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apiary.apib
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FORMAT: 1A
HOST: http://kb.phenoscape.org/api/
# Phenoscape Knowledgebase web API
**This is an out-of-date web API description. For the latest, please see http://kb.phenoscape.org/apidocs/ **
The Phenoscape Knowledgebase web API is an HTTP interface for searching ontology terms, retrieving term info, and querying data from the KB.
Most of the services return data in JSON format. Other formats you may encounter inlcude plain text (usually tab-delimited), and NeXML. The available formats for a given service are listed in the Response section of the service detail. As multiple formats may be available for one service, be sure to scroll through to see all supported formats.
When plain-text is available, it is usually the default response, to provide a simple format for service results being directly reviewed.
Set the appropriate media type value in your request's `Accept` header to ensure you receive the desired response format.
# Group Knowledgebase status
## KB annotation summary [/annotation_summary]
### Return summary counts of annotated data matrices, taxa, characters, and states [GET]
+ Response 200 (application/json)
{
"annotated_matrices": 154,
"annotated_taxa": 5071,
"annotated_characters": 9602,
"annotated_states": 21182
}
## KB annotation report [/annotation_report]
### Return table of character state EQ annotations for curator review [GET]
The columns are tab-separated.
+ Response 200 (text/plain)
?matrix_file ?character_number ?character_text ?state_symbol ?state_text ?entity_id ?entity_name ?quality_id ?quality_name ?related_entity_id ?related_entity_name ?attributes
"Bowne, P. S. (1994)" "7" "Interorbital commissure" "1" "medially opening pore" "http://data.bioontology.org/provisional_classes/3a694e40-e12b-0132-ac85-005056010074" "" "http://purl.obolibrary.org/obo/PATO_0000025" "composition" "http://purl.obolibrary.org/obo/UBERON_0008915" "pore" "composition, structure"
"McLennan, D. A., & Mattern, M. Y. (2001)" "12" "Interorbital commisure" "1" "medially opening pore" "http://data.bioontology.org/provisional_classes/3a694e40-e12b-0132-ac85-005056010074" "" "http://purl.obolibrary.org/obo/PATO_0000025" "composition" "http://purl.obolibrary.org/obo/UBERON_0008915" "pore" "composition, structure"
# Group Terms
## Term detail [/term{?iri}]
### Return detail info for a given term. Currently this is the label and an optional definition [GET]
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/UBERON_0011618`) ... the term IRI
+ Response 200 (application/json)
## Term search [/term/search{?text,type,property}]
### Search for terms in the KB by text match on a property value. [GET]
Specifying the property is optional; `rdfs:label` is searched by default.
The `matchType` value in the return format can be any of `exact` (case insensitive), `partial`, or `broad`.
+ Parameters
+ text (required, string, `basihyal`) ... the input text to search
+ type (optional, URI, `http://www.w3.org/2002/07/owl#Class`) ... the type of term to search for
+ property (optional, URI, `http://www.w3.org/2000/01/rdf-schema#label`)
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/UBERON_3000957",
"label": "basihyal",
"matchType": "exact"
}, {
"@id": "http://purl.obolibrary.org/obo/XAO_0004358",
"label": "basihyal",
"matchType": "exact"
}, {
"@id": "http://purl.obolibrary.org/obo/UBERON_0011618",
"label": "basihyal bone",
"matchType": "partial"
}, {
"@id": "http://purl.obolibrary.org/obo/ZFA_0000316",
"label": "basihyal bone",
"matchType": "partial"
}, {
"@id": "http://purl.obolibrary.org/obo/UBERON_0011615",
"label": "basihyal cartilage",
"matchType": "partial"
}, {
"@id": "http://purl.obolibrary.org/obo/ZFA_0001510",
"label": "basihyal cartilage",
"matchType": "partial"
}
]
}
## Ontology class search [/term/search_classes{?text,definedBy,limit}]
### Search for classes from a particular ontology [GET]
+ Parameters
+ text (required, string, `basihyal`) ... the input text to search
+ definedBy (URI, `http://purl.obolibrary.org/obo/uberon.owl`) ... the ontology identifier IRI in which the search terms are defined
+ limit (optional, integer, `10`)
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/UBERON_3000957",
"label": "basihyal",
"matchType": "exact"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011618",
"label": "basihyal bone",
"matchType": "partial"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011615",
"label": "basihyal cartilage",
"matchType": "partial"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011614",
"label": "basihyal element",
"matchType": "partial"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011620",
"label": "basihyal lingual process",
