https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&user=JenniferVendetti&feedformat=atomNCBO Wiki - User contributions [en]2024-03-28T13:26:31ZUser contributionsMediaWiki 1.35.9https://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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12936SKOSSupport2017-12-01T02:35:47Z<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 />
<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more concept assertions. 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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12935SKOSSupport2017-12-01T02:35:22Z<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 />
<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more concept assertions. See the W3C's SKOS System Primer and SKOS Reference for SKOS 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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12934SKOSSupport2017-12-01T02:34:35Z<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 />
<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more SKOS concept assertions. See the W3C's SKOS System Primer and SKOS Reference for SKOS 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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12933SKOSSupport2017-12-01T02:32:52Z<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 />
<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for SKOS 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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12932SKOSSupport2017-12-01T02:32:04Z<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 />
<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12931SKOSSupport2017-12-01T02:25:38Z<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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. <br />
<br />
This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to handle the submission properly.<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12930SKOSSupport2017-12-01T02:24:56Z<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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to handle the submission properly.<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12929SKOSSupport2017-12-01T02:19:50Z<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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12928SKOSSupport2017-12-01T02:16:49Z<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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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 vocabulaires submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. More documentation and examples of concept schemes and top concepts is available in the SKOS System Primer and SKOS Reference:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12927SKOSSupport2017-12-01T02:15:30Z<p>JenniferVendetti: Incremental save</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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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 />
<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 vocabulaires submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. More documentation and examples of concept schemes and top concepts is available in the SKOS System Primer and SKOS Reference:<br />
<br />
https://www.w3.org/TR/2009/NOTE-skos-primer-20090818/#secscheme<br />
<br />
https://www.w3.org/TR/skos-reference/#schemes</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12926SKOSSupport2017-12-01T02:11:07Z<p>JenniferVendetti: Incremental save</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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
SKOS vocabularies submitted to BIoPortal must contain one or more skos:Concept assertions. See the W3C's SKOS System Primer and SKOS Reference for skos: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 />
<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 />
<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.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=File:Plos_thesaurus_class_tree.png&diff=12925File:Plos thesaurus class tree.png2017-12-01T01:43:22Z<p>JenniferVendetti: Screenshot of the PLOS Thesaurus class tree in BioPortal</p>
<hr />
<div>Screenshot of the PLOS Thesaurus class tree in BioPortal</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12924SKOSSupport2017-12-01T00:43:34Z<p>JenniferVendetti: </p>
<hr />
<div><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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
<br />
[[File:Snomedct_class_tree.png|border|The Classes tab for the SNOMED CT ontology in BioPortal]]<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12923SKOSSupport2017-12-01T00:43:01Z<p>JenniferVendetti: Incremental save</p>
<hr />
<div>__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 fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
<br />
[[File:Snomedct_class_tree.png|border|The Classes tab for the SNOMED CT ontology in BioPortal]]<br />
<br />
<br />
==== Required SKOS constructs ====<br />
<br />
===== skos:Concept =====<br />
<br />
===== skos:ConceptScheme & skos:hasTopConcept =====</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=SKOSSupport&diff=12922SKOSSupport2017-12-01T00:28:44Z<p>JenniferVendetti: Incremental save</p>
<hr />
<div>== Support for SKOS vocabularies in BioPortal ==<br />
<br />
BioPortal is a web-based portal for accessing and sharing ontologies. The application fully supports ontology submissions in OWL and OBO format, and offers partial support for SKOS vocabularies. To follow is documentation of the minimum number of SKOS constructs that a SKOS vocabulary must contain in order to display well in BioPortal.<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 />
<br />
[[File:Snomedct_class_tree.png|border|Screenshot of the SNOMED CT class tree in BioPortal]]</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=File:Snomedct_class_tree.png&diff=12921File:Snomedct class tree.png2017-12-01T00:23:48Z<p>JenniferVendetti: Screenshot of the SNOMEDCT class tree in BioPortal.</p>
<hr />
<div>Screenshot of the SNOMEDCT class tree in BioPortal.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=Main_Page&diff=12920Main Page2017-11-18T03:17:07Z<p>JenniferVendetti: </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 />
* [[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=Main_Page&diff=12919Main Page2017-11-18T03:16:01Z<p>JenniferVendetti: Update Ontology Development Projects section</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 the NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about the NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
To follow is a list of software developed and maintained by the 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 the NCBO technologies in your project]] - get ideas for how to employ the NCBO technologies in your website or application<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=Main_Page&diff=12918Main Page2017-11-18T02:58:24Z<p>JenniferVendetti: Update Ontology Development Projects section</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 the NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about the NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
To follow is a list of software developed and maintained by the 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 the NCBO technologies in your project]] - get ideas for how to employ the NCBO technologies in your website or application<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=Main_Page&diff=12917Main Page2017-11-18T02:50:24Z<p>JenniferVendetti: Update documentation section</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 the NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about the NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
To follow is a list of software developed and maintained by the 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 the NCBO technologies in your project]] - get ideas for how to employ the NCBO technologies in your website or application<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 />
* [[BRO:Main_Page]] - Biomedical Resource Ontology<br />
* [[TMO:]] - Translational Medicine Ontology <br />
* [[NPO:Main_Page]] - NanoParticle Ontology<br />
* [[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
* [[RO:Main_Page]] - OBO Relations ontology<br />
* [[CARO:Main_Page]] - Reference anatomical ontology<br />
* [[CL:Main_Page]] - OBO Cell ontology<br />
* [[SO:Main_Page]] - Sequence 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=Main_Page&diff=12916Main Page2017-11-18T02:24:22Z<p>JenniferVendetti: Update software section</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 the NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about the NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
To follow is a list of software developed and maintained by the 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 REST 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 />
== User Support Documentation ==<br />
<br />
*[[BioPortal Help]] - General BioPortal help documentation. <br />
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project<br />
<br />
<br />
== Technical Documentation ==<br />
<br />
* [http://data.bioontology.org/documentation NCBO REST Web services] - Listing of all NCBO web services with usage documentation<br />
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_Developer_Documentation Developer Documentation] - Some documentation for developers<br />
<br />
<br />
== Ontology Development Projects ==<br />
<br />
These are some of the ontology development projects that NCBO has participated in:<br />
<br />
* [[BRO:Main_Page]] - Biomedical Resource Ontology<br />
* [[TMO:]] - Translational Medicine Ontology <br />
* [[NPO:Main_Page]] - NanoParticle Ontology<br />
* [[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
* [[RO:Main_Page]] - OBO Relations ontology<br />
