NCBO Wiki - User contributions [en]

RDF in BioPortal

2010-08-25T19:47:43Z

Plependu: /* Accessing RDF content */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the [http://sparql.bioontology.org/webui/ SPARQL Endpoint WebUI], paste the following queries into the appropriate text box and press "Submit Query." For several of the examples below, we use the NEMO ontology as an example. Using the "List all named graphs" query example, please find the named graph for your ontology of interest and substitute appropriately.

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
For the NEMO ontology, filter for the object having string "ERP_spatiotemporal_pattern."

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
For the NEMO ontology, list all subject-property-object triples.

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
For the NEMO ontology, list only the subclass properties, i.e., the child-parent relationships.

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
For the NEMO ontology, filter by class identifiers and list each property of the class.

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:39:25Z

Plependu: /* Sample Queries */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the [http://sparql.bioontology.org/webui/ SPARQL Endpoint WebUI], paste the following queries into the appropriate text box and press "Submit Query." For several of the examples below, we use the NEMO ontology as an example. Using the "List all named graphs" query example, please find the named graph for your ontology of interest and substitute appropriately.

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
For the NEMO ontology, filter for the object having string "ERP_spatiotemporal_pattern."

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
For the NEMO ontology, list all subject-property-object triples.

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
For the NEMO ontology, list only the subclass properties, i.e., the child-parent relationships.

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
For the NEMO ontology, filter by class identifiers and list each property of the class.

Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:32:29Z

Plependu: /* List all named graphs */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the [http://sparql.bioontology.org/webui/ SPARQL Endpoint WebUI], paste the following queries into the appropriate text box and press "Submit Query." For several of the examples below, we use the NEMO ontology as an example. Using the "List all named graphs" query example, please find the named graph for your ontology of interest and substitute appropriately.

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:28:18Z

Plependu: /* SPARQL Endpoint */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the [http://sparql.bioontology.org/webui/ SPARQL Endpoint WebUI], paste the following queries into the appropriate text box and press "Submit Query." For several of the examples below, we use the NEMO ontology as an example. Using the "List all named graphs" query example, please find the named graph for your ontology of interest and substitute appropriately.

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
Graph URI (e.g., NEMO):
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:27:16Z

Plependu: /* Sample Queries */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the [http://sparql.bioontology.org/webui/ SPARQL Endpoint WebUI], paste the following queries into the appropriate text box and press "Submit Query." For several of the examples below, we use the NEMO ontology as an example. Using the "List all named graphs" query example, please find the named graph for your ontology of interest and substitute appropriately.

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:24:39Z

Plependu: /* Sample Queries */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the [http://sparql.bioontology.org/webui/ SPARQL Endpoint WebUI], paste the following queries into the appropriate text box and press "Submit Query":

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:23:48Z

Plependu: /* SPARQL Endpoint */

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store. For more information, please see the [http://www.mulgara.org/trac/wiki Mulgara documentation].

== Sample Queries ==
Using the Mulgara [http://sparql.bioontology.org/webui/ WebUI], paste the following queries into the appropriate text box and press "Submit Query":

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:21:49Z

Plependu:

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

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

= Goals for generating RDF for BioPortal content =

We had the following goals in generating RDF for BioPortal:

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

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

= Providing URIs =

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

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

= Accessing RDF content =

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

= Content of the RDF graph =

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

* id (including the original id, using skos:notation)
* preferred name
* synonyms
* superclasses (for OWL, Protege, and OBO)
* skos:broader for terms from RRF ontologies
* CUI, TUI and UMLS code for RRF ontologies

We also use the [http://purl.bioontology.org/ontology/BPMetadata BioPortal Metadata Ontology] to represent the following information about the ontology being described by the RDF:

* id (i.e., BioPortal version id)
* name (i.e., display label)
* acronym (i.e., abbreviation)
* ontology language (i.e., format such as OBO, OWL or RRF)
* description
* URI (the persistent URL or purl)

= SPARQL Endpoint =

The BioPortal [http://sparql.bioontology.org SPARQL Endpoint] currently uses the [http://www.mulgara.org Mulgara] RDF store.

== Sample Queries ==
Using the Mulgara [http://sparql.bioontology.org/webui/ WebUI], paste the following queries into the appropriate text box and press "Submit Query":

=== List all named graphs ===
For every BioPortal ontology, list its named graph, display label, version id, virtual id and format.

Graph URI:
<pre>
sys:default
</pre>

Query Text:
<pre>
SELECT ?graphURI ?label ?versionId ?virtualId ?format
WHERE {
GRAPH ?graphURI {
?s <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label .
?s <http://purl.bioontology.org/ontology/bioportal/id> ?versionId .
?s <http://purl.bioontology.org/ontology/bioportal/ontologyId> ?virtualId .
?s <http://purl.bioontology.org/ontology/bioportal/format> ?format
}
}
</pre>

=== Filter for a specific object ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
?subject ?property ?object
FILTER regex(?object, "ERP_spatiotemporal_pattern", "i")
}
</pre>

=== List all triples ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?subject ?property ?object
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?subject ?property ?object}
</pre>

=== List all subclass relationships ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?child ?parent
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {?child <http://www.w3.org/2000/01/rdf-schema#subClassOf> ?parent}
</pre>

=== List properties of each class ===
Graph URI:
<pre>
http://purl.bioontology.org/virtual/rdf/download/1321.rdf
</pre>

Query Text:
<pre>
SELECT ?s ?p ?o
FROM <http://purl.bioontology.org/virtual/rdf/download/1321.rdf>
WHERE {
{
?ontoid <http://purl.bioontology.org/ontology/bioportal/displayLabel> ?label
FILTER regex(?label, "Neural ElectroMagnetic Ontologies", "i") .
?s <http://www.w3.org/2004/02/skos/core#notation> ?classid
FILTER regex(?classid, "NEMO_0") .
?s ?p ?o
}
}
</pre>