"matchType": "partial"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_2001649",
"label": "basihyal tooth",
"matchType": "partial"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_2001648",
"label": "basihyal tooth plate",
"matchType": "partial"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0003999",
"label": "hyoid bone body",
"matchType": "broad"
}
]
}
## Term label [/term/label{?iri}]
### Retrieve a label for a given term IRI [GET]
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/UBERON_0011618`) ... the term IRI
+ Response 200 (application/json)
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011618",
"label": "basihyal bone"
}
## Term labels [/term/labels{?iris}]
### Retrieve a label for each term IRI in a list [GET]
+ Parameters
+ iris (required, URI, `http://purl.obolibrary.org/obo/UBERON_0011618,http://purl.obolibrary.org/obo/UBERON_0011615`) ... comma-separated list of term IRIs (no spaces)
+ Response 200 (application/json)
{
"results": [{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011615",
"label": "basihyal cartilage"
}, {
"@id": "http://purl.obolibrary.org/obo/UBERON_0011618",
"label": "basihyal bone"
}]
}
## Classification [/term/classification{?iri}]
### Return direct superclasses, direct subclasses, and equivalent classes of a given term [GET]
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/UBERON_0011618`) ... the term IRI
+ Response 200 (application/json)
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011618",
"label": "basihyal bone",
"subClassOf": [{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011614",
"label": "basihyal element"
}, {
"@id": "http://purl.obolibrary.org/obo/UBERON_0002513",
"label": "endochondral bone"
}],
"equivalentTo": [],
"superClassOf": [{
"@id": "http://purl.obolibrary.org/obo/ZFA_0000316",
"label": "basihyal bone"
}]
}
## Ancestors [/term/all_ancestors{?iri}]
### Return all ancestor superclasses of a given term [GET]
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/UBERON_0011618`) ... the term IRI
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/BFO_0000040",
"label": "material entity"
},
{
"@id": "http://purl.obolibrary.org/obo/BFO_0000040",
"label": "material entity"
},
{
"@id": "http://purl.obolibrary.org/obo/CARO_0000003",
"label": "anatomical structure"
},
{
"@id": "http://purl.obolibrary.org/obo/CARO_0000003",
"label": "anatomical structure"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0001474",
"label": "bone element"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0000061",
"label": "anatomical structure"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0000062",
"label": "organ"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0000465",
"label": "material anatomical entity"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0004119",
"label": "endoderm-derived structure"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0004765",
"label": "skeletal element"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0010000",
"label": "multicellular anatomical structure"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0010314",
"label": "structure with developmental contribution from neural crest"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0001062",
"label": "anatomical entity"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0010363",
"label": "endochondral element"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0002513",
"label": "endochondral bone"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0011614",
"label": "basihyal element"
},
{
"@id": "http://purl.obolibrary.org/obo/CARO_0000000",
"label": "anatomical entity"
},
{
"@id": "http://purl.obolibrary.org/obo/CARO_0000006",
"label": "material anatomical entity"
},
{
"@id": "http://purl.obolibrary.org/obo/CARO_0000006",
"label": "material anatomical entity"
},
{
"@id": "http://purl.obolibrary.org/obo/CARO_0010000",
"label": "multicellular anatomical structure"
},
{
"@id": "http://purl.obolibrary.org/obo/BFO_0000002",
"label": "continuant"
},
{
"@id": "http://purl.obolibrary.org/obo/BFO_0000004",
"label": "independent continuant"
}
]
}
## Descendants [/term/all_descendants{?iri}]
### Return all descendant subclasses of a given term [GET]
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/UBERON_0011618`) ... the term IRI
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/ZFA_0000316",
"label": "basihyal bone"
}
]
}
## Least common subsumers [/term/least_common_subsumers{?iris,definedBy}]
### Return the set of least common subsumers for a set of terms [GET]
For any set of input terms, there may be more than one least common subsumer. This is because the Phenoscape KB class hierarchy is not a strict tree, but more generally a directed acyclic graph with multiple axes of classification.
