NCBO Wiki - User contributions [en]

RDF in BioPortal

2010-07-12T19:13:52Z

Natasha: /* Accessing RDF content */

This page describes representation of ontologies in the [http://bioportal.bioontology.org NCBO BioPortal] and individual classes in these ontologies in [http://www.w3.org/RDF/ RDF]. Please send comments and questions to [mailto:support@bioontology.org support@bioontology.org].

You can access RDF graphs for all BioPortal ontologies at our prototype [http://sparql.bioontology.org SPARQL endpoint].

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

# Provide RDF for each class in BioPortal so that we can have a URL to a concept that resolves to a set of RDF triples that provide essential information about the term.
# Provide an RDF dump of each ontology in BioPortal to put them in a tripelstore to enable SPARQL access to the ontologies

Our goal was ''not'' to provide an RDF graph that covers the complete content of each ontology. Rather, we wanted to provide uniform RDF format for all the terms from the ontologies that were originally developed in different formats.

= Providing URIs =

In order to have an RDF graph for each term, we must have an http URI for the term. We used the following approach to determine the URIs for the terms for ontologies in different formats:

* '''OWL and RDF ontologies''': these ontologies already have http URIs for each resource that they define. We used the URIs provided by ontology authors.
* '''OBO ontologies''': terms in the ontologies in the OBO format do not have http URIs. We used the same URIs that the [http://docs.google.com/Doc?docid=0Acx6Blq96uycZHpwcm5td18wZGtkMmdiZ3Y&hl=en OBO library uses for these terms]
** <tt>http://purl.obolibrary.org/obo/IDSPACE_LOCALID</tt>
** For example: http://purl.obolibrary.org/obo/GO_0050918
* '''RRF and Protege ontologies''': terms in these ontologies do not have http URIs. We generate the URIs in the following form for these terms:
** <tt>http://purl.bioontology.org/ontology/{Acronym}/{ID}</tt>

= Accessing RDF content =

There are two ways to access the RDF content that we generate for BioPortal ontologies and their terms:
# Use the [http://sparwl.bioontology.org NCBO prototype SPARQL endpoint]
# Use the [http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Term_Service RDF Term Service] to get an RDF snippet for a single term or several terms and the
[http://www.bioontology.org/wiki/index.php/NCBO_REST_services#RDF_Download_Service RDF Download Service] to download the whole ontology in RDF. Note that the second service will provide only some basic information about each term, not all the relations that are defined in the ontology.

= Content of the RDF graph =

For each term in BioPortal, we provide the following information in the RDF graph:

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader and skos:narrower for terms from RRF ontologies
* all annotation properties for terms in OWL ontologies
* part-of relations for OBO terms

RDF in BioPortal

2010-07-12T19:11:38Z

Natasha: New page: This page describes representation of ontologies in the [http://bioportal.bioontology.org NCBO BioPortal] and individual classes in these ontologies in [http://www.w3.org/RDF/ RDF]. Please...

BioPortal Mappings

2010-07-12T18:49:26Z

Natasha: /* Mappings in BioPortal */

This page defines common mappings types in the [http://bioportal.bioontology.org NCBO BioPortal] and provides examples of different mappings that already exist in BioPortal. We welcome comments on this set of mapping relations. Please send email to [mailto:support@bioontology.org support@bioontology.org].

= BioPortal Mapping Types =

There are mappings of the following types in BioPortal:

* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual
* '''exact match''': [http://www.w3.org/2008/05/skos#exactMatch skos:exactMatch]
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. <tt>skos:exactMatch</tt> is a transitive property, and is a sub-property of <tt>skos:closeMatch</tt>.
* '''close match''': [http://www.w3.org/2008/05/skos#closeMatch skos:closeMatch]
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property.
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource.
* '''homologous to''' (for anatomical terms): ''not defined yet''
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).

= Survey of BioPortal Mappings =
The table below presents the statistics and examples of BioPortal mappings as of July 2010.