RDF in BioPortal

2010-08-25T19:01:52Z

Plependu: /* SPARQL Endpoint */

RDF in BioPortal

2010-08-25T18:43:08Z

Plependu: /* Accessing RDF content */

RDF in BioPortal

2010-08-25T18:41:41Z

Plependu: /* Accessing RDF content */

RDF in BioPortal

2010-08-25T18:41:21Z

Plependu:

RDF in BioPortal

2010-08-25T18:33:48Z

Plependu:

RDF in BioPortal

2010-07-28T01:36:33Z

Plependu: /* Content of the RDF graph */

RDF in BioPortal

2010-07-28T01:35:36Z

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RDF in BioPortal

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RDF in BioPortal

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BioPortal REST services

2010-07-23T17:35:53Z

Plependu: /* RDF Term Service */

This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services.

The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/

* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''

= Overview - Using NCBO Technology in Your Project =
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.

= Code Examples =
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.

*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.

= BioPortal Announce Mailing List =
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''Signature''': ./ontologies?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org

== List all ontology categories ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./categories?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/categories

== List all ontology groups ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./groups?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/groups

= Services to access ontology views and ontology view versions =

Since all the views on ontologies are ontologies themselves all the services that work on ontologies do
work for ontology views also with the same signature.

For example to get a specific ontology view based on a version id would be possible by using the signature:

'''./ontologies/download/{view version id}?email={email_address}'''

or for getting all view versions of a virtual view can be achieved called using the signature:

'''./ontologies/versions/{view id}?email={email_address}'''

However, there are a couple of services that are special for views:

== List all the latest version of views ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./views?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org

== Get all versions of views from a virtual ontology id ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]
* '''Optional arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).

* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/search/cutaneous%20mela
</accessedResource>
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>3</pageSize>
<numResultsPage>3</numResultsPage>
<numResultsTotal>3</numResultsTotal>
<contents
class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://www.ebi.ac.uk/efo/EFO_0000389
</conceptId>
<conceptIdShort>EFO_0000389</conceptIdShort>
<preferredName>
cutaneous melanoma
</preferredName>
<contents>cutaneous melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
</conceptId>
<conceptIdShort>
Cutaneous_Melanoma
</conceptIdShort>
<preferredName>
Cutaneous Melanoma
</preferredName>
<contents>Cutaneous Melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>DOID:2418</conceptId>
<conceptIdShort>DOID:2418</conceptIdShort>
<preferredName>
Cutaneous Melanocytic Neoplasm
</preferredName>
<contents>
Cutaneous Melanocytic Neoplasm
</contents>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
</ontologyHitList>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
* '''Examples''':
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>/bioportal/concepts/40644/</accessedResource>
<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
<data>
<classBean>
<id>Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
<label>Melanoma</label>
<type>Class</type>
<synonyms>
<string>Malignant Melanoma</string>
<string>Melanoma</string>
<string>melanoma</string>
</synonyms>
<definitions>
<string>A malignant, usually aggressive tumor composed of atypical,
neoplastic melanocytes.</string>
</definitions>
<relations>
<entry>
<string>UMLS_CUI</string>
<list>
<string>C0025202</string>
</list>
</entry>
<entry>
<string>owl:equivalentClass</string>
<list>
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
</list>
</entry>
<entry>
<string>ALT_DEFINITION</string>
<list>
<string>
<def-source>NCI-GLOSS</def-source>
<def-definition>A form of skin cancer that arises in
melanocytes, the cells that produce pigment.</def-definition>
</string>
</list>
</entry>
<entry>
<string>ICD-O-3_Code</string>
<list>
<string>8720/3</string>
</list>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Neoplastic Process</string>
</list>
</entry>
<entry>
<string>SubClass</string>
<list>
<classBean>
<id>Non-Cutaneous_Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
<label>Non-Cutaneous Melanoma</label>
<type>Class</type>
<synonyms>
<string>Extracutaneous Melanoma</string>
<string>Non-Cutaneous Melanoma</string>
</synonyms>
<definitions>
<string>Melanoma is a malignant tumor of melanocytes,
cells that are derived from the neural crest.</string>
</definitions>
<relations>
<entry>
<string>code</string>
<list>
<string>C8711</string>
</list>
</entry>
</relations>
</classBean>
</list>
</entry>
</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org

== Get term for latest ontology version id ==
'''NOTE''': ''This signature will change in BioPortal release 2.2''
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org

* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org

== Get all terms using the specific ontology version id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Get all terms using the virtual ontology id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Changes to the Get all terms service ==

Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
*** '''pagenum:''' An integer indicating which page of results to return.

* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

'''NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''

== Get parents/children of a given concept in a specific ontology version ==
* '''Signature''': ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional args}]