+ Parameters
+ iris (required, URI, `http://purl.obolibrary.org/obo/UBERON_4200115,http://purl.obolibrary.org/obo/UBERON_4000160`) ... comma-separated list of term IRIs (no spaces)
+ definedBy (optional, URI, `http://purl.obolibrary.org/obo/uberon.owl`) ... limit the returned subsumers to those defined by this ontology
+ Response 200 (application/json)
{
"results": [{
"@id": "http://purl.obolibrary.org/obo/UBERON_0007829"
}, {
"@id": "http://purl.obolibrary.org/obo/UBERON_0008907"
}]
}
## Property neighbors for object [/term/property_neighbors/object{?term,property}]
### Return subjects of existential relations to the given object [GET]
For a subject `S` with an existential 'part_of' relation to the object `O`, it means that
`S` SubClassOf `part_of` some `O`. The only currently supported property is `http://purl.obolibrary.org/obo/BFO_0000050` (part_of).
+ Parameters
+ term (required, URI, `http://purl.obolibrary.org/obo/UBERON_0001442`) ... IRI of focal term
+ property (required, URI, `http://purl.obolibrary.org/obo/BFO_0000050`) ... IRI of property
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0005897",
"label": "manus bone"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0009880",
"label": "carpal skeleton"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0012151",
"label": "skeleton of manual digitopodium"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_4200179",
"label": "manual claw"
}
]
}
## Property neighbors for subject [/term/property_neighbors/subject{?term,property}]
### Return objects of existential relations to the given subject [GET]
For a subject `S` with an existential 'part_of' relation to the object `O`, it means that
`S` SubClassOf `part_of` some `O`. The only currently supported property is `http://purl.obolibrary.org/obo/BFO_0000050` (part_of).
+ Parameters
+ term (required, URI, `http://purl.obolibrary.org/obo/UBERON_0001442`) ... IRI of focal term
+ property (required, URI, `http://purl.obolibrary.org/obo/BFO_0000050`) ... IRI of property
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0001440",
"label": "forelimb skeleton"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0002398",
"label": "manus"
},
{
"@id": "http://purl.obolibrary.org/obo/UBERON_0006717",
"label": "autopodial skeleton"
}
]
}
# Group OntoTrace
## OntoTrace [/ontotrace{?taxon,entity,variable_only}]
### Generate matrix of inferred presence/absence associations for anatomical structures subsumed by the provided entity class expression, for any taxa within the provided taxon class expression [GET]
Returns a NeXML-format evolutionary character matrix.
