This page details the data services that query the Phenoscape OBD
database and transfer the retrieved results to the Phenoscape UI. Each
service may support multiple media types. The desired media type can be
specified by appending ?media=json or similar to the request URL. URI
specifications are defined (loosely) using URI
Templates.
These are available at the base URI http://fish.phenoscape.org/OBD-WS.
URI
/timestamp
This service returns the date on which the Knowledgebase content was refreshed.
Returns
JSON:
</javascript>
URI
/term/{term_id}
This is a generic term info service returning basic properties and relationships of a term, given its ID. The returned relationships are those included in the source ontology for the term, not all links to the term in the Knowledgebase.
Returns
JSON:
"id": "TAO:0000620",
"definition": "Endochondral bone that is part of the antero-lateral region of the palate.
Commonly, it articulates with the maxilla anterolaterally and with the ethmoidal region medially. It may also articulate with the dermopalatine ventro-laterally and with the entopterygoid posteriorly. The autopalatine is paired.”,
"name": "autopalatine",
"synonyms": [
{
"name": "palatine bone", "scope": "EXACT", "type": {"id":"COMMONNAME"}
}],
"parents": [
{
"relation": {
"id": "OBO_REL:part_of",
"name": "part_of"
},
"target": {
"id": "TAO:0001272",
"name": "palatoquadrate arch"
}
},
{
"relation": {
"id": "develops_from",
"name": "develops from"
},
"target": {
"id": "TAO:0001399",
"name": "palatoquadrate cartilage"
}
},
{
"relation": {
"id": "OBO_REL:is_a",
"name": "is_a"
},
"target": {
"id": "TAO:0001591",
"name": "endochondral bone"
}
},
{
"relation": {
"id": "overlaps",
"name": "overlaps"
},
"target": {
"id": "TAO:0001942",
"name": "autopalatine-maxillary joint"
}
},
{
"relation": {
"id": "overlaps",
"name": "overlaps"
},
"target": {
"id": "TAO:0001784",
"name": "autopalatine-vomer joint"
}
},
{
"relation": {
"id": "overlaps",
"name": "overlaps"
},
"target": {
"id": "TAO:0001608",
"name": "autopalatine-lateral ethmoid joint"
}
}],
"children": [
{
"relation": {
"id": "develops_from",
"name": "develops from"
},
"target": {
"id": "TAO:0002158",
"name": "palatine"
}
},
{
"relation": {
"id": "OBO_REL:part_of",
"name": "part_of"
},
"target": {
"id": "TAO:0001578",
"name": "anterior dorsomedial process of autopalatine"
}
}]
} </javascript>
Error
If there is no term with the given ID, the service should return “404 Not Found”.
URI
/term/{term_id}/path
This returns an array of term info objects from the ontology root to the given term.
Returns
JSON:
"path":[
//sequence of term info objects as returned by the term info service
]
} </javascript>
Error
If there is no term with the given ID, the service should return “404 Not Found”.
URI
/term/taxon/{term_id}
This is a specialized term info service which returns data in a format customized for taxa.
Returns
JSON:
"id": "TTO:101020",
"extinct": false,
"rank": {
"id": "TAXRANK:0000005",
"name": "genus"
},
"name": "Ictalurus",
"species_count": 231,
"common_names":[{"scope":"RELATED","name":"Zebra danio","type":{"id":"COMMONNAME"}}]
"synonyms": [{
"name": "Villarius"
},
{
"name": "Haustor"
},
{
"name": "Elliops"
},
{
"name": "Istlarius"
},
{
"name": "Synechoglanis"
}],
"parent": {
"id": "TTO:10930",
"extinct": false,
"rank": {
"id": "TAXRANK:0000004",
"name": "family"
},
"name": "Ictaluridae"
},
"children": [{
"id": "TTO:10000452",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus sp. (Vigliotta 2008)"
},
{
"id": "TTO:1004548",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus lupus"
},