* '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/concepts/children/42331/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?level=1&offset=1&limit=10&email=example@example.org
* '''Description''': returns all parents of the concept, with the level indicating how far away the parent is from the concept. For instance, direct parents have level 1; their direct parents have level 2, etc. If no level is specified, the service returns all the levels up to the root. If the level is specified, the service returns only the parents at that level.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/parents/42331/Melanoma
</accessedResource>
<accessDate>20100408 17:58:14.230 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm
</fullId>
<label>Common Neoplasm</label>
<synonyms>
<string>Common Tumor</string>
<string>Common Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Melanocytic_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanocytic_Neoplasm
</fullId>
<label>Melanocytic Neoplasm</label>
<synonyms>
<string>Melanocytic Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get parents/children of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get paths to roots/leaves from a concept in a specific ontology version ==
* '''Signature''': ./concepts/[rootpath|leafpath]/{ontologyVersionId}/{conceptId}[?email={email_address}&{optional args}]
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies
* '''Example''': http://rest.bioontology.org/bioportal/concepts/rootpath/42693/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/concepts/leafpath/42693/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': return a set of path to the roots (resp. leaves) for a given concept in a specific ontology version. Paths are represented as a list of conceptIds, separated by periods (.) The first one in the list is a root (resp. leaf) in the hierarchy; the last one in the list is the direct parent (resp. direct child) of the concept.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/concepts/rootpath/40644/Melanoma
</accessedResource>
<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>40644</ontologyVersionId>
<id>Melanoma</id>
<relations>
<entry>
<string>Path</string>
<string>
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
</string>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>40644</ontologyVersionId>
<id>Melanoma</id>
<relations>
<entry>
<string>Path</string>
<string>
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
</string>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get siblings of a given concept in a specific ontology version ==
* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/42331/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/siblings/42331/Melanoma
</accessedResource>
<accessDate>20100408 18:06:16.868 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Germ_Cell_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Germ_Cell_Neoplasm
</fullId>
<label>Common Germ Cell Tumor</label>
<synonyms>
<string>Common Germ Cell Tumor</string>
<string>Common Germ Cell Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Hematopoietic_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Hematopoietic_Neoplasm
</fullId>
<label>Common Hematopoietic Neoplasm</label>
<synonyms>
<string>Common Hematopoietic Neoplasm</string>
<string>Common Hematopoietic Tumor</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get siblings of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.

= Bio2RDF Dump Service =

This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org

= Annotator Service =

The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others.

The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.

= Resource Index Service =

The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.

= Prototypes =

== RDF Term Service ==
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org
* '''Required arguments:'''
** ontology version id
** concept id
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"

...

<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf">
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description>
<bioportal:abbreviation>NEMO</bioportal:abbreviation>
<bioportal:format>OWL</bioportal:format>
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date>
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri>
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel>
<bioportal:versionNumber>.95</bioportal:versionNumber>
<bioportal:id>42743</bioportal:id>
<bioportal:ontologyId>1321</bioportal:ontologyId>
</owl:Ontology>

...

<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023">
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/>
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader>
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation>
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel>
</owl:Class>
</rdf:RDF>


</pre>

== RDF Download Service ==
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org
* '''Required arguments:'''
** ontology version id
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

== Notes Service ==
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].

== Mapping Service ==
* '''Prototype'''
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/
** '''Required arguments:'''
*** ontology_id
** '''Optional arguments:'''
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]
** '''Sample Output:'''
<pre>
<hash>
<mapping-from type="array">
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:25:23</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>

<source-name>Carbon</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:27594</destination-id>
<id>98216</id>
<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>

<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Carbon</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Carbon</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:27:05</created-at>

<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Gold</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:29287</destination-id>
<id>98218</id>
<user-id>38139</user-id>

<relationship-type nil="true"></relationship-type>
<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Gold</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Gold</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
</mapping-from>
<mapping-to type="array">
<mapping-to>
<comment nil="true"></comment>
<map-type>Human</map-type>

<created-at>2008-05-09 08:35:27</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Carbohydrate</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>Carbohydrate</destination-id>
<id>98219</id>

<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
<destination-name>Carbohydrate</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1083</destination-ont>
<source-id>Carbohydrate</source-id>

<destination-version-id>29531</destination-version-id>
<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-to>
</mapping-to>
</hash>

</pre>



= XML Schema Definitions for the REST services =

XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.

BioPortal REST services

2010-07-23T17:35:00Z

Plependu: /* RDF Term Service */

This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services.

The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/

* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''

= Overview - Using NCBO Technology in Your Project =
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.

= Code Examples =
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.

*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.

= BioPortal Announce Mailing List =
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''Signature''': ./ontologies?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org

== List all ontology categories ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./categories?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/categories

== List all ontology groups ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./groups?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/groups

= Services to access ontology views and ontology view versions =

Since all the views on ontologies are ontologies themselves all the services that work on ontologies do
work for ontology views also with the same signature.

For example to get a specific ontology view based on a version id would be possible by using the signature:

'''./ontologies/download/{view version id}?email={email_address}'''

or for getting all view versions of a virtual view can be achieved called using the signature:

'''./ontologies/versions/{view id}?email={email_address}'''

However, there are a couple of services that are special for views:

== List all the latest version of views ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./views?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org

== Get all versions of views from a virtual ontology id ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]
* '''Optional arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).

* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/search/cutaneous%20mela
</accessedResource>
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>3</pageSize>
<numResultsPage>3</numResultsPage>
<numResultsTotal>3</numResultsTotal>
<contents
class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://www.ebi.ac.uk/efo/EFO_0000389
</conceptId>
<conceptIdShort>EFO_0000389</conceptIdShort>
<preferredName>
cutaneous melanoma
</preferredName>
<contents>cutaneous melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
</conceptId>
<conceptIdShort>
Cutaneous_Melanoma
</conceptIdShort>
<preferredName>
Cutaneous Melanoma
</preferredName>
<contents>Cutaneous Melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>DOID:2418</conceptId>
<conceptIdShort>DOID:2418</conceptIdShort>
<preferredName>
Cutaneous Melanocytic Neoplasm
</preferredName>
<contents>
Cutaneous Melanocytic Neoplasm
</contents>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
</ontologyHitList>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
* '''Examples''':
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>/bioportal/concepts/40644/</accessedResource>
<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
<data>
<classBean>
<id>Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
<label>Melanoma</label>
<type>Class</type>
<synonyms>
<string>Malignant Melanoma</string>
<string>Melanoma</string>
<string>melanoma</string>
</synonyms>
<definitions>
<string>A malignant, usually aggressive tumor composed of atypical,
neoplastic melanocytes.</string>
</definitions>
<relations>
<entry>
<string>UMLS_CUI</string>
<list>
<string>C0025202</string>
</list>
</entry>
<entry>
<string>owl:equivalentClass</string>
<list>
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
</list>
</entry>
<entry>
<string>ALT_DEFINITION</string>
<list>
<string>
<def-source>NCI-GLOSS</def-source>
<def-definition>A form of skin cancer that arises in
melanocytes, the cells that produce pigment.</def-definition>
</string>
</list>
</entry>
<entry>
<string>ICD-O-3_Code</string>
<list>
<string>8720/3</string>
</list>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Neoplastic Process</string>
</list>
</entry>
<entry>
<string>SubClass</string>
<list>
<classBean>
<id>Non-Cutaneous_Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
<label>Non-Cutaneous Melanoma</label>
<type>Class</type>
<synonyms>
<string>Extracutaneous Melanoma</string>
<string>Non-Cutaneous Melanoma</string>
</synonyms>
<definitions>
<string>Melanoma is a malignant tumor of melanocytes,
cells that are derived from the neural crest.</string>
</definitions>
<relations>
<entry>
<string>code</string>
<list>
<string>C8711</string>
</list>
</entry>
</relations>
</classBean>
</list>
</entry>
</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org