+ Parameters
+ taxon (required, string, `<http://purl.obolibrary.org/obo/VTO_0036217>`) ... Taxonomic class expression in [OWL Manchester syntax](http://www.w3.org/TR/owl2-manchester-syntax/)
+ entity (required, string `<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/UBERON_0008897>`) ... Anatomical class expression in [OWL Manchester syntax](http://www.w3.org/TR/owl2-manchester-syntax/)
+ variable_only (optional, boolean, `true`) ... whether to restrict the matrix to characters with both 'present' and 'absent' values in the matrix
+ Response 200 (application/xml)
<?xml version="1.0" encoding="UTF-8"?>
<nexml xmlns="http://www.nexml.org/2009" xmlns:dc="http://purl.org/dc/terms/" xmlns:dwc="http://rs.tdwg.org/dwc/terms/" xmlns:obo="http://purl.obolibrary.org/obo/" xmlns:ps="http://vocab.phenoscape.org/" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="0.9" xsi:schemaLocation="http://www.nexml.org/2009 http://www.nexml.org/2009/nexml.xsd http://www.bioontologies.org/obd/schema/pheno http://purl.org/phenoscape/phenoxml.xsd">
<meta xsi:type="LiteralMeta" property="dc:creator" />
<meta xsi:type="LiteralMeta" property="dc:description">Generated from the Phenoscape Knowledgebase on 2015-10-20 by Ontotrace query:
* taxa: <http://purl.obolibrary.org/obo/VTO_0036217>
* entities: <http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/UBERON_0008897></meta>
<otus id="ta2272552-0b69-46ce-ac61-c653f7fb8e73">
<otu id="VTO_0036225" label="Ictalurus punctatus" about="#VTO_0036225">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0036225" />
</otu>
<otu id="VTO_0061498" label="Ictalurus mexicanus" about="#VTO_0061498">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0061498" />
</otu>
<otu id="VTO_0061495" label="Ictalurus australis" about="#VTO_0061495">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0061495" />
</otu>
<otu id="VTO_0036221" label="Ictalurus balsanus" about="#VTO_0036221">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0036221" />
</otu>
<otu id="VTO_0036218" label="Ictalurus pricei" about="#VTO_0036218">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0036218" />
</otu>
<otu id="VTO_0036223" label="Ictalurus furcatus" about="#VTO_0036223">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0036223" />
</otu>
<otu id="VTO_0036220" label="Ictalurus lupus" about="#VTO_0036220">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0036220" />
</otu>
<otu id="VTO_0061497" label="Ictalurus dugesii" about="#VTO_0061497">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0061497" />
</otu>
<otu id="VTO_0061496" label="Ictalurus sp. (Mo 1991)" about="#VTO_0061496">
<meta xsi:type="ResourceMeta" rel="dwc:taxonID" href="http://purl.obolibrary.org/obo/VTO_0061496" />
</otu>
</otus>
<characters id="cf52803f-e302-4ae7-9242-4d8c8daf7bde" xsi:type="StandardCells" otus="ta2272552-0b69-46ce-ac61-c653f7fb8e73">
<format>
<states id="s62693495-2c47-4a2d-ae7c-10e1b033cc99">
<state id="UBERON_2002002_1" label="present" symbol="1" />
<state id="UBERON_2002002_0" label="absent" symbol="0" />
<polymorphic_state_set id="sb2f789a5-1727-4db4-a8bf-b7260742575d" symbol="1 and 0">
<member state="UBERON_2002002_1" />
<member state="UBERON_2002002_0" />
</polymorphic_state_set>
</states>
<states id="s8ddf6f6e-b946-456f-9906-0dc41966f1c4">
<state id="UBERON_2001788_1" label="present" symbol="1" />
<state id="UBERON_2001788_0" label="absent" symbol="0" />
<polymorphic_state_set id="s70c8320f-d62a-47a4-b7ca-4ad7455fd2b0" symbol="1 and 0">
<member state="UBERON_2001788_1" />
<member state="UBERON_2001788_0" />
</polymorphic_state_set>
</states>
<states id="s80e10fab-6506-4b72-892b-8e4ac261eb4a">
<state id="UBERON_2002001_1" label="present" symbol="1" />
<state id="UBERON_2002001_0" label="absent" symbol="0" />
</states>
<char id="UBERON_2002002" label="anterior distal serration of pectoral fin spine" about="#UBERON_2002002" states="s62693495-2c47-4a2d-ae7c-10e1b033cc99">
