ConceptScheme;<br />
skos:hasTopConcept ex:mammals;<br />
skos:hasTopConcept ex:fish.<br />
<br />
SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes</div>JenniferVendetti