== Get term for latest ontology version id ==
'''NOTE''': ''This signature will change in BioPortal release 2.2''
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org

* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org

== Get all terms using the specific ontology version id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Get all terms using the virtual ontology id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Changes to the Get all terms service ==

Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
*** '''pagenum:''' An integer indicating which page of results to return.

* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

'''NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''

== Get parents/children of a given concept in a specific ontology version ==
* '''Signature''': ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional args}]

* '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/concepts/children/42331/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?level=1&offset=1&limit=10&email=example@example.org
* '''Description''': returns all parents of the concept, with the level indicating how far away the parent is from the concept. For instance, direct parents have level 1; their direct parents have level 2, etc. If no level is specified, the service returns all the levels up to the root. If the level is specified, the service returns only the parents at that level.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/parents/42331/Melanoma
</accessedResource>
<accessDate>20100408 17:58:14.230 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm
</fullId>
<label>Common Neoplasm</label>
<synonyms>
<string>Common Tumor</string>
<string>Common Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Melanocytic_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanocytic_Neoplasm
</fullId>
<label>Melanocytic Neoplasm</label>
<synonyms>
<string>Melanocytic Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get parents/children of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get paths to roots/leaves from a concept in a specific ontology version ==
* '''Signature''': ./concepts/[rootpath|leafpath]/{ontologyVersionId}/{conceptId}[?email={email_address}&{optional args}]
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies
* '''Example''': http://rest.bioontology.org/bioportal/concepts/rootpath/42693/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/concepts/leafpath/42693/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': return a set of path to the roots (resp. leaves) for a given concept in a specific ontology version. Paths are represented as a list of conceptIds, separated by periods (.) The first one in the list is a root (resp. leaf) in the hierarchy; the last one in the list is the direct parent (resp. direct child) of the concept.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/concepts/rootpath/40644/Melanoma
</accessedResource>
<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>40644</ontologyVersionId>
<id>Melanoma</id>
<relations>
<entry>
<string>Path</string>
<string>
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
</string>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>40644</ontologyVersionId>
<id>Melanoma</id>
<relations>
<entry>
<string>Path</string>
<string>
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
</string>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get siblings of a given concept in a specific ontology version ==
* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/42331/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/siblings/42331/Melanoma
</accessedResource>
<accessDate>20100408 18:06:16.868 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Germ_Cell_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Germ_Cell_Neoplasm
</fullId>
<label>Common Germ Cell Tumor</label>
<synonyms>
<string>Common Germ Cell Tumor</string>
<string>Common Germ Cell Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Hematopoietic_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Hematopoietic_Neoplasm
</fullId>
<label>Common Hematopoietic Neoplasm</label>
<synonyms>
<string>Common Hematopoietic Neoplasm</string>
<string>Common Hematopoietic Tumor</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get siblings of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.

= Bio2RDF Dump Service =

This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org

= Annotator Service =

The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others.

The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.

= Resource Index Service =

The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.

= Prototypes =

== RDF Term Service ==
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org
* '''Required arguments:'''
** ontology version id
** concept id
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}</nowiki>
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki>
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"

...

<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf">
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description>
<bioportal:abbreviation>NEMO</bioportal:abbreviation>
<bioportal:format>OWL</bioportal:format>
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date>
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri>
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel>
<bioportal:versionNumber>.95</bioportal:versionNumber>
<bioportal:id>42743</bioportal:id>
<bioportal:ontologyId>1321</bioportal:ontologyId>
</owl:Ontology>

...

<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023">
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/>
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader>
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation>
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel>
</owl:Class>
</rdf:RDF>


</pre>

== RDF Download Service ==
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org
* '''Required arguments:'''
** ontology version id
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

== Notes Service ==
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].

== Mapping Service ==
* '''Prototype'''
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/
** '''Required arguments:'''
*** ontology_id
** '''Optional arguments:'''
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]
** '''Sample Output:'''
<pre>
<hash>
<mapping-from type="array">
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:25:23</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>

<source-name>Carbon</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:27594</destination-id>
<id>98216</id>
<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>

<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Carbon</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Carbon</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:27:05</created-at>

<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Gold</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:29287</destination-id>
<id>98218</id>
<user-id>38139</user-id>

<relationship-type nil="true"></relationship-type>
<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Gold</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Gold</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
</mapping-from>
<mapping-to type="array">
<mapping-to>
<comment nil="true"></comment>
<map-type>Human</map-type>

<created-at>2008-05-09 08:35:27</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Carbohydrate</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>Carbohydrate</destination-id>
<id>98219</id>

<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
<destination-name>Carbohydrate</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1083</destination-ont>
<source-id>Carbohydrate</source-id>

<destination-version-id>29531</destination-version-id>
<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-to>
</mapping-to>
</hash>

</pre>



= XML Schema Definitions for the REST services =

XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.