<meta xsi:type="ResourceMeta" rel="obo:IAO_0000219" href="http://purl.obolibrary.org/obo/UBERON_2002002" />
</char>
<char id="UBERON_2001788" label="pelvic splint" about="#UBERON_2001788" states="s8ddf6f6e-b946-456f-9906-0dc41966f1c4">
<meta xsi:type="ResourceMeta" rel="obo:IAO_0000219" href="http://purl.obolibrary.org/obo/UBERON_2001788" />
</char>
<char id="UBERON_2002001" label="anterior dentation of pectoral fin spine" about="#UBERON_2002001" states="s80e10fab-6506-4b72-892b-8e4ac261eb4a">
<meta xsi:type="ResourceMeta" rel="obo:IAO_0000219" href="http://purl.obolibrary.org/obo/UBERON_2002001" />
</char>
</format>
<matrix>
<row id="re5c991ac-0568-4d62-82e1-e54a3a88c296" otu="VTO_0036225">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="s70c8320f-d62a-47a4-b7ca-4ad7455fd2b0" />
<cell char="UBERON_2002001" state="UBERON_2002001_1" />
</row>
<row id="re98d83f4-cc23-4014-a011-6b28e7fa876d" otu="VTO_0061498">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
</row>
<row id="r3b75c894-6efc-46d7-96ae-bdc327f00c7b" otu="VTO_0061495">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
<cell char="UBERON_2002001" state="UBERON_2002001_1" />
</row>
<row id="r13b318e3-309d-4e6b-9306-68e1ed765cc6" otu="VTO_0036221">
<cell char="UBERON_2002002" state="sb2f789a5-1727-4db4-a8bf-b7260742575d" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
<cell char="UBERON_2002001" state="UBERON_2002001_0" />
</row>
<row id="rc80b1386-ea71-4f28-a26f-a442bb75ae6d" otu="VTO_0036218">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
<cell char="UBERON_2002001" state="UBERON_2002001_1" />
</row>
<row id="rb855c9cc-8594-41f3-bb1e-f85ca1b5ce94" otu="VTO_0036223">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
<cell char="UBERON_2002001" state="UBERON_2002001_0" />
</row>
<row id="redbdfca0-ca69-4710-a887-b9429c3faf67" otu="VTO_0036220">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
<cell char="UBERON_2002001" state="UBERON_2002001_1" />
</row>
<row id="r4378658a-901f-464f-9320-c9375ead4638" otu="VTO_0061497">
<cell char="UBERON_2002002" state="UBERON_2002002_1" />
<cell char="UBERON_2001788" state="UBERON_2001788_1" />
</row>
<row id="r0034d445-b7ec-4246-af54-68a90afc718d" otu="VTO_0061496">
<cell char="UBERON_2001788" state="UBERON_2001788_0" />
</row>
</matrix>
</characters>
<trees id="td2cf438a-4bef-49b0-93cf-7a0a97660a58" otus="ta2272552-0b69-46ce-ac61-c653f7fb8e73" />
</nexml>
# Group Semantic Similarity
## Semantic similarity query [/similarity/query{?iri,limit,offset}]
### Retrieve taxon variation profile similarity scores for this gene, ordered with best matches first [GET]
+ Parameters
+ iri (required, URI, `http://www.informatics.jax.org/marker/MGI:1202401`) ... Gene IRI
+ limit (optional, integer `20`)
+ offset (optional, integer, `0`)
+ Response 200 (text/plain)
taxon IRI taxon label median score expect score
http://purl.obolibrary.org/obo/VTO_0037378 Gymnotiformes 0.7506756923676524 0.0014462288121
http://purl.obolibrary.org/obo/VTO_0037490 Eigenmannia 0.6217930498438566 0.00352135614022
+ Response 200 (application/json)
{
"results": [{
"match_profile": {
"@id": "http://purl.obolibrary.org/obo/VTO_0037378",
"label": "Gymnotiformes"
},
"median_score": 0.7506756923676524,
"expect_score": 0.0014462288121
}, {
"match_profile": {
"@id": "http://purl.obolibrary.org/obo/VTO_0037490",
"label": "Eigenmannia"
},
"median_score": 0.6217930498438566,
"expect_score": 0.00352135614022
}]
}
## Best annotation matches for comparison [/similarity/best_matches{?query_iri,corpus_iri}]
### Retrieve the top matching phenotype annotations, with their most informative common subsumer, for a given pair of profiles, e.g. a gene and a taxon [GET]
+ Parameters
+ query_iri (required, URI, `http://www.informatics.jax.org/marker/MGI:1202401`) ... IRI for query profile
+ `corpus_iri` (required, URI, `http://purl.obolibrary.org/obo/VTO_0037378`) ... IRI for matched profile in corpus
+ Response 200 (application/json)