{| border="1" cellpadding="2"
| align="center" style="background:#f0f0f0;"|'''relationship'''
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Total mappings'''
| align="center" style="background:#f0f0f0;"|'''Notes'''
|-
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings
|-
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym
|-
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings
|-
| skos:closeMatch||lexical similarity||Automatic with manual review||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology
|-
| owl:sameAs||shared id||Manual||LOOM||271,000||Mappings between the terms that share the same ID
|-
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms
|-
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs
|-
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO
|-
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings
|-
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface
|-
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT
|-
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity
|-
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT
|}

BioPortal Mappings

2010-07-12T18:39:42Z

Natasha: /* Survey of BioPortal Mappings */

= Mappings in BioPortal =

This page defines common mappings types in the [http://bioportal.bioontology.org NCBO BioPortal] and provides examples of different mappings that already exist in BioPortal. We welcome comments on this set of mapping relations. Please send email to [mailto:support@bioontology.org support@bioontology.org].

== BioPortal Mapping Types ==

There are mappings of the following types in BioPortal:

* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual
* '''exact match''': [http://www.w3.org/2008/05/skos#exactMatch skos:exactMatch]
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. <tt>skos:exactMatch</tt> is a transitive property, and is a sub-property of <tt>skos:closeMatch</tt>.
* '''close match''': [http://www.w3.org/2008/05/skos#closeMatch skos:closeMatch]
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property.
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource.
* '''homologous to''' (for anatomical terms): ''not defined yet''
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).

== Survey of BioPortal Mappings ==
The table below presents the statistics and examples of BioPortal mappings as of July 2010.

{| border="1" cellpadding="2"
| align="center" style="background:#f0f0f0;"|'''relationship'''
| width="125" align="center" style="background:#f0f0f0;"|'''basis'''
| align="center" style="background:#f0f0f0;"|'''Manual/Automatic'''
| align="center" style="background:#f0f0f0;"|'''Source'''
| align="center" style="background:#f0f0f0;"|'''Total mappings'''
| align="center" style="background:#f0f0f0;"|'''Notes'''
|-
| skos:closeMatch||identical UMLS CUIs||Manual||LEXEVS_UMLS_MAPPER||2,028,186||Mappings between terms in UMLS ontologies that were created automatically, linking terms with the same CUI. Because CUIs were assigned manually by UMLS editors, we treat these mapings as manual mappings
|-
| skos:closeMatch||lexical similarity||Automatic||LOOM||1,449,303||Mappings were generated by the LOOM algorithm automatically based on close lexical match between preferred names of terms or a preferred name and a synonym
|-
| skos:closeMatch||lexical similarity||Automatic||||2,562||Mappings were generated automatically based on the exact match of preferred names or synonyms for terms in FMA, ZFA, and mouse anatomy. Note: These mappings are likely homology mappings
|-
| skos:closeMatch||lexical similarity||Automatic with manual review||||628||Mappings were generated manually by a user and uploaded to BioPortal. The mappings were generated automatically based on lexical similarity but later manually reviewed by a domain expert. All mappings involve terms in the MGED ontology
|-
| owl:sameAs||shared id||Manual||LOOM||271,000||Mappings between the terms that share the same ID
|-
| rdfs:seeAlso||OBO xref||Manual||||17,776||Mappings based on OBO xref mappings, which indicate related terms
|-
| skos:exactMatch||Dbxref||Manual||||7,028||Mappings based on the use of Dbxref to indicate term reuse in OBO Foundry ontologies. Very close to having identical ids, but because the ids are different, we use exact match rather than owl:sameAs
|-
| skos:exactMatch||||Manual||||68||Mappings generated manually by a user; all involve terms from NEMO
|-
| skos:closeMatch||identical UMLS CUIs||Manual||||902||Mappings between non-UMLS ontologies where concepts do have cui. So, technically, similar to inter-cui mappings
|-
| skos:closeMatch||||Manual||BioPortal UI||117||Mappings created by users through the BioPortal user interface
|-
| skos:closeMatch||||Manual||NCICB||3078||Manual mappings between Mouse anatomy and NCIT
|-
| skos:closeMatch||lexical similarity||Automatic||EFO||673||Mappings generated automatically based on lexical similarity
|-
| skos:closeMatch||||Manual||NLM||2,662||Manual mappings between Mouse anatomy and NCIT
|}

BioPortal Mappings

2010-07-12T18:21:24Z

Natasha: /* BioPortal Mapping Types */

BioPortal Mappings

2010-07-12T18:16:46Z

Natasha: New page: = BioPortal Mapping Types = There are mappings of the following types in BioPortal: * '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs] ** '''Definition''' (f...