RDF in BioPortal

2010-07-23T17:33:14Z

Plependu: /* Providing URIs */

RDF in BioPortal

2010-07-23T17:32:51Z

Plependu: /* Providing URIs */

RDF in BioPortal

2010-07-23T17:23:05Z

Plependu: /* Goals for generating RDF for BioPortal content */

BioPortal REST services

2010-07-23T17:20:51Z

Plependu: /* RDF Download Service */

This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services.

The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/

* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter.

* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''

= Overview - Using NCBO Technology in Your Project =
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.

= Code Examples =
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.

*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.

= BioPortal Announce Mailing List =
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.

= Services to access ontologies and ontology versions =

== List all the latest version of ontologies ==

* '''Signature''': ./ontologies?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org

== Get a specific ontology based on a version id ==
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org

== Download an ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org

== Download the latest ontology file ==
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org

== Get all versions of an ontology from a virtual ontology id ==
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org

== Get latest version of an ontology id ==
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org

== List all ontology categories ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./categories?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/categories

== List all ontology groups ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./groups?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/groups

= Services to access ontology views and ontology view versions =

Since all the views on ontologies are ontologies themselves all the services that work on ontologies do
work for ontology views also with the same signature.

For example to get a specific ontology view based on a version id would be possible by using the signature:

'''./ontologies/download/{view version id}?email={email_address}'''

or for getting all view versions of a virtual view can be achieved called using the signature:

'''./ontologies/versions/{view id}?email={email_address}'''

However, there are a couple of services that are special for views:

== List all the latest version of views ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Signature''': ./views?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org

== Get all versions of views from a virtual ontology id ==
'''NOTE''': ''To be released in BioPortal version 2.2''
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.
* '''Signature''': ./views/versions/{ontology id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org

= Search services =

== Search BioPortal ==
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]
* '''Optional arguments:'''
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)
** isexactmatch=[1/0] – match the entire concept name (default: 0)
** includeproperties=[1/0] – include attributes in the search (default: 0)
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.
* '''Description:'''
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).

In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).

* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/search/cutaneous%20mela
</accessedResource>
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>1</numPages>
<pageSize>3</pageSize>
<numResultsPage>3</numResultsPage>
<numResultsTotal>3</numResultsTotal>
<contents
class="org.ncbo.stanford.bean.search.SearchResultListBean">
<searchResultList>
<searchBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://www.ebi.ac.uk/efo/EFO_0000389
</conceptId>
<conceptIdShort>EFO_0000389</conceptIdShort>
<preferredName>
cutaneous melanoma
</preferredName>
<contents>cutaneous melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma
</conceptId>
<conceptIdShort>
Cutaneous_Melanoma
</conceptIdShort>
<preferredName>
Cutaneous Melanoma
</preferredName>
<contents>Cutaneous Melanoma</contents>
</searchBean>
<searchBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<recordType>
RECORD_TYPE_PREFERRED_NAME
</recordType>
<conceptId>DOID:2418</conceptId>
<conceptIdShort>DOID:2418</conceptIdShort>
<preferredName>
Cutaneous Melanocytic Neoplasm
</preferredName>
<contents>
Cutaneous Melanocytic Neoplasm
</contents>
</searchBean>
</searchResultList>
<ontologyHitList>
<ontologyHitBean>
<ontologyVersionId>39715</ontologyVersionId>
<ontologyId>1136</ontologyId>
<ontologyDisplayLabel>
Experimental Factor Ontology
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39833</ontologyVersionId>
<ontologyId>1009</ontologyId>
<ontologyDisplayLabel>
Human disease
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
<ontologyHitBean>
<ontologyVersionId>39478</ontologyVersionId>
<ontologyId>1032</ontologyId>
<ontologyDisplayLabel>
NCI Thesaurus
</ontologyDisplayLabel>
<numHits>1</numHits>
</ontologyHitBean>
</ontologyHitList>
</contents>
</page>
</data>
</success>
</pre>

= Term services =
(formerly referred to as Concept services)

== Get term ==
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI.
* '''Optional arguments:'''
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.
* '''Examples''':
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org 
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org
* '''Sample Output''':
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>/bioportal/concepts/40644/</accessedResource>
<accessDate>2009-12-16 10:06:10.727 PST</accessDate>
<data>
<classBean>
<id>Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId>
<label>Melanoma</label>
<type>Class</type>
<synonyms>
<string>Malignant Melanoma</string>
<string>Melanoma</string>
<string>melanoma</string>
</synonyms>
<definitions>
<string>A malignant, usually aggressive tumor composed of atypical,
neoplastic melanocytes.</string>
</definitions>
<relations>
<entry>
<string>UMLS_CUI</string>
<list>
<string>C0025202</string>
</list>
</entry>
<entry>
<string>owl:equivalentClass</string>
<list>
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string>
</list>
</entry>
<entry>
<string>ALT_DEFINITION</string>
<list>
<string>
<def-source>NCI-GLOSS</def-source>
<def-definition>A form of skin cancer that arises in
melanocytes, the cells that produce pigment.</def-definition>
</string>
</list>
</entry>
<entry>
<string>ICD-O-3_Code</string>
<list>
<string>8720/3</string>
</list>
</entry>
<entry>
<string>Semantic_Type</string>
<list>
<string>Neoplastic Process</string>
</list>
</entry>
<entry>
<string>SubClass</string>
<list>
<classBean>
<id>Non-Cutaneous_Melanoma</id>
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId>
<label>Non-Cutaneous Melanoma</label>
<type>Class</type>
<synonyms>
<string>Extracutaneous Melanoma</string>
<string>Non-Cutaneous Melanoma</string>
</synonyms>
<definitions>
<string>Melanoma is a malignant tumor of melanocytes,
cells that are derived from the neural crest.</string>
</definitions>
<relations>
<entry>
<string>code</string>
<list>
<string>C8711</string>
</list>
</entry>
</relations>
</classBean>
</list>
</entry>
</relations>
</classBean>
</data>
</success>
</pre>

== Get all root terms for an ontology version id ==
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org

== Get term for latest ontology version id ==
'''NOTE''': ''This signature will change in BioPortal release 2.2''
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org

* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org

== Get all terms using the specific ontology version id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Get all terms using the virtual ontology id ==

'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.

* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org
* '''Arguments:'''
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
** '''pagenum:''' An integer indicating which page of results to return.

== Changes to the Get all terms service ==

Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.

* '''Examples''': A preview of the new service can be seen on the NCBO staging site:
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500

* '''Signature'''
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)
*** '''pagenum:''' An integer indicating which page of results to return.

* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.

= Instance Services =

== Get all direct instances for a given term ==
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address}
* '''Optional arguments:'''
** pagesize=<pagesize> - the number of results to display in a single request (default: all)
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)

* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org
* '''Description''': returns all direct instances for a given term.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/instances/38801
</accessedResource>
<accessDate>20100408 18:17:21.226 PDT</accessDate>
<data>
<page>
<pageNum>1</pageNum>
<numPages>5</numPages>
<pageSize>1</pageSize>
<numResultsPage>1</numResultsPage>
<numResultsTotal>5</numResultsTotal>
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean">
<list>
<instanceBean>
<id>unknown_substrate_type</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</fullId>
<label>unknown_substrate_type</label>
<relations>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>

<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_484</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>

<list>
<string>SubstrateType of unknown type.</string>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</contents>
</page>
</data>
</success>
</pre>

== Get an instance and its property/value pairs ==
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]

* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org
* '''Description''': returns information about an instance and a list of property/value pairs.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/instance/38801
</accessedResource>
<accessDate>20100408 18:10:48.760 PDT</accessDate>
<data>
<instanceBean>
<id>glass</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</fullId>
<label>glass</label>
<relations>
<entry>
<propertyBean>
<id>:NAME</id>
<fullId>:NAME</fullId>
<label>:NAME</label>
<relations />
</propertyBean>
<list>
<string>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass
</string>
</list>
</entry>
<entry>
<propertyBean>
<id>unique_identifier</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier
</fullId>
<label>unique_identifier</label>
<relations />
</propertyBean>
<list>
<string>MO_742</string>
</list>
</entry>
<entry>
<propertyBean>
<id>rdfs:comment</id>
<fullId>http://www.w3.org/2000/01/rdfschema#comment
</fullId>
<label>rdfs:comment</label>
<relations />
</propertyBean>
<list>
<string>The array is made on a glass slide.</string>
</list>
</entry>
<entry>
<propertyBean>
<id>:DIRECTTYPE</id>
<fullId>:DIRECTTYPE</fullId>
<label>:DIRECTTYPE</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
<entry>
<propertyBean>
<id>rdf:type</id>
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type
</fullId>
<label>rdf:type</label>
<relations />
</propertyBean>
<list>
<instanceBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<relations />
<instanceType>
<list>
<classBean>
<id>owl:Class</id>
<fullId>http://www.w3.org/2002/07/owl#Class
</fullId>
<label>owl:Class</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</list>
</entry>
</relations>
<instanceType>
<list>
<classBean>
<id>SubstrateType</id>
<fullId>
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType
</fullId>
<label>SubstrateType</label>
<type>Class</type>
<relations />
</classBean>
</list>
</instanceType>
</instanceBean>
</data>
</success>
</pre>

= Hierarchy Services =

'''NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.'''

== Get parents/children of a given concept in a specific ontology version ==
* '''Signature''': ./concepts/[parents|children]/{ontlogyVersionId}/{conceptId}[?email={email_address}&{optional args}]

* '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/concepts/children/42331/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?level=1&offset=1&limit=10&email=example@example.org
* '''Description''': returns all parents of the concept, with the level indicating how far away the parent is from the concept. For instance, direct parents have level 1; their direct parents have level 2, etc. If no level is specified, the service returns all the levels up to the root. If the level is specified, the service returns only the parents at that level.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/parents/42331/Melanoma
</accessedResource>
<accessDate>20100408 17:58:14.230 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Neoplasm
</fullId>
<label>Common Neoplasm</label>
<synonyms>
<string>Common Tumor</string>
<string>Common Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Melanocytic_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanocytic_Neoplasm
</fullId>
<label>Melanocytic Neoplasm</label>
<synonyms>
<string>Melanocytic Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get parents/children of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get paths to roots/leaves from a concept in a specific ontology version ==
* '''Signature''': ./concepts/[rootpath|leafpath]/{ontologyVersionId}/{conceptId}[?email={email_address}&{optional args}]
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies
* '''Example''': http://rest.bioontology.org/bioportal/concepts/rootpath/42693/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/concepts/leafpath/42693/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': return a set of path to the roots (resp. leaves) for a given concept in a specific ontology version. Paths are represented as a list of conceptIds, separated by periods (.) The first one in the list is a root (resp. leaf) in the hierarchy; the last one in the list is the direct parent (resp. direct child) of the concept.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF-8" ?>
<success>
<accessedResource>
/bioportal/concepts/rootpath/40644/Melanoma
</accessedResource>
<accessDate>2009-04-21 11:06:23.439 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>40644</ontologyVersionId>
<id>Melanoma</id>
<relations>
<entry>
<string>Path</string>
<string>
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm
</string>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>40644</ontologyVersionId>
<id>Melanoma</id>
<relations>
<entry>
<string>Path</string>
<string>
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm
</string>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get paths to root/leaves from a concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
** limit=<integer> – limits the number of results
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.