{
"results": [{
"query_annotation": {
"@id": "http://purl.obolibrary.org/obo/MP_0009038",
"label": "decreased inferior colliculus size"
},
"corpus_annotation": {
"@id": "http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000140%3E+and+%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000052%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_2002106%3E%29+and+%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2Fpato%23towards%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0001945%3E%29#ca1edf06-51cb-40f5-8858-0b266e906ca2",
"label": "position and (inheres in some eminentia granularis) and (towards some superior colliculus)"
},
"best_subsumer": {
"term": {
"@id": "http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051%3E+some+%28%3Chttp%3A%2F%2Fpurl.org%2Fphenoscape%2Fvocab.owl%23phenotype_of%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0002950%3E%29",
"label": "has part some (phenotype of some regional part of midbrain)"
},
"ic": 0.8926218653448688,
"disparity": 0.47824477007017246
}
}]
}
## Best subsumers for comparison [/similarity/best_subsumers{?query_iri,corpus_iri}]
### Retrieve only the most informative subsumers for the top matching phenotype annotations for a given pair of profiles, e.g. a gene and a taxon [GET]
+ Parameters
+ query_iri (required, URI, `http://www.informatics.jax.org/marker/MGI:1202401`) ... IRI for query profile
+ `corpus_iri` (required, URI, `http://purl.obolibrary.org/obo/VTO_0037378`) ... IRI for matched profile in corpus
+ Response 200 (application/json)
{
"results": [{
"term": {
"@id": "http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051%3E+some+%28%3Chttp%3A%2F%2Fpurl.org%2Fphenoscape%2Fvocab.owl%23phenotype_of%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0002950%3E%29",
"label": "has part some (phenotype of some regional part of midbrain)"
},
"ic": 0.8926218653448688
}, {
"term": {
"@id": "http://purl.org/phenoscape/expression?value=%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000051%3E+some+%28%3Chttp%3A%2F%2Fpurl.org%2Fphenoscape%2Fvocab.owl%23phenotype_of%3E+some+%28%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FBFO_0000050%3E+some+%3Chttp%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0003528%3E%29%29",
"label": "has part some (phenotype of some (part of some brain grey matter))"
},
"ic": 0.7506756923676524
}]
}
## Subsumed annotations [/similarity/subsumed_annotations{?subsumer,instance}]
### Retrieve all annotations for a given profile which are subsumed by a phenotype class [GET]
+ Parameters
+ subsumer (required, URI, `http://purl.obolibrary.org/obo/MP_0001265`) ... IRI for query profile
+ instance (required, URI, `http://www.informatics.jax.org/marker/MGI:1202401`) ... IRI for matched profile in corpus
+ Response 200 (application/json)
{
"results": [{
"@id": "http://purl.obolibrary.org/obo/MP_0009038",
"label": "decreased inferior colliculus size"
}]
}
## Profile size [/similarity/profile_size{?iri}]
### Retrieve number of phenotype annotations for a given profile, e.g. gene or taxon [GET]
+ Parameters
+ iri (required, URI, `http://www.informatics.jax.org/marker/MGI:1202401`) ... IRI for profile
+ Response 200 (application/json)
{
"total": 5
}
## Corpus size [/similarity/corpus_size]
### Retrieve number of instances in the similarity search corpus (currently, taxon nodes) [GET]
+ Response 200 (application/json)
{
"total": 659
}
## IC disparity [/similarity/ic_disparity{?iri}]
### Query information content disparity for a phenotype class between taxon and gene corpora [GET]
The disparity for a class is the taxon-based IC minus the gene-based IC.
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/PATO_0000052`) ... IRI for phenotype class
+ Response 200 (application/json)
{
"value": -0.19564677483705345
}
# Group Taxa
## Taxon info [/taxon{?iri}]
### Return detail info for a given taxon. [GET]
Currently this is the label, extinction status, and an optional rank.