* [[CARO:Main_Page]] - Reference anatomical ontology<br />
* [[CL:Main_Page]] - OBO Cell ontology<br />
* [[SO:Main_Page]] - Sequence 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=Main_Page&diff=12915Main Page2017-11-18T01:55:34Z<p>JenniferVendetti: Remove link to NCBO-OOR page, which is obsolete</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 the NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about the NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
<br />
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page of the BioPortal application<br />
* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries ''(obsolete)''<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Recommender<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements] <br />
<br />
<br />
== User Support Documentation ==<br />
<br />
*[[BioPortal Help]] - General BioPortal help documentation. <br />
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project<br />
<br />
<br />
== Technical Documentation ==<br />
<br />
* [http://data.bioontology.org/documentation NCBO REST Web services] - Listing of all NCBO web services with usage documentation<br />
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_Developer_Documentation Developer Documentation] - Some documentation for developers<br />
<br />
<br />
== Ontology Development Projects ==<br />
<br />
These are some of the ontology development projects that NCBO has participated in:<br />
<br />
* [[BRO:Main_Page]] - Biomedical Resource Ontology<br />
* [[TMO:]] - Translational Medicine Ontology <br />
* [[NPO:Main_Page]] - NanoParticle Ontology<br />
* [[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
* [[RO:Main_Page]] - OBO Relations ontology<br />
* [[CARO:Main_Page]] - Reference anatomical ontology<br />
* [[CL:Main_Page]] - OBO Cell ontology<br />
* [[SO:Main_Page]] - Sequence 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=Main_Page&diff=12914Main Page2017-11-18T01:47:46Z<p>JenniferVendetti: Format and content updates</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 the NCBO.<br />
<br />
Please visit our [http://www.bioontology.org main site] for more information about the NCBO.<br />
<br />
<br />
__TOC__<br />
<br />
== Software ==<br />
<br />
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page of the BioPortal application<br />
* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries ''(obsolete)''<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Recommender<br />
* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements] <br />
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.<br />
<br />
<br />
== User Support Documentation ==<br />
<br />
*[[BioPortal Help]] - General BioPortal help documentation. <br />
* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project<br />
<br />
<br />
== Technical Documentation ==<br />
<br />
* [http://data.bioontology.org/documentation NCBO REST Web services] - Listing of all NCBO web services with usage documentation<br />
* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation<br />
* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.<br />
* [http://www.bioontology.org/wiki/index.php/NCBO_Developer_Documentation Developer Documentation] - Some documentation for developers<br />
<br />
<br />
== Ontology Development Projects ==<br />
<br />
These are some of the ontology development projects that NCBO has participated in:<br />
<br />
* [[BRO:Main_Page]] - Biomedical Resource Ontology<br />
* [[TMO:]] - Translational Medicine Ontology <br />
* [[NPO:Main_Page]] - NanoParticle Ontology<br />
* [[PATO:Main_Page]] - An ontology of phenotypic qualities<br />
* [[RO:Main_Page]] - OBO Relations ontology<br />
* [[CARO:Main_Page]] - Reference anatomical ontology<br />
* [[CL:Main_Page]] - OBO Cell ontology<br />
* [[SO:Main_Page]] - Sequence 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=BioPortal_Release_Notes&diff=12906BioPortal Release Notes2017-05-24T19:11:04Z<p>JenniferVendetti: </p>
<hr />
<div>''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 />
== 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_Release_3_Release_Notes&diff=12905BioPortal Release 3 Release Notes2017-05-24T18:56:03Z<p>JenniferVendetti: Reformat for readability</p>
<hr />
<div>''This page contains software release notes for the 3.x series of [http://bioportal.bioontology.org/ BioPortal].''<br />
<br />
Please see the [[BioPortal_Release_Notes|main release notes page]] to access release notes for other versions.<br />
<br />
<br />
__TOC__<br />
<br />
<br />
== BioPortal Release 3.12 (2013-Feb) ==<br />
<br />
* Implemented the display of the OBO part-of relationship in the term neighborhood visualization.<br />
* Improved some default layouts in the visualization system.<br />
* Updated automated mappings for all ontologies.<br />
* Regenerated the annotator hierarchy database. The versions of ontologies in this database are now much more current.<br />
* Implemented support for federated queries in the [http://sparql.bioontology.org BioPortal SPARQL endpoint].<br />
* Moved the mappings from the BioPortal endpoint into a separate public endpoint. This change allows us to update automated mappings more cleanly.<br />
* Added the following resources to the Resource Index. All of these resources are the results of our collaboration with the [http://www.neuinfo.org/ Neuroscience Information Framework] (NIF) group.<br />
** NIF PubMed Health: Tests<br />
** NIF Drug Related Gene Database<br />
** NIF Gemma<br />
** NIF Integrated Disease View<br />
* Fixed “Maximum Depth” metric for a number of ontologies. Was incorrectly displaying “1” in some cases.<br />
* Fixed web service failure when attempting to retrieve all concepts from several ontologies.<br />
* Fixed annotator to return all ancestor terms. Was missing some ancestors for some ontologies.<br />
* Fixed Search to work correctly in MeSH.<br />
* Fixed problem with SPARQL query to BioPortal endpoint on queries that include ORDER and LIMIT clauses<br />
<br />
<br />
== BioPortal Release 3.10 (2012-Jul) ==<br />
* Revised UI for the Resource Index. This new UI supports the BioPortal slice mechanism. The new UI is also much faster than the previous one.<br />
* Updated ontologies available for use with the Annotator which includes newer ontologies and more recent versions of existing ontologies.<br />
* Fixed a longstanding bug in the Annotator that caused paths from a term to root nodes to occasionally be truncated.<br />
* Allow submission of Notes on ontology terms by anonymous users. Previously a user had to be logged in to submit a note.<br />
<br />
<br />
== BioPortal Release 3.9 (2012-Jun) ==<br />
<br />
* We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better” ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support@bioontology.org. *<br />
<br />
* We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *<br />
<br />
* We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).<br />
<br />
<br />
== BioPortal Release 3.8 (2012-May) == <br />
<br />
* We have regenerated all mappings based on UMLS CUIs. Thus terms in different UMLS ontologies which share the same CUI are now mapped to each other. The mapping created is of type skos:closeMatch. There are now 3,000,000 of these UMLS CUI mappings in the system.*<br />
* We have regenerated all mappings based on xrefs (OBO cross-reference) in OBO ontologies. A mapping is now generated when a term in an OBO ontology has an xref to a term in another ontology. The mapping created is of type skos:relatedMatch. There are 35,000 of these xref mappings in the system.*<br />
* We have regenerated all mappings based on terms which have identical unique identifiers (IRIs). A mapping is now generated when term in an ontology has a unique identifier that is identical to the identifier of a term in another ontology. The mapping created is of type skos:exactMatch. There are 700,000 of these identical IRI mappings in the system.*<br />
<br />
We also fixed a number of bugs which were causing performance, stability, and ontology upload problems.<br />
<br />
<br />
== BioPortal Release 3.7 (2012-Apr) ==<br />
<br />
* Updated term mappings generated by LOOM <br />
* Added boolean functionality to Search Web service and UI<br />
* Updated ontology content for the Resource Index<br />
* BioPortal SPARQL endpoint beta release, http://sparql.bioontology.org <br />
* Modified response of Annotator UI to not fail if input text contains returns or results do not have any term matches*<br />
* Bug fix for Term Autocomplete widget to remove namespace collision with jQuery widgets*<br />
<br />
<br />
== BioPortal Release 3.6 (2012-Jan) ==<br />
<br />
* Created “alternate entry points” for BioPortal. These URL’s limit the ontologies that are visible in BioPortal, allowing users to focus on a shared, smaller set of ontologies. The entry points which are currently available are:<br />
** OBO-Foundry: http://obo-foundry.bioportal.bioontology.org<br />
** Unified Medical Language Systems: http://umls.bioportal.bioontology.org<br />
** Cancer Biomedical Informatics Grid: http://cabig.bioportal.bioontology.org<br />
** Clinical and Translational Science Awards: http://ctsa.bioportal.bioontology.org<br />
** CTSA Health Ontology Mapper: http://ctsa-hom.bioportal.bioontology.org<br />
** Proteomics Standards Initiative: http://psi.bioportal.bioontology.org<br />
** WHO Family of International Classifications: http://who-fic.bioportal.bioontology.org<br />
** Consultative Group on Intl Agricultural Research: http://cgiar.bioportal.bioontology.org<br />
** Please contact us on the support mailing list if you would like us to configure an entry point for another set of ontologies.<br />
<br />
* Major Updates and Fixes<br />
** Updated the ontologies used by the Annotator Web Services*<br />
** Improved the reliability and robustness of the parsing of OWL 2 ontologies*<br />
<br />
<br />