== Get siblings of a given concept in a specific ontology version ==
* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/42331/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.
* '''Sample Output:'''
<pre>
<?xml version="1.0" encoding="UTF8" ?>
<success>
<accessedResource>/bioportal/concepts/siblings/42331/Melanoma
</accessedResource>
<accessDate>20100408 18:06:16.868 PDT</accessDate>
<data>
<list>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Germ_Cell_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Germ_Cell_Neoplasm
</fullId>
<label>Common Germ Cell Tumor</label>
<synonyms>
<string>Common Germ Cell Tumor</string>
<string>Common Germ Cell Neoplasm</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
<classBean>
<ontologyVersionId>42331</ontologyVersionId>
<id>Common_Hematopoietic_Neoplasm</id>
<fullId>
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Hematopoietic_Neoplasm
</fullId>
<label>Common Hematopoietic Neoplasm</label>
<synonyms>
<string>Common Hematopoietic Neoplasm</string>
<string>Common Hematopoietic Tumor</string>
</synonyms>
<relations>
<entry>
<string>Level</string>
<int>1</int>
</entry>
</relations>
</classBean>
</list>
</data>
</success>
</pre>

== Get siblings of a given concept in the latest version of a given ontology ==
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org
* '''Required arguments:'''
** level=<integer> - limits results to a given level in the hierarchy
* '''Optional arguments:'''
** offset=<integer> – results offset (used for pagination)
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.

= Bio2RDF Dump Service =

This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.

* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org

= Annotator Service =

The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others.

The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.

= Resource Index Service =

The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.

= Prototypes =

== RDF Term Service ==
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org
* '''Required arguments:'''
** ontology version id
** concept id
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}
* '''Sample Output:'''
<pre>
<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"

...

<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf">
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description>
<bioportal:abbreviation>NEMO</bioportal:abbreviation>
<bioportal:format>OWL</bioportal:format>
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date>
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri>
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel>
<bioportal:versionNumber>.95</bioportal:versionNumber>
<bioportal:id>42743</bioportal:id>
<bioportal:ontologyId>1321</bioportal:ontologyId>
</owl:Ontology>

...

<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023">
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label>
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/>
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader>
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation>
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel>
</owl:Class>
</rdf:RDF>


</pre>

== RDF Download Service ==
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org
* '''Examples''':
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org
* '''Required arguments:'''
** ontology version id
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce].
** The RDF dump will use URIs that are based on which format the ontology is in:
*** '''OWL/RDF(S)''': preserve original URIs
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}

== Notes Service ==
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].

== Mapping Service ==
* '''Prototype'''
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/
** '''Required arguments:'''
*** ontology_id
** '''Optional arguments:'''
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]
** '''Sample Output:'''
<pre>
<hash>
<mapping-from type="array">
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:25:23</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>

<source-name>Carbon</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:27594</destination-id>
<id>98216</id>
<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>

<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Carbon</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Carbon</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
<mapping-from>
<comment nil="true"></comment>
<map-type>Human</map-type>
<created-at>2008-05-09 08:27:05</created-at>

<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Gold</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>CHEBI:29287</destination-id>
<id>98218</id>
<user-id>38139</user-id>

<relationship-type nil="true"></relationship-type>
<destination-ont-name>Chemical entities of biological interest</destination-ont-name>
<destination-name>Gold</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1007</destination-ont>
<source-id>Gold</source-id>
<destination-version-id>38377</destination-version-id>

<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-from>
</mapping-from>
<mapping-to type="array">
<mapping-to>
<comment nil="true"></comment>
<map-type>Human</map-type>

<created-at>2008-05-09 08:35:27</created-at>
<updated-at>2008-08-05 17:26:06</updated-at>
<source-name>Carbohydrate</source-name>
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name>
<destination-id>Carbohydrate</destination-id>
<id>98219</id>

<user-id>38139</user-id>
<relationship-type nil="true"></relationship-type>
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name>
<destination-name>Carbohydrate</destination-name>
<map-source nil="true"></map-source>
<destination-ont>1083</destination-ont>
<source-id>Carbohydrate</source-id>

<destination-version-id>29531</destination-version-id>
<source-version-id>29531</source-version-id>
<source-ont>1083</source-ont>
</mapping-to>
</mapping-to>
</hash>

</pre>



= XML Schema Definitions for the REST services =

XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.

RDF in BioPortal

2010-07-23T17:20:05Z

Plependu: /* Accessing RDF content */

Metrics Study

2010-07-07T02:37:45Z

Plependu: /* Download Benchmark Ontologies */

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010. (NOTE: powered, in part, by the [http://owlapi.sourceforge.net OWL API].)
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

References and materials such as source code for the tool will be forthcoming.

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 10, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-27T07:13:38Z

Plependu: /* Download Metrics Files */

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010. (NOTE: powered, in part, by the [http://owlapi.sourceforge.net OWL API].)
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

References and materials such as source code for the tool will be forthcoming.

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-27T07:13:04Z

Plependu: /* Download Metrics Files */

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010. (NOTE: powered, in part, by the [http://owlapi.sourceforge.net | OWL API].)
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

References and materials such as source code for the tool will be forthcoming.

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-22T23:20:38Z

Plependu: /* Download Benchmark Ontologies */

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010.
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

References and materials such as source code for the tool will be forthcoming.

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-21T22:32:53Z

Plependu: /* Download Benchmark Ontologies */

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010.
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

References and materials for the tool will be forthcoming.