= BioPortal Mapping Types =

There are mappings of the following types in BioPortal:

* '''identical, the same''' : [http://www.w3.org/2002/07/owl#sameAs owl:sameAs]
** '''Definition''' (from [http://www.w3.org/TR/owl-ref/#sameAs-def OWL]): <tt>owl:sameAs</tt> is used to state that two URI references refer to the same individual
* '''exact match''': [http://www.w3.org/2008/05/skos#exactMatch skos:exactMatch]
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS]): The property <tt>skos:exactMatch</tt> is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. <tt>skos:exactMatch</tt> is a transitive property, and is a sub-property of <tt>skos:closeMatch</tt>.
* '''close match''': [http://www.w3.org/2008/05/skos#closeMatch skos:closeMatch]
** '''Definition''' (from [http://www.w3.org/TR/skos-reference/#mapping SKOS]): The property <tt>skos:closeMatch</tt> is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, <tt>skos:closeMatch</tt> is not declared to be a transitive property.
* '''related''' (but not necessarily similar): [http://www.w3.org/2000/01/rdf-schema#seeAlso rdfs:seeAlso]
** '''Definition''' (from [http://www.w3.org/TR/2000/CR-rdf-schema-20000327/#s2.3.4 RDFS]): The property <tt>rdfs:seeAlso</tt> specifies a resource that might provide additional information about the subject resource.
* '''homologous to''' (for anatomical terms): ''not defined yet''
** '''Definition''': The property links two anatomical terms from different species that refer to terms that have a common ancestor (evolutionary derived form a common ancestor).

BioPortal 2.0.1 (Label 1005) Release Notes

2008-09-20T00:19:27Z

Natasha: /* New features */

Author: Misha Dorf
9/19/2008

We have completed a production release of the latest version of BioPortal 2.0 (labeled “1005”), designed to address numerous critical issues as well as implement a number of server optimizations, UI fixes, and performance enhancements. Here is the list of resolved issues and new features:

=Bugs Fixes=

Bug #703: Very large XML path to root document for TAO:0000578

Bug #541: BP should have the NCIT version that is available on the NCICB site and *not* pull it from OBO foundry

Bug #472: "Lost your password" doesn't work

Bug #531: URLs for BioPortal concepts

Bug #465: Uploaded ontology doesn't show up in list

Bug #562: When downloading mapping the user list is not up to date

Bug #515: After registration failure, can still edit metadata -- But no edits saved

Bug #644: Problem with Root to concept when on a top level node

Bug #490: Get a mapping icon next to a class that has no mappings

Bug #651: Cell Cycle Ontology - Incorrect Relationship and Ontology Navigation

Bug #496: Marginal note icon appears when there are no marginal notes

Bug #656: The "download" link for remote ontologies points to a wrong URL

Bug #493: Commas in the wrong place for properties with multiple values

Bug #560: The term "Element" in the resource tab must be replaced by "Annotations"

Bug #677: Flex visualization problem with deep paths

Bug #662: Cell Cycle Ontology Search and User problems

Bug #679: BioPortal hangs when clicking on some "Latest marginal notes"

Bug #593: Many ontology (ex Cell Type) have Explore links that are broken

Bug #482: Search Results - Concept does not load for NCI Thesaurus:Aspirin_Clopidogrel-Bisulfate

Bug #652: Exploring big ontologies in the Tree has very large lag time

Bug #550: Simply closing an ontology browsing tab can sometime take hours

Bug #521: Strip out language prefix (e.g. "~#en") from Owl rdfs:comment fields in the REST XML

Support #691: URL Links to an existing TAO concepts is not working

Support #699: Proxy Error - Human Disease Ontolgoy - Prostate Cancer

Support #705: earch not finding terms containing 2+ words in name

=New features=

1. The "Browse ontologies" page now shows the latest mappings and marginal notes that users added to BioPortal

2. The new "Projects" tab enables users to describe their projects and link to them. When describing their project, users can link the description to the BioPortal ontologies that they use in the project.

3. Search results for OWL ontologies are now correctly ordered by ranking

4. "My Projects" page enables users to edit the projects descriptions that they have submitted previously.

5. On the "All Mappings" page, only ontologies that have any mappings defined appear in the pull-down list. The list contains the number of mappings for each ontology.

=New REST Service Base URL=
Note that we have updated the URL to rest services to a more permanent and intuitive version: http://rest.bioontology.org/bioportal and the port has changed from 8080 to the standard, 80. The old REST service links will still work, but going forward, we should distribute the above base URL for all our RESTful services.