== BioPortal Release 3.5 (2011-Dec) ==<br />
<br />
* Added ability for logged-in users to filter which ontologies appear in their BioPortal display<br />
* Updated Annotator page to simplify the selection of options, to clarify the annotation results, and to remove Flash from the implementation<br />
* Improved Annotator Web service response performance by 5-10x* <br />
* Added ability for the ontology Web services API to optionally return JSON (rather than XML)* <br />
* Updated Ontology Recommender algorithm to provide better recommendations*<br />
* Added display of matched terms for Ontology Recommender*<br />
* Added Web service to get all namespaces for an ontology*<br />
* Bug Fixes <br />
** Display user-friendly names for RxNorm ontology properties<br />
<br />
<br />
== BioPortal Release 3.4 (2011-Oct) ==<br />
<br />
* Revised the Term Mappings tab to ease the creation of term-to-term mappings*<br />
* Limited access to “Private” ontologies via the Browse and Search pages<br />
* Added backend support to allow multiple administrators for a single ontology*<br />
* Added ability to copy to the clipboard a permanent link to any BioPortal term* <br />
* Bug Fixes <br />
** Resolved issue causing search to not display all matching terms* <br />
** Fixed Term Mappings tab display for IE 7 & 8* <br />
** Fixed RDF Ontology Download Web service<br />
** Fixed link to the list of resources included in the Resource Index* <br />
<br />
<br />
== BioPortal Release 3.3 (2011-Sep) == <br />
<br />
New features include updates to the Web interface and Web services:<br />
<br />
* Added Get Properties Web service, http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Property_Services <br />
* Updated Search page to remove Flash<br />
* Handling of obsolete terms, part 2 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OWL ontologies. <br />
* Added Help documentation <br />
* Implemented a feature to allow ontology submitters to flag their ontology as “licensed”. This feature allows the ontology submitter to require users to provide license information before they are allowed to access the ontology.<br />
* Bug Fix<br />
** Fixed the Filter by Account on the Mappings tab<br />
<br />
<br />
== BioPortal Release 3.2 ==<br />
<br />
New features include updates to the Web interface and Web services:<br />
* Added Ontology Recommender feature, http://bioportal.bioontology.org/recommender <br />
** Web service documentation: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Web_service<br />
** Sample client information: http://www.bioontology.org/wiki/index.php/Ontology_Recommender_Client_Examples<br />
* Added support for access control for viewing ontologies <br />
* Added link to subscribe to BioPortal Notes emails <br />
* Synchronized “Jump To” feature with ontology parsing and display <br />
* Added documentation on Ontology Groups<br />
* Annotator Web service – disabled use of “longest only” parameter when also selecting “ontologies to expand” parameter <br />
* Removed the metric "Number of classes without an author" <br />
* Handling of obsolete terms, part 1 – term name is grayed out and <is_obsolete> element is returned in Web service response for obsolete terms from OBO and RRF ontologies. This feature will be extended to cover OWL ontologies in a subsequent release. <br />
* Bug Fixes<br />
** Fixed calculation of “Classes with no definition” metric<br />
** Added re-direct from old BioPortal URL format to new URL format to provide working links from archived search results <br />
<br />
<br />
'''''Firefox Extension for NCBO API Key''''':<br />
To make it easier to test Web service calls from your browser, we have released the NCBO API Key Firefox Extension. This extension will automatically add your API Key to NCBO REST URLs any time you visit them in Firefox. The extension is available at Mozilla's Add-On site. To use the extension, follow the installation directions, restart Firefox, and add your API Key into the “Options” dialog menu on the Add-Ons management screen. After that, the extension will automatically append your stored API Key any time you visit http://rest.bioontology.org. <br />
<br />
'''''Upcoming software license change''''':<br />
The next release of NCBO software will be under the two-clause BSD license rather than under the currently used three-clause BSD license. This change should not affect anyone’s use of NCBO software and this change is to a less restrictive license. More information about these licenses is available at the site: http://www.opensource.org/licenses. Please contact support@bioontology.org with any questions concerning this change.<br />
<br />
<br />
== BioPortal Release 3.1 (2011-Jul) ==<br />
<br />
New features include updates to the Web interface and Web services:<br />
<br />
* Support for loading OWL 2 ontologies<br />
* Security Framework, part 2 - The apikey parameter is now required for all Web services. Login to BioPortal to get your API Key. <br />
* Browsing of ontologies that contain large numbers of sibling terms<br />
* Icons for is_a and part_of are displayed for OBO format ontologies <br />
* Display of the “occurs_in” relationship used in the Extended version of the Gene Ontology <br />
<br />
Bug Fix<br />
<br />
* Added informative error message when incompatible parameter values are used in the Annotator Web service and updated Perl client to capture this error response<br />
<br />
<br />
== BioPortal Release 3.0 (2011-May) ==<br />
<br />
New features include updates to the Web interface and Web services:<br />
* Web interface updates<br />
* Browse page now displays ontology features, e.g. size of the ontology, number of notes added to the ontology, number of projects that use the ontology, and number of reviews of the ontology<br />
* New ontology summary details page highlights the ontology metrics, reviews, projects, and derived views of the ontology<br />
* Security Framework, part 1 - Added apikey parameter to all Web services. The apikey parameter is optional until June 15, 2011, after this time the apikey parameter will be required for usage of the Web services. Login to BioPortal to get your API key.<br />
* Provisional Term Web service - New term proposals now receive a provisional term id. Additional Web services are now available for submitting provisional terms. For more details, see: http://www.bioontology.org/wiki/index.php/BioPortal_Provisional_Terms<br />
* Form auto-complete Widget - Option to include term definition in display<br />
* Resource Index<br />
** Data indexed with new ontologies from BioPortal<br />
** PubMed data now available for abstracts published in 2010</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_4_Release_Notes&diff=12904BioPortal 4 Release Notes2017-05-23T00:52:09Z<p>JenniferVendetti: Moved VA release notes to separate page</p>
<hr />
<div>''This page contains software release notes for the 4.x series of [http://bioportal.bioontology.org/ BioPortal].''<br />
<br />
Please see the [[BioPortal_Release_Notes|main release notes page]] to access release notes for other versions.<br />
<br />
<br />
__TOC__<br />
<br />
<br />
== BioPortal Release 4.29 Interim (January 2017) ==<br />
<br />
Recommender improvements:<br />
<br />
* Added sorting to table that contains recommended ontologies.<br />
* Tool tips added to explain the header columns in more detail. Mouse over the column to see the tool tip.<br />
<br />
<br />
== BioPortal Release 4.29 (Oct 2016) ==<br />
<br />
* Loaded 2016AA version of the UMLS terminologies into BioPortal (NCBO-1711).<br />
* Fixed an issue on the BioPortal home page that prevented the Facebook Like button and Cite Us link from working (NCBO-1746).<br />
* Fixed a bug in the Recommender algorithm that caused NCIT to always show up as the top recommended ontology (NCBO-1794).<br />
* Fixed a bug that prevented the annotation process from succeeding during parsing of the ECSO ontology (NCBO-1813).<br />
* Performed software upgrades for the BioPortal application and REST endpoint:<br />
** Rails 4.2.6 (NCBO-1759)<br />
** Ruby 2.2.5 (NCBO-1782)<br />
* Fixed parsing issues for the following ontologies:<br />
** AAO (NCBO-1690)<br />
** ATMO (NCBO-1783)<br />
** BCTTV1 (NCBO-1700)<br />
** BT (NCBO-1786)<br />
** BTO (NCBO-1787)<br />
** CHEBI (NCBO-1780)<br />
** CIINTEADO (NCBO-1702<br />
** CISAVIADO (NCBO-1698)<br />
** EFO (NCBO-1788)<br />
** ENVO (NCBO-1791)<br />
** HAROREADO, HAAURAADO (NCBO-1695)<br />
** MOOCCUADO, MOOCCIADO, MOOCULADO (NCBO-1688)<br />
** MS (NCBO-1579)<br />
** ORDO (NCBO-1771)<br />
** PHMAMMADO, PHFUMIADO (NCBO-1692)<br />
** RNAO (NCBO-1795)<br />
<br />
<br />
== BioPortal Release 4.28 (June 2016) ==<br />
<br />
* Modified several areas of code to eliminate long running SPARQL count queries that hampered overall performance (NCBO-1741).<br />
* Tweaked the size of cache limits to ensure that frequently requested data is cached appropriately (NCBO-1757).<br />
* Fixed an issue that prevented the BioPortal site from setting correct HTTP status codes for Internal Server and Not Found errors. Previously, BioPortal always set status codes to 200 (NCBO-1548).<br />
* Fixed an issue that prevented the Sequence Types and Features Ontology (SO) ontology from parsing (NCBO-1739).<br />
* Cleaned up and removed 249 failed submissions of the GoMapMan (GMM) ontology that resulted from an invalid ontology pull location (NCBO-1743).<br />
<br />
<br />
== BioPortal Release 4.27 (May 2016) ==<br />
<br />
* Made improvements to the code that calculates ontology popularity, which is the default sort order for search results in BioPortal (NCBO-1718).<br />
* Modified the code that calculates ontology metrics to reduce occurrences of long running SPARQL count queries (NCBO-1652, NCBO-1724, NCBO-1736).<br />
* BioPortal will now display preferred names with English ("en") language tags by default. Previously, preferred names were chosen at random without regard to language tags (NCBO-1662). <br />