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-21T22:32:13Z

Plependu:

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010.
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters--randomization seed, no. individuals, depth, span, density. When fed the listed parameters, the tool should generate the corresponding file listed.

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-21T22:30:39Z

Plependu:

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010.
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
These ontologies were generated using the OntoGenerate tool using the given input parameters (randomization seed, no. individuals, depth, span, density).

* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (100, 1000000, 10, 4, 40)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 20, 2, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Medium_mid.obo.zip|Medium-Mid]] (100, 1000000, 10, 4, 60)
** [[Media:Medium_deep.obo.zip|Medium-Deep]] (7, 1000000, 20, 6, 28)

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]] (7, 1000000, 5, 11, 60)
** [[Media:Large_mid.obo.zip|Large-Mid]] (7, 1000000, 6, 40)
** [[Media:Large_deep.obo.zip|Large-Deep]] (7, 1000000, 20, 3, 52)

Metrics Study

2010-06-21T21:29:08Z

Plependu:

= Introduction =
We performed a metrics analysis of the BioPortal to quantify the effects of ontology variation, evolution and instance density on various tools such as bechmarking suites, Resource Index optimization, and SPARQL query optimization. The data for these analyses are archived below.

Publication materials and references will be forthcoming.

= Download Metrics Files =
These ontologies were generated using the OntoGenerate tool using the given input parameters (seed, individuals, depth, span, density).

* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]] - metrics for all of the BioPortal ontologies taken on May 5, 2010.
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]] - metrics for the NCBO Resource Index taken on June 3, 2010.

= Download Benchmark Ontologies =
* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]] (7, 1000000, 5, 6, 30)
** [[Media:Small_mid.obo.zip|Small-Mid]] (7, 1000000, 7, 60)
** [[Media:Small_deep.obo.zip|Small-Deep]] (7, 1000000, 11, 60)

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]]
** [[Media:Medium_mid.obo.zip|Medium-Mid]]
** [[Media:Medium_deep.obo.zip|Medium-Deep]]

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]]
** [[Media:Large_mid.obo.zip|Large-Mid]]
** [[Media:Large_deep.obo.zip|Large-Deep]]

Metrics Study

2010-06-21T21:22:34Z

Plependu: /* Introduction */

Metrics Study

2010-06-21T21:21:41Z

Plependu:

File:Large deep.obo.zip

2010-06-21T21:19:06Z

Plependu:

File:Large mid.obo.zip

2010-06-21T21:18:53Z

Plependu:

File:Large shallow.obo.zip

2010-06-21T21:18:36Z

Plependu:

File:Medium deep.obo.zip

2010-06-21T21:18:12Z

Plependu:

File:Medium mid.obo.zip

2010-06-21T21:17:54Z

Plependu:

File:Medium shallow.obo.zip

2010-06-21T21:17:39Z

Plependu:

Metrics Study

2010-06-21T21:17:24Z

Plependu:

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]]
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]]

= Download Benchmark Ontologies =
* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]]
** [[Media:Small_mid.obo.zip|Small-Mid]]
** [[Media:Small_deep.obo.zip|Small-Deep]]

* Medium
** [[Media:Medium_shallow.obo.zip|Medium-Shallow]]
** [[Media:Medium_mid.obo.zip|Medium-Mid]]
** [[Media:Medium_deep.obo.zip|Medium-Deep]]

* Large
** [[Media:Large_shallow.obo.zip|Large-Shallow]]
** [[Media:Large_mid.obo.zip|Large-Mid]]
** [[Media:Large_deep.obo.zip|Large-Deep]]

File:Small deep.obo.zip

2010-06-21T21:15:52Z

Plependu:

File:Small mid.obo.zip

2010-06-21T21:11:31Z

Plependu:

File:Small shallow.obo.zip

2010-06-21T21:10:57Z

Plependu:

Metrics Study

2010-06-21T21:09:36Z

Plependu:

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]]
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]]

= Download Benchmark Ontologies =
* Small
** [[Media:Small_shallow.obo.zip|Small-Shallow]]
** [[Media:Small_mid.obo.zip|Small-Mid]]
** [[Media:Small_deep.obo.zip|Small-Deep]]

* Medium
** [[Media:Medium_deep.obo.zip|Medium-Deep]]
** [[Media:Small_shallow.obo.zip|Medium-Shallow]]
** [[Media:Medium_mid.obo.zip|Medium-Mid]]

* Large
** [[Media:Small_shallow.obo.zip|Large-Shallow]]
** [[Media:Large_mid.obo.zip|Large-Mid]]
** [[Media:Large_deep.obo.zip|Large-Deep]]

Metrics Study

2010-06-21T20:05:23Z

Plependu:

= Download Metrics Files =
* [[Media:Ontology_metrics.txt.zip|Ontology Metrics]]
* [[Media:Annotation_metrics.txt.zip|Annotation Metrics]]

Metrics Study

2010-06-21T19:59:11Z

Plependu:

= Metrics Files =
* Ontology Metrics [[Image:Ontology_metrics.txt.zip]]
* Annotation Metrics [[Image:Annotation_metrics.txt.zip]]

Metrics Study

2010-06-21T19:58:59Z

Plependu:

= Metrics Files =
* Ontology Metrics [[Image:Ontology_metrics.txt.zip]]
* Annotation Metrics [[File:Annotation_metrics.txt.zip]]

File:Annotation metrics.txt.zip

2010-06-21T19:58:34Z

Plependu: Resource Index metrics summary taken June 10, 2010.

Resource Index metrics summary taken June 10, 2010.

Metrics Study

2010-06-21T19:57:27Z

Plependu:

= Metrics Files =
* Ontology Metrics [[Image:Ontology_metrics.txt.zip]]
* Annotation Metrics [[File:annotation_metrics.txt]]