+ Parameters
+ iri (required, URI, `http://purl.obolibrary.org/obo/VTO_9020379`) ... the taxon IRI
+ Response 200 (application/json)
{
"@id": "http://purl.obolibrary.org/obo/VTO_9020379",
"label": "Diplocaulus",
"extinct": true,
"rank": {
"@id": "http://purl.obolibrary.org/obo/TAXRANK_0000005",
"label": "genus"
}
}
## Taxa with rank [/taxon/with_rank{?rank,in_taxon}]
### Retrieve all taxa with a given taxonomic rank, within the given super-taxon. [GET]
Ranks are terms from the taxonomic rank ontology such as [order](http://purl.obolibrary.org/obo/TAXRANK_0000003), [family](http://purl.obolibrary.org/obo/TAXRANK_0000004), [genus](http://purl.obolibrary.org/obo/TAXRANK_0000005), [species](http://purl.obolibrary.org/obo/TAXRANK_0000006).
+ Parameters
+ rank (required, URI, `http://purl.obolibrary.org/obo/TAXRANK_0000003`) ... taxonomic rank IRI
+ `in_taxon` (required, URI, `http://purl.obolibrary.org/obo/VTO_0033666`) ... taxonomic group within which to search
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/VTO_0041714",
"label": "Polymixiiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0041730",
"label": "Stephanoberyciformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0041825",
"label": "Dactylopteriformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0041834",
"label": "Tetraodontiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0079702",
"label": "Cetomimiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0042306",
"label": "Perciformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0070136",
"label": "Gobiesociformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0052503",
"label": "Scorpaeniformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0053586",
"label": "Synbranchiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0053669",
"label": "Syngnathiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0053907",
"label": "Gasterosteiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0053945",
"label": "Mugiliformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0054071",
"label": "Cyprinodontiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0071639",
"label": "Elassomatiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0055028",
"label": "Beloniformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0055262",
"label": "Atheriniformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0055603",
"label": "Pleuronectiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0056166",
"label": "Beryciformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0056319",
"label": "Zeiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0056375",
"label": "Lophiiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0056592",
"label": "Gadiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0056946",
"label": "Percopsiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0056976",
"label": "Batrachoidiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0057041",
"label": "Ophidiiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0057204",
"label": "Lampriformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0057251",
"label": "Myctophiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0057490",
"label": "Aulopiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0057725",
"label": "Ateleopodiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0057738",
"label": "Stomiiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0058011",
"label": "Esociformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0058036",
"label": "Salmoniformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0058256",
"label": "Osmeriformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0066344",
"label": "Ellimmichthyiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9029595",
"label": "Lampridiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9031428",
"label": "Alepisauriformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9027864",
"label": "Tselfatiiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9031963",
"label": "Crossognathiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9030589",
"label": "Ionoscopiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9031087",
"label": "Ctenothrissiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9032978",
"label": "Pachycormiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_9010506",
"label": "Incertae"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0033668",
"label": "Osteoglossiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0066731",
"label": "Hiodontiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0033927",
"label": "Elopiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0033946",
"label": "Notacanthiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0033969",
"label": "Albuliformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0034001",
"label": "Anguilliformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0034544",
"label": "Clupeiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0067542",
"label": "Saccopharyngiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0034955",