* Upgraded to Java 8 (NCBO-1697).<br />
* Fixed an issue that prevented the PE-O ontology from parsing correctly (NCBO-1716).<br />
* Fixed an issue that prevented the PHENX ontology from parsing correctly (NCBO-1708).<br />
* Removed assets from BioPortal home page from non HTTPS sources, which caused browsers to report BioPortal as an insecure site (NCBO-1567).<br />
* Fixed corrupt creation dates for a number of projects on the Projects page (NCBO-1535).<br />
<br />
<br />
== BioPortal Release 4.26 (April 2016) ==<br />
* Upgraded to version 4.2.1 of the OWL API (NCBO-1676).<br />
* Generated metrics data for a number of ontologies with missing metrics (NCBO-1687).<br />
* Reparsed the FMA ontology to fix an issue with missing values for preferred labels, synonyms, and definitions (NCBO-1679).<br />
* Fixed an issue that caused parsing errors with the latest versions of the NCIT ontology (NCBO-1664).<br />
* Fixed a bug in the Recommender's score aggregation function for ontology sets (NCBO-1682).<br />
* Fixed an issue with the PO ontology that resulted in a series of bad submissions and failed indexing (NCBO-1678).<br />
* Fixed an issue that prevented the MS ontology from parsing correctly (NCBO-1579).<br />
<br />
<br />
== BioPortal Release 4.25 (March 2016) ==<br />
<br />
In this release we fixed problems that were causing regular outages of the [[BioPortal_Help#Recommender_Tab|Recommender]], and sometimes affecting the main BioPortal system. Our troubleshooting documentation has been updated based on our experience.<br />
<br />
* Fixed an issue that prevented users from getting "ready" submissions from the REST API (NCBO-1673)<br />
* Fixed an issue that caused the Metrics REST endpoint to fail (NCBO-1660).<br />
* Flattened and reparsed the DRON ontology to address SPARQL query performance issues (NCBO-1651).<br />
* Fixed a bug that caused the Recommender to fail when dealing with ontologies with no submissions (NCBO-1650).<br />
* Modified several BioPortal components to retrieve ontology class counts from metrics data instead of directly querying the backend to address performance issues (NCBO-1648).<br />
* Fixed an issue was preventing the latest versions of the NCIT ontology from being pulled into BioPortal (NCBO-1655).<br />
<br />
<br />
== BioPortal Release 4.24 (February 2016) ==<br />
<br />
'''Enhancements'''<br />
<br />
* Implemented an ability to create and manage provisional relations on a provisional class (NCBO-1614)<br />
* Implemented an ability to search for all subclasses of a class, including provisional classes (NCBO-1624)<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a subtree root search to properly include provisional classes when an appropriate parameter is passed to the endpoint<br />
* Fixed an issue with CHEBI ontology not being pulled from its download location (NCBO-1639)<br />
* Fixed a display issue where BioPortal displayed a nested 404 page when an error occured rendering the class tree (NCBO-1623)<br />
* Fixed a bug in NCBO Tree widget that ommitted a "+" sign for classes that have children (NCBO-1574)<br />
* Fixed an issue with search not returning entries for some existing classes of NCBI Taxonomy (NCBITAXON) (NCBO-1591)<br />
* Added sample link to this section of the API documentation (NCBO-1612)<br />
* Updated the Resource Index UI to default to hierarchical classes (classes and descendants) (NCBO-1622)<br />
* Fixed a broken pull location for ONLIRA ontology (NCBO-1627)<br />
<br />
<br />
== BioPortal Release 4.23 (January 2016) ==<br />
<br />
* Added an additional server to the group that serves the BioPortal UI for improved performance.<br />
* Fixed an issue with the ontology analytics REST endpoint returning an empty set.<br />
* Fixed an issue that caused a breakage of the ontology submissions REST endpoint (NCBO-1590).<br />
* Fixed an issue that prevented search from returning some terms in the DOID and NCBITAXON ontologies (NCBO-1578, NCBO-1588).<br />
* Fixed an issue that caused some of the mapping display dialogs to freeze (NCBO-1562).<br />
* Fixed an issue where using the "Jump To:" search box on the ontology classes page caused the UI to hang (NCBO-1506).<br />
* Fixed an issue that prevented the DDO ontology from parsing (NCBO-1603).<br />
* Fixed an issue that caused an error in the virtual appliance if ontology analytics data is empty. Thanks to Vincent Emonet for the contribution.<br />
* Fixed an issue on the Annotator page with an incorrect parameter in the REST API link to retrieve results formatted as JSON. Thanks (again!) Vincent Emonet for the contribution.<br />
<br />
<br />
== BioPortal Release 4.22.1 (December 2015) ==<br />
<br />
This is a minor release that addresses an issue of system instability caused by a bug in our HTTP caching layer that resulted in a significant load on our backend services.<br />
<br />
'''Enhancements'''<br />
<br />
* Added configuration parameters at the UI layer that allow for a greater control over debugging issues with HTTP caching.<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a bug in the HTTP caching code that caused multiple identical requests to bypass the cache and trigger extraneous requests to the REST API. The bug fix resulted in a significant performance boost to both the front- and back-end services.<br />
<br />
<br />
== BioPortal Release 4.22 (November 2015) ==<br />
<br />
'''Enhancements'''<br />
<br />
* New functionality at the REST API level in support of our collaboration with the [http://www.metadatacenter.org/ CEDAR] project:<br />
** Added the ability to search for, and retrieve all value sets.<br />
** Implemented search for value set items ([http://data.bioontology.org/search?q=melanoma&also_search_provisional=true&valueset_exclude_roots=true&ontology_types=VALUE_SET_COLLECTION example link]).<br />
** Implemented search for ontology classes and value set items ([http://data.bioontology.org/search?q=melanoma&also_search_provisional=true&valueset_exclude_roots=true example link]).<br />
** Added the ability to exclude value set collections from search ([http://data.bioontology.org/search?q=melanoma&ontology_types=ONTOLOGY&also_search_provisional=true example link]).<br />
** Added the ability to search for value set values across all value sets in an ontology.<br />
* Ontologies are now sortable by creation date on the Admin page.<br />
* Clicking the Add Comment and/or Add Proposal buttons in the Notes sections for ontologies will navigate unauthenticated users to the login page.<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed an issue that caused [http://bioportal.bioontology.org/projects Projects page] load times in excess of 3 minutes.<br />
* Fixed an issue that caused the UI to go blank after selecting the root node of the CCO ontology.<br />
* Admin page: the ontologies table now refreshes after deleting an ontology.<br />
* Fixed an issue that caused a 404 error when trying to view the DINTO ontology.<br />
* Fixed an inconsistency in the metadata for the CHMO ontology that caused the parsing process to fail.<br />
<br />
<br />
== BioPortal Release 4.21 (October 2015) ==<br />
<br />
'''Bug Fixes'''<br />
* Fixed an issue that caused class trees to reload every time a class was selected.<br />
* Fixed an issue with BioPortal's term selection widget that caused raw HTML to be displayed in search results.<br />
* Fixed a problem in the REST API that caused an internal server error when accessing nonexistent users. The API now correctly displays a 404 not found message.<br />
* Fixed a bug that prevented flat tree ontologies from displaying in BioPortal.<br />
* Fixed an issue that prevented the latest versions of the Gazetteer and Chemical Entities of Biological Interest ontologies from parsing.<br />
* Fixed a problem that prevented visualization from working with private ontologies (thanks go to Eric Verbeek for this).<br />
<br />
<br />
== BioPortal Release 4.20 (August 2015) ==<br />
<br />
''This release includes minor fixes from several previous releases.''<br />
<br />
* Released a new version of the Ontology Recommender. This version is more flexible than the previous version and allows users to assign weights to the scores for various factors that influence the recommendation. In addition, some edge cases in the old system that resulted in bad recommendations have been addressed. This new recommendation system was developed independently by Marcos Martinez and then incorporated into our base code.<br />
* Instances (individuals) in an ontology can now be accessed through the API. Documentation for this is available at: http://data.bioontology.org/documentation#Instance.<br />
* Components have been added to the Annotator UI to allow users to exercise additional options available through the API.<br />
* Icons now indicate non-subclass relationships in OBO ontologies. Previously it was not possible to distinguish visually OBO subclass from other OBO relations displayed in the tree (such as OBO part-of).<br />
* The UMLS MeSH vocabulary is now displayed hierarchically. Previously it was displayed as a flat list of terms because of some problems with the hierarchical relation in the source that we were using.<br />
* The Search API now allows search-by-name of provisional classes assigned to an ontology.<br />
* The UMLS ontologies have all been updated to the latest 2015AA release.<br />
* A new version of BioMixer with a simpler user interface has been incorporated into the system. This work was done by our collaborators at the University of Victoria.<br />
* Created both a REST service and a UI for BioPortal application administration. This interface is automatically visible to VM administrators.<br />
* Updated the framework of our system from RAILS version 2 to version 4.<br />
* Fixed many bugs, especially those causing failures when parsing an ontology.<br />
<br />
<br />
== BioPortal Release 4.14 (February 2015) ==<br />
<br />
''This release includes minor fixes from several previous releases.''<br />
<br />
* The ontology summary page for each ontology now has a graph of recent history of the level of user-interface (UI) web traffic (number of page views) for that ontology. This graph is available under the “Metrics” box. See, for example, http://bioportal.bioontology.org/ontologies/SNOMEDCT . The raw data is also available for download in CSV format from the same location.<br />
* The BioPortal home page now has a link that displays all ontologies in the system and the number of UI views for each ontology. Previously usage of only the top 5 ontologies were available.<br />
* Users of our virtual machine now have the ability to plug in alternate concept recognizers for use by the annotator. To support these custom annotators, arbitrary parameters can be passed via the rest interface to the underlying concept recognizer. Documentation for how to make use of this feature is available on [https://github.com/ncbo/ncbo_annotator/wiki/Extending-Annotator-with-a-Custom-Concept-Recognizer GitHub]. Previously the “mgrep” concept recognizer was hardwired into the system and code modifications were required to employ another recognizer.<br />
* Ontologies views can now be used for annotation. Previously only top level ontologies were available for use by the annotation system.<br />
* All of PubMed has been indexed for use by the Resource Index for all terms in all ontologies in BioPortal. Previously only 18 months of PubMed data was indexed.<br />
* We now provide for download, for all resources in BioPortal, files containing counts for term occurrence and co-occurrence (occurrence of pairs of terms in a document). These files can be used for research in enrichment analysis. Documentation of the files and how they might be used is available on [https://github.com/ncbo/resource_index/wiki/Term-Occurence GitHub].<br />
* The ontology browse page now has a faceted interface that allows the list of displayed ontologies to be narrowed as desired. Previously all ontologies appeared in an alphabetical list but this became unwieldy with the 400+ ontologies that we now have.<br />
* There is now a user-interface for displaying all of the properties in an ontology. If the properties were created in a hierarchy then this hierarchy is displayed. Previously only the class hierarchy was displayed. Properties were available programmatically though the REST interface but this information was not surfaced in the UI.<br />
* Ontologies defined using SKOS are now supported. For these ontologies, the hierarchy is determined by the SKOS “broader” and “narrower” properties.<br />
* We now allow download of all publically available ontologies in RDF. UMLS ontologies with restrictive licenses are excluded.<br />
* We fixed a number of non-parsing ontologies and removed a bunch of low-content (“test”) ontologies.<br />
* The system now contains the latest versions (2014AB) of all UMLS ontologies.<br />
* We now treat all OBO synonym types as a BioPortal synonyms. Previously only the OBO “exact” synonym type was treated as a BioPortal synonym.<br />
* We now notify by email the ontology authors if the nightly pull of their ontology fails.<br />
<br />
<br />
== BioPortal Release 4.10 (September 2014) ==<br />
<br />
''This release includes minor fixes from several previous releases.''<br />
<br />
* Reengineered the entire Resource Index to achieve better and more consistent performance and to align the Resource Index with the new BioPortal backend (released last year). In addition to allowing us to support additional resources, this revision removes a number of inconsistencies that resulted from the Resource Index using the old BioPortal backend.<br />
* Upgraded the OWL and OBO parser to the latest version and reparsed all OBO and OWL ontologies. This reprocessing fixed a large number of problems with ontologies that either did not parse or that failed search indexing or metrics calculations.<br />
* We now create and make available for download a comma-separated value (CSV) file for most ontologies. These files have one row/class and a standard set of properties in the columns. We cannot make these files available for ontologies if the license for the ontology does not permit it (e.g. SNOMED-CT and MedDRA).<br />
* Fixed PURLS for all ontologies. There were a large number of ontologies for which the PURLs we created, in the old system or the new one, no longer worked correctly.<br />
* Reworked the entire mappings system so that mappings will be always up-to-date with the latest version of the ontologies.<br />
* Created a web page (http://bioportal.bioontology.org/validate_ontology_file) so that users can validate that their ontologies parse correctly with the latest version of the OWL/OBO parser.<br />
* Removed a number of bogus ontologies and spam notes.<br />
* Fixed implementation of “longest only” parameter in Annotator.<br />
* We now reparse and reindex an ontology if the administrator of the ontology changes the metadata for the ontology. The reparse is necessary because the metadata contains information, such as the properties that contain synonyms or definitions, that influence the parsing and indexing.<br />
* Recalculated metrics for all ontologies. This process filled in metrics for many ontologies that lacked them, and corrected the calculations of some metrics in other ontologies.<br />
* We now allow the download of RDF (Turtle) files for UMLS ontologies whose license allows users to download them.<br />
* Reindexing ontologies for search no longer interferes with the use of search on those ontologies. Previously search for an ontology was either broken or incomplete for an ontology that was being indexed.<br />
* Added an ontology properties endpoint to the REST API. This endpoint allows a user to query for the properties used by an ontology.<br />
<br />
As previously noted, we have permanently retired the old NCBO BioPortal API. New API documentation is available at<br />
http://data.bioontology.org/documentation.<br />
<br />
<br />
== BioPortal Release 4.6 (May 2014) ==<br />
<br />
* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.<br />
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.<br />
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)<br />
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)<br />
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything. <br />
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.<br />
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.<br />
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.<br />
* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.<br />
* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.<br />
* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.<br />
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.<br />
<br />
<br />
We've shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We've provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at: http://data.bioontology.org/documentation.<br />
<br />
<br />
== BioPortal Release 4.0 (September 2013) ==<br />
<br />
The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.<br />
<br />
The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at <br />
http://data.bioontology.org/documentation<br />
<br />
BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.<br />
<br />
With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.<br />
<br />
Temporary Changes <br />
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.<br />
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet<br />
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type. <br />
* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.<br />
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.<br />
<br />
Permanent Additions<br />
* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.<br />
* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.<br />
<br />
Permanent Subtractions<br />
* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.<br />
* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.<br />
* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Virtual_Appliance_Release_Notes&diff=12903BioPortal Virtual Appliance Release Notes2017-05-23T00:51:18Z<p>JenniferVendetti: </p>
<hr />
<div>''This page contains software release notes for the [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance].''<br />
<br />
Please see the [[BioPortal_Release_Notes|main release notes page]] to access release notes for the Stanford-hosted [http://bioportal.bioontology.org/ BioPortal application].<br />
<br />
<br />
== BioPortal Virtual Appliance 2.4 (2015-Apr) ==<br />
<br />
This release contains the following components:<br />
<br />
* Ontologies API (REST service) v4.15.3<br />
* Annotator<br />
* Recommender<br />
* BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI) v4.15.5<br />
* BioMixer <br />
<br />
Note that release 4.15 was a silent release, implying that it contained bug fixes and other non-visible changes, and the third release number (.3, .5) indicates a patch number.<br />
<br />
Application server stack:<br />
<br />
* CentOS 6.6<br />
* Apache httpd 2.2.15<br />
* Apache Tomcat 6.0.24<br />
* Solr 4.10.4<br />
* MySQL 5.1.73<br />
* Ruby 2.1.5<br />
* Passenger 4.0.57<br />
* Redis 2.8.18<br />
* Memcached 1.4.4<br />
* 4store v1.1.5-122-g1788d29<br />
* nginx 1.6.3</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Virtual_Appliance_Release_Notes&diff=12902BioPortal Virtual Appliance Release Notes2017-05-23T00:45:49Z<p>JenniferVendetti: </p>
<hr />
<div>== BioPortal Virtual Appliance 2.4 (2015-Apr) ==<br />
<br />
This release contains the following components:<br />
<br />
* Ontologies API (REST service) v4.15.3<br />
* Annotator<br />
* Recommender<br />
* BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI) v4.15.5<br />
* BioMixer <br />
<br />
Note that release 4.15 was a silent release, implying that it contained bug fixes and other non-visible changes, and the third release number (.3, .5) indicates a patch number.<br />
<br />
Application server stack:<br />
<br />
* CentOS 6.6<br />
* Apache httpd 2.2.15<br />
* Apache Tomcat 6.0.24<br />
* Solr 4.10.4<br />
* MySQL 5.1.73<br />
* Ruby 2.1.5<br />
* Passenger 4.0.57<br />
* Redis 2.8.18<br />
* Memcached 1.4.4<br />
* 4store v1.1.5-122-g1788d29<br />
* nginx 1.6.3</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_Release_Notes&diff=12901BioPortal Release Notes2017-05-23T00:41:57Z<p>JenniferVendetti: Add link to VA release notes page</p>
<hr />
<div>''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 />
== 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_Virtual_Appliance_Release_Notes&diff=12900BioPortal Virtual Appliance Release Notes2017-05-23T00:40:04Z<p>JenniferVendetti: Create separate page for BP VA release notes</p>
<hr />
<div>The Virtual Appliance 2.4 has been released with the following components:<br />
<br />
Ontologies API (REST service) v4.15.3<br />
Annotator<br />
Recommender<br />
BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI) v4.15.5<br />
BioMixer <br />
<br />
Note that release 4.15 was a silent release, implying that it contained bug fixes and other non-visible changes, and the third release number (.3, .5) indicates a patch number.<br />
<br />
Application Server Stack:<br />
<br />
CentOS 6.6<br />
Apache httpd 2.2.15<br />
Apache Tomcat 6.0.24<br />
Solr 4.10.4<br />
MySQL 5.1.73<br />
Ruby 2.1.5<br />
Passenger 4.0.57<br />
Redis 2.8.18<br />
Memcached 1.4.4<br />
4store v1.1.5-122-g1788d29<br />
nginx 1.6.3</div>JenniferVendettihttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_4_Release_Notes&diff=12899BioPortal 4 Release Notes2017-05-23T00:36:46Z<p>JenniferVendetti: </p>
<hr />
<div>''This page contains software release notes for the 4.x series of [http://bioportal.bioontology.org/ BioPortal].''<br />
<br />
Please see the [[BioPortal_Release_Notes|main release notes page]] to access release notes for other versions.<br />
<br />
<br />
__TOC__<br />
<br />
<br />
== BioPortal Release 4.29 Interim (January 2017) ==<br />
<br />
Recommender improvements:<br />
<br />
* Added sorting to table that contains recommended ontologies.<br />
* Tool tips added to explain the header columns in more detail. Mouse over the column to see the tool tip.<br />
<br />
<br />
== BioPortal Release 4.29 (Oct 2016) ==<br />
<br />
* Loaded 2016AA version of the UMLS terminologies into BioPortal (NCBO-1711).<br />
* Fixed an issue on the BioPortal home page that prevented the Facebook Like button and Cite Us link from working (NCBO-1746).<br />
* Fixed a bug in the Recommender algorithm that caused NCIT to always show up as the top recommended ontology (NCBO-1794).<br />
* Fixed a bug that prevented the annotation process from succeeding during parsing of the ECSO ontology (NCBO-1813).<br />
* Performed software upgrades for the BioPortal application and REST endpoint:<br />
** Rails 4.2.6 (NCBO-1759)<br />
** Ruby 2.2.5 (NCBO-1782)<br />
* Fixed parsing issues for the following ontologies:<br />
** AAO (NCBO-1690)<br />
** ATMO (NCBO-1783)<br />
** BCTTV1 (NCBO-1700)<br />
** BT (NCBO-1786)<br />
** BTO (NCBO-1787)<br />
** CHEBI (NCBO-1780)<br />
** CIINTEADO (NCBO-1702<br />
** CISAVIADO (NCBO-1698)<br />
** EFO (NCBO-1788)<br />
** ENVO (NCBO-1791)<br />
** HAROREADO, HAAURAADO (NCBO-1695)<br />
** MOOCCUADO, MOOCCIADO, MOOCULADO (NCBO-1688)<br />
** MS (NCBO-1579)<br />
** ORDO (NCBO-1771)<br />
** PHMAMMADO, PHFUMIADO (NCBO-1692)<br />
** RNAO (NCBO-1795)<br />
<br />
<br />
== BioPortal Release 4.28 (June 2016) ==<br />
<br />
* Modified several areas of code to eliminate long running SPARQL count queries that hampered overall performance (NCBO-1741).<br />
* Tweaked the size of cache limits to ensure that frequently requested data is cached appropriately (NCBO-1757).<br />
* Fixed an issue that prevented the BioPortal site from setting correct HTTP status codes for Internal Server and Not Found errors. Previously, BioPortal always set status codes to 200 (NCBO-1548).<br />
* Fixed an issue that prevented the Sequence Types and Features Ontology (SO) ontology from parsing (NCBO-1739).<br />
* Cleaned up and removed 249 failed submissions of the GoMapMan (GMM) ontology that resulted from an invalid ontology pull location (NCBO-1743).<br />
<br />
<br />
== BioPortal Release 4.27 (May 2016) ==<br />
<br />
* Made improvements to the code that calculates ontology popularity, which is the default sort order for search results in BioPortal (NCBO-1718).<br />
* Modified the code that calculates ontology metrics to reduce occurrences of long running SPARQL count queries (NCBO-1652, NCBO-1724, NCBO-1736).<br />
* BioPortal will now display preferred names with English ("en") language tags by default. Previously, preferred names were chosen at random without regard to language tags (NCBO-1662). <br />
* Upgraded to Java 8 (NCBO-1697).<br />
* Fixed an issue that prevented the PE-O ontology from parsing correctly (NCBO-1716).<br />
* Fixed an issue that prevented the PHENX ontology from parsing correctly (NCBO-1708).<br />
* Removed assets from BioPortal home page from non HTTPS sources, which caused browsers to report BioPortal as an insecure site (NCBO-1567).<br />
* Fixed corrupt creation dates for a number of projects on the Projects page (NCBO-1535).<br />
<br />
<br />
== BioPortal Release 4.26 (April 2016) ==<br />
* Upgraded to version 4.2.1 of the OWL API (NCBO-1676).<br />
* Generated metrics data for a number of ontologies with missing metrics (NCBO-1687).<br />
* Reparsed the FMA ontology to fix an issue with missing values for preferred labels, synonyms, and definitions (NCBO-1679).<br />
* Fixed an issue that caused parsing errors with the latest versions of the NCIT ontology (NCBO-1664).<br />
* Fixed a bug in the Recommender's score aggregation function for ontology sets (NCBO-1682).<br />
* Fixed an issue with the PO ontology that resulted in a series of bad submissions and failed indexing (NCBO-1678).<br />
* Fixed an issue that prevented the MS ontology from parsing correctly (NCBO-1579).<br />
<br />
<br />
== BioPortal Release 4.25 (March 2016) ==<br />
<br />
In this release we fixed problems that were causing regular outages of the [[BioPortal_Help#Recommender_Tab|Recommender]], and sometimes affecting the main BioPortal system. Our troubleshooting documentation has been updated based on our experience.<br />
<br />
* Fixed an issue that prevented users from getting "ready" submissions from the REST API (NCBO-1673)<br />
* Fixed an issue that caused the Metrics REST endpoint to fail (NCBO-1660).<br />
* Flattened and reparsed the DRON ontology to address SPARQL query performance issues (NCBO-1651).<br />
* Fixed a bug that caused the Recommender to fail when dealing with ontologies with no submissions (NCBO-1650).<br />
* Modified several BioPortal components to retrieve ontology class counts from metrics data instead of directly querying the backend to address performance issues (NCBO-1648).<br />
* Fixed an issue was preventing the latest versions of the NCIT ontology from being pulled into BioPortal (NCBO-1655).<br />
<br />
<br />
== BioPortal Release 4.24 (February 2016) ==<br />
<br />
'''Enhancements'''<br />
<br />
* Implemented an ability to create and manage provisional relations on a provisional class (NCBO-1614)<br />
* Implemented an ability to search for all subclasses of a class, including provisional classes (NCBO-1624)<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a subtree root search to properly include provisional classes when an appropriate parameter is passed to the endpoint<br />
* Fixed an issue with CHEBI ontology not being pulled from its download location (NCBO-1639)<br />
* Fixed a display issue where BioPortal displayed a nested 404 page when an error occured rendering the class tree (NCBO-1623)<br />
* Fixed a bug in NCBO Tree widget that ommitted a "+" sign for classes that have children (NCBO-1574)<br />
* Fixed an issue with search not returning entries for some existing classes of NCBI Taxonomy (NCBITAXON) (NCBO-1591)<br />
* Added sample link to this section of the API documentation (NCBO-1612)<br />
* Updated the Resource Index UI to default to hierarchical classes (classes and descendants) (NCBO-1622)<br />
* Fixed a broken pull location for ONLIRA ontology (NCBO-1627)<br />
<br />
<br />
== BioPortal Release 4.23 (January 2016) ==<br />
<br />
* Added an additional server to the group that serves the BioPortal UI for improved performance.<br />
* Fixed an issue with the ontology analytics REST endpoint returning an empty set.<br />
* Fixed an issue that caused a breakage of the ontology submissions REST endpoint (NCBO-1590).<br />
* Fixed an issue that prevented search from returning some terms in the DOID and NCBITAXON ontologies (NCBO-1578, NCBO-1588).<br />
* Fixed an issue that caused some of the mapping display dialogs to freeze (NCBO-1562).<br />
* Fixed an issue where using the "Jump To:" search box on the ontology classes page caused the UI to hang (NCBO-1506).<br />
* Fixed an issue that prevented the DDO ontology from parsing (NCBO-1603).<br />
* Fixed an issue that caused an error in the virtual appliance if ontology analytics data is empty. Thanks to Vincent Emonet for the contribution.<br />
* Fixed an issue on the Annotator page with an incorrect parameter in the REST API link to retrieve results formatted as JSON. Thanks (again!) Vincent Emonet for the contribution.<br />
<br />
<br />
== BioPortal Release 4.22.1 (December 2015) ==<br />
<br />
This is a minor release that addresses an issue of system instability caused by a bug in our HTTP caching layer that resulted in a significant load on our backend services.<br />
<br />
'''Enhancements'''<br />
<br />
* Added configuration parameters at the UI layer that allow for a greater control over debugging issues with HTTP caching.<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed a bug in the HTTP caching code that caused multiple identical requests to bypass the cache and trigger extraneous requests to the REST API. The bug fix resulted in a significant performance boost to both the front- and back-end services.<br />
<br />
<br />
== BioPortal Release 4.22 (November 2015) ==<br />
<br />
'''Enhancements'''<br />
<br />
* New functionality at the REST API level in support of our collaboration with the [http://www.metadatacenter.org/ CEDAR] project:<br />
** Added the ability to search for, and retrieve all value sets.<br />
** Implemented search for value set items ([http://data.bioontology.org/search?q=melanoma&also_search_provisional=true&valueset_exclude_roots=true&ontology_types=VALUE_SET_COLLECTION example link]).<br />
** Implemented search for ontology classes and value set items ([http://data.bioontology.org/search?q=melanoma&also_search_provisional=true&valueset_exclude_roots=true example link]).<br />
** Added the ability to exclude value set collections from search ([http://data.bioontology.org/search?q=melanoma&ontology_types=ONTOLOGY&also_search_provisional=true example link]).<br />
** Added the ability to search for value set values across all value sets in an ontology.<br />
* Ontologies are now sortable by creation date on the Admin page.<br />
* Clicking the Add Comment and/or Add Proposal buttons in the Notes sections for ontologies will navigate unauthenticated users to the login page.<br />
<br />
'''Bug Fixes'''<br />
<br />
* Fixed an issue that caused [http://bioportal.bioontology.org/projects Projects page] load times in excess of 3 minutes.<br />
* Fixed an issue that caused the UI to go blank after selecting the root node of the CCO ontology.<br />
* Admin page: the ontologies table now refreshes after deleting an ontology.<br />
* Fixed an issue that caused a 404 error when trying to view the DINTO ontology.<br />
* Fixed an inconsistency in the metadata for the CHMO ontology that caused the parsing process to fail.<br />
<br />
<br />
== BioPortal Release 4.21 (October 2015) ==<br />
<br />
'''Bug Fixes'''<br />
* Fixed an issue that caused class trees to reload every time a class was selected.<br />
* Fixed an issue with BioPortal's term selection widget that caused raw HTML to be displayed in search results.<br />
* Fixed a problem in the REST API that caused an internal server error when accessing nonexistent users. The API now correctly displays a 404 not found message.<br />
* Fixed a bug that prevented flat tree ontologies from displaying in BioPortal.<br />
* Fixed an issue that prevented the latest versions of the Gazetteer and Chemical Entities of Biological Interest ontologies from parsing.<br />
* Fixed a problem that prevented visualization from working with private ontologies (thanks go to Eric Verbeek for this).<br />
<br />
<br />
== BioPortal Release 4.20 (August 2015) ==<br />
<br />
''This release includes minor fixes from several previous releases.''<br />
<br />
* Released a new version of the Ontology Recommender. This version is more flexible than the previous version and allows users to assign weights to the scores for various factors that influence the recommendation. In addition, some edge cases in the old system that resulted in bad recommendations have been addressed. This new recommendation system was developed independently by Marcos Martinez and then incorporated into our base code.<br />
* Instances (individuals) in an ontology can now be accessed through the API. Documentation for this is available at: http://data.bioontology.org/documentation#Instance.<br />
* Components have been added to the Annotator UI to allow users to exercise additional options available through the API.<br />
* Icons now indicate non-subclass relationships in OBO ontologies. Previously it was not possible to distinguish visually OBO subclass from other OBO relations displayed in the tree (such as OBO part-of).<br />
* The UMLS MeSH vocabulary is now displayed hierarchically. Previously it was displayed as a flat list of terms because of some problems with the hierarchical relation in the source that we were using.<br />
* The Search API now allows search-by-name of provisional classes assigned to an ontology.<br />
* The UMLS ontologies have all been updated to the latest 2015AA release.<br />
* A new version of BioMixer with a simpler user interface has been incorporated into the system. This work was done by our collaborators at the University of Victoria.<br />
* Created both a REST service and a UI for BioPortal application administration. This interface is automatically visible to VM administrators.<br />
* Updated the framework of our system from RAILS version 2 to version 4.<br />
* Fixed many bugs, especially those causing failures when parsing an ontology.<br />
<br />
== Virtual Appliance 2.4 Release (April 2015) ==<br />
<br />
The Virtual Appliance 2.4 has been released with the following components:<br />
<br />
* Ontologies API (REST service) v4.15.3<br />
* Annotator <br />
* Recommender<br />
* BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI) v4.15.5<br />
* BioMixer<br />
<br />
Note that release 4.15 was a silent release, implying that it contained bug fixes and other non-visible changes, and the third release number (.3, .5) indicates a patch number.<br />
<br />
Application Server Stack:<br />
<br />
* CentOS 6.6<br />
* Apache httpd 2.2.15<br />
* Apache Tomcat 6.0.24<br />
* Solr 4.10.4<br />
* MySQL 5.1.73<br />
* Ruby 2.1.5<br />
* Passenger 4.0.57<br />
* Redis 2.8.18<br />
* Memcached 1.4.4<br />
* 4store v1.1.5-122-g1788d29<br />
* nginx 1.6.3<br />
<br />
== BioPortal Release 4.14 (February 2015) ==<br />
<br />
''This release includes minor fixes from several previous releases.''<br />
<br />
* The ontology summary page for each ontology now has a graph of recent history of the level of user-interface (UI) web traffic (number of page views) for that ontology. This graph is available under the “Metrics” box. See, for example, http://bioportal.bioontology.org/ontologies/SNOMEDCT . The raw data is also available for download in CSV format from the same location.<br />
* The BioPortal home page now has a link that displays all ontologies in the system and the number of UI views for each ontology. Previously usage of only the top 5 ontologies were available.<br />
* Users of our virtual machine now have the ability to plug in alternate concept recognizers for use by the annotator. To support these custom annotators, arbitrary parameters can be passed via the rest interface to the underlying concept recognizer. Documentation for how to make use of this feature is available on [https://github.com/ncbo/ncbo_annotator/wiki/Extending-Annotator-with-a-Custom-Concept-Recognizer GitHub]. Previously the “mgrep” concept recognizer was hardwired into the system and code modifications were required to employ another recognizer.<br />
* Ontologies views can now be used for annotation. Previously only top level ontologies were available for use by the annotation system.<br />
* All of PubMed has been indexed for use by the Resource Index for all terms in all ontologies in BioPortal. Previously only 18 months of PubMed data was indexed.<br />
* We now provide for download, for all resources in BioPortal, files containing counts for term occurrence and co-occurrence (occurrence of pairs of terms in a document). These files can be used for research in enrichment analysis. Documentation of the files and how they might be used is available on [https://github.com/ncbo/resource_index/wiki/Term-Occurence GitHub].<br />
* The ontology browse page now has a faceted interface that allows the list of displayed ontologies to be narrowed as desired. Previously all ontologies appeared in an alphabetical list but this became unwieldy with the 400+ ontologies that we now have.<br />
* There is now a user-interface for displaying all of the properties in an ontology. If the properties were created in a hierarchy then this hierarchy is displayed. Previously only the class hierarchy was displayed. Properties were available programmatically though the REST interface but this information was not surfaced in the UI.<br />
* Ontologies defined using SKOS are now supported. For these ontologies, the hierarchy is determined by the SKOS “broader” and “narrower” properties.<br />
* We now allow download of all publically available ontologies in RDF. UMLS ontologies with restrictive licenses are excluded.<br />
* We fixed a number of non-parsing ontologies and removed a bunch of low-content (“test”) ontologies.<br />
* The system now contains the latest versions (2014AB) of all UMLS ontologies.<br />
* We now treat all OBO synonym types as a BioPortal synonyms. Previously only the OBO “exact” synonym type was treated as a BioPortal synonym.<br />
* We now notify by email the ontology authors if the nightly pull of their ontology fails.<br />
<br />
<br />
== BioPortal Release 4.10 (September 2014) ==<br />
<br />
''This release includes minor fixes from several previous releases.''<br />
<br />
* Reengineered the entire Resource Index to achieve better and more consistent performance and to align the Resource Index with the new BioPortal backend (released last year). In addition to allowing us to support additional resources, this revision removes a number of inconsistencies that resulted from the Resource Index using the old BioPortal backend.<br />
* Upgraded the OWL and OBO parser to the latest version and reparsed all OBO and OWL ontologies. This reprocessing fixed a large number of problems with ontologies that either did not parse or that failed search indexing or metrics calculations.<br />
* We now create and make available for download a comma-separated value (CSV) file for most ontologies. These files have one row/class and a standard set of properties in the columns. We cannot make these files available for ontologies if the license for the ontology does not permit it (e.g. SNOMED-CT and MedDRA).<br />
* Fixed PURLS for all ontologies. There were a large number of ontologies for which the PURLs we created, in the old system or the new one, no longer worked correctly.<br />
* Reworked the entire mappings system so that mappings will be always up-to-date with the latest version of the ontologies.<br />
* Created a web page (http://bioportal.bioontology.org/validate_ontology_file) so that users can validate that their ontologies parse correctly with the latest version of the OWL/OBO parser.<br />
* Removed a number of bogus ontologies and spam notes.<br />
* Fixed implementation of “longest only” parameter in Annotator.<br />
* We now reparse and reindex an ontology if the administrator of the ontology changes the metadata for the ontology. The reparse is necessary because the metadata contains information, such as the properties that contain synonyms or definitions, that influence the parsing and indexing.<br />
* Recalculated metrics for all ontologies. This process filled in metrics for many ontologies that lacked them, and corrected the calculations of some metrics in other ontologies.<br />
* We now allow the download of RDF (Turtle) files for UMLS ontologies whose license allows users to download them.<br />
* Reindexing ontologies for search no longer interferes with the use of search on those ontologies. Previously search for an ontology was either broken or incomplete for an ontology that was being indexed.<br />
* Added an ontology properties endpoint to the REST API. This endpoint allows a user to query for the properties used by an ontology.<br />
<br />
As previously noted, we have permanently retired the old NCBO BioPortal API. New API documentation is available at<br />
http://data.bioontology.org/documentation.<br />
<br />
<br />
== BioPortal Release 4.6 (May 2014) ==<br />
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* Improved Search Result Display – Many ontologies contain classes that are references to a canonical ontology that “owns” the class. The system now automatically tries to identify the “owning” ontology and emphasize it in the results while displaying the ontologies that contain references to that ontology as subordinate (for that class). This feature is easier to try out than to explain. Type in “cancer” into the search box on the Search Tab and scan through the results to see what it is all about. This sort of display has been requested by a number of users for quite a while and we are happy to finally provide it.<br />
* Implemented Search for ID (URI), UMLS CUI, UMLS TUI, and skos:notation – The search system now will use the input search to find a class URI, a class skos:notation field (“short id” in the old system) or a UMLS “concept unique identifier” or semantic type. All of these fields are available through the default search mechanism. There is still an optional “all properties” parameter to search these property values along with all other property values.<br />
* Released New Version of BioMixer visualization system – The BioMixer system has been updated to improve performance and be more robust. (Work performed by our University of Victoria collaborators.)<br />
* Implemented New Mapping Visualization – Mappings system now allows a user to visualize the strength of mappings relationships between ontologies. Go to the mappings tab, select an ontology, and hit the visualization radio button to try this out. (Work performed by our University of Victoria collaborators.)<br />
* Implemented Configurable REST API calls – The Annotator and Search REST calls now allow a user specify which fields of a class the system should return. The user can also specify “all” to get everything. <br />
* Updated UMLS Ontologies – All UMLS ontologies have been updated to the latest (2013 AB) version.<br />
* Improved Autocomplete – The autocomplete in the ontology “Jump To” box, and in the widgets, now works more reliably with results that are more intuitive than previously.<br />
* Provide Access Control for Mappings – We have implemented access control to prevent people other than the author from deleting a mapping.<br />
* Reimplemented Annotator “Longest Only” Parameter – We have reimplemented the annotator “longest only” parameter to work in all situations. This parameter allows the user to limit the returned results to only those matches which are longer than other matches for a given ontology. In the old system this parameter did not work correctly.<br />
* Reimplemented Widgets to not use Flash – We have reimplemented the widgets to not use the Adobe Flash technology. Requiring the use of this technology was unpopular among our user community.<br />
* Enabled Upload and Download Large Ontologies – We have fixed various timeout problems which prevented users from uploading or downloading large ontologies.<br />
* Fixed Bugs! – Fixed a very large number of bugs, some new with the new system, and some carried forward from the old system.<br />
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We've shut down access to the old BioPortal REST API and will be turning off the old system entirely in the near future. We've provided 7 months for application developers to move to the new system and the vast majority have already done so. The overwhelming response from developers has been the that new system is now (after a few post release glitches!) much easier to use and much more reliable than the old system. Documentation for the new API is available at: http://data.bioontology.org/documentation.<br />
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== BioPortal Release 4.0 (September 2013) ==<br />
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The primary distinguishing feature of this release is the replacement of several backend storage and caching mechanisms with a single triple-store based backend built with on the open source 4store platform. In addition we are simultaneously releasing a new version of the BioPortal REST API. This API is also built on top of the triple store. It provides a much more uniform and REST-full interface to the underlying BioPortal data than our previous REST API.<br />
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The old API will continue to function through the end of 2013. This API will only be able to access “old content” (that is, ontologies submitted or updated before today). We encourage API users to transition as quickly as possible to the new API. The new API is the only way to access both new content (submitted after today) and old content. The reports from beta users of the new API have been uniformly positive. Draft documentation for the new API is available at <br />
http://data.bioontology.org/documentation<br />
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BioPortal users will note a few changes from the previous version. Some of these changes are temporary (we didn’t quite get everything done…) while others are permanent. There are also a number of minor and cosmetic changes. The list of the more important changes is available below.<br />
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With a release of this size, it is inevitable that some bugs have crept in. Please report any that you run across to the support@bioontology.org mailing list. Have confidence that we will be working diligently to prioritize and fix the problems that arise.<br />
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Temporary Changes <br />
* All handling of obsolete classes in UI and API is not supported yet. Obsolete classes are currently indistinguishable from normal classes.<br />
* “Slices” and ontology sets (user defined lists of ontologies of interest) are not supported yet<br />
* The tree browse UI does not yet distinguish between is-a and part-of relations for OBO ontologies. Previously (and probably in the future) icons next to the class name indicated the relationship type. <br />
* We do not yet have a VM version for this release. We expect to produce a new VM version by the end of the year. This VM will include the triple-store based storage mechanism. In addition VM users will be able to query the VM triple-store directly with SPARQL.<br />
* Parsing of new ontologies and new versions remains disabled for the next few days. We will re-enable parsing by early next week.<br />
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Permanent Additions<br />
* New ontologies and new versions of ontologies will be typically available for text annotation the next day after submission. Previously the process took several weeks to several months.<br />
* We now have the latest versions UMLS ontologies. Previously we updated UMLS ontologies on request only, which left us with some very old versions. Going forward we will try to update our set of UMLS ontologies within a month of the UMLS release.<br />
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Permanent Subtractions<br />
* Programmatic and browse access to classes in non-current versions of ontologies is removed. We still retain metadata about older versions of ontologies and we still allow you to download the source files for old versions.<br />
* We no longer support Protégé Frames format ontologies. Owners of these ontologies will need to convert them to OWL or OBO to load them.<br />
* We now use the owlAPI (http://owlapi.sourceforge.net/) to load OWL and OBO ontologies. This API supports OWL version 2.0. For almost all features, OWL 2.0 is a superset of OWL 1.0. There are some edge cases though where ontologies that marginally parsed with an OWL 1.0 parser will not parse at all with the OWL 2.0 parser. We leave it to OWL ontology owners to provide valid OWL 2.0 ontologies.</div>JenniferVendetti