"label": "Gonorynchiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0034991",
"label": "Siluriformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0037378",
"label": "Gymnotiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0037519",
"label": "Characiformes"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0038678",
"label": "Cypriniformes"
}
]
}
## Taxa with phenotype [/taxon/with_phenotype{?entity,quality,in_taxon,parts,limit,offset,total}]
### Retrieve taxa with annotated phenotypes related to the given anatomical entity or quality. [GET]
+ Parameters
+ entity (optional, string `<http://purl.obolibrary.org/obo/BFO_0000050> some <http://purl.obolibrary.org/obo/UBERON_0003097>`) ... Anatomical class expression in [OWL Manchester syntax](http://www.w3.org/TR/owl2-manchester-syntax/)
+ quality (optional, string `<http://purl.obolibrary.org/obo/PATO_0000052>`) ... Quality class expression in [OWL Manchester syntax](http://www.w3.org/TR/owl2-manchester-syntax/)
+ `in_taxon` (optional, URI, `http://purl.obolibrary.org/obo/VTO_0034991`) ... A taxon group to limit the results
+ parts (optional, boolean, `false`) ... whether to include parts of the entity in the query
+ limit (optional, integer `20`)
+ offset (optional, integer, `0`)
+ total (optional, boolean, `false`) ... whether to return the total result count rather than the results
+ Response 200 (application/json)
{
"results": [
{
"@id": "http://purl.obolibrary.org/obo/VTO_0059975",
"label": "Acanthicus hystrix"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0061854",
"label": "Acanthocleithron chapini"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0061312",
"label": "Acrochordonichthys ischnosoma"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0061314",
"label": "Acrochordonichthys pachyderma"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0035553",
"label": "Acrochordonichthys rugosus"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0061318",
"label": "Acrochordonichthys sp. (de Pinna 1993)"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0036705",
"label": "Agamyxis albomaculatus"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0035046",
"label": "Ageneiosus atronasus"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060572",
"label": "Ageneiosus cf. guianensis (Mo 1991)"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0035045",
"label": "Ageneiosus inermis"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060583",
"label": "Ageneiosus magoi"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060581",
"label": "Ageneiosus pardalis"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060575",
"label": "Ageneiosus sp. (de Pinna 1993)"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060571",
"label": "Ageneiosus sp. 1 (Mo 1991)"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060580",
"label": "Ageneiosus sp. 2 (Mo 1991)"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0060570",
"label": "Ageneiosus sp. 3 (Mo 1991)"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0035047",
"label": "Ageneiosus ucayalensis"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0036184",
"label": "Ailia coila"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0061478",
"label": "Ailiichthys punctata"
},
{
"@id": "http://purl.obolibrary.org/obo/VTO_0061303",
"label": "Akysis sp. (Friel 1994)"
}
]
}
+ Response 200 (text/plain)
IRI label
http://purl.obolibrary.org/obo/VTO_0059975 Acanthicus hystrix
http://purl.obolibrary.org/obo/VTO_0061854 Acanthocleithron chapini
http://purl.obolibrary.org/obo/VTO_0061312 Acrochordonichthys ischnosoma
http://purl.obolibrary.org/obo/VTO_0061314 Acrochordonichthys pachyderma
http://purl.obolibrary.org/obo/VTO_0035553 Acrochordonichthys rugosus
http://purl.obolibrary.org/obo/VTO_0061318 Acrochordonichthys sp. (de Pinna 1993)
http://purl.obolibrary.org/obo/VTO_0036705 Agamyxis albomaculatus
http://purl.obolibrary.org/obo/VTO_0035046 Ageneiosus atronasus
http://purl.obolibrary.org/obo/VTO_0060572 Ageneiosus cf. guianensis (Mo 1991)
http://purl.obolibrary.org/obo/VTO_0035045 Ageneiosus inermis
http://purl.obolibrary.org/obo/VTO_0060583 Ageneiosus magoi
http://purl.obolibrary.org/obo/VTO_0060581 Ageneiosus pardalis
http://purl.obolibrary.org/obo/VTO_0060575 Ageneiosus sp. (de Pinna 1993)
http://purl.obolibrary.org/obo/VTO_0060571 Ageneiosus sp. 1 (Mo 1991)
http://purl.obolibrary.org/obo/VTO_0060580 Ageneiosus sp. 2 (Mo 1991)
http://purl.obolibrary.org/obo/VTO_0060570 Ageneiosus sp. 3 (Mo 1991)
http://purl.obolibrary.org/obo/VTO_0035047 Ageneiosus ucayalensis
http://purl.obolibrary.org/obo/VTO_0036184 Ailia coila
http://purl.obolibrary.org/obo/VTO_0061478 Ailiichthys punctata
http://purl.obolibrary.org/obo/VTO_0061303 Akysis sp. (Friel 1994)
## Count of annotated taxa [/taxon/annotated_taxa_count{?in_taxon}]
### Retrieve count of taxa with direct annotations within the given super-taxon [GET]
+ Parameters
+ `in_taxon` (optional, URI, `http://purl.obolibrary.org/obo/VTO_0034991`) ... A taxon group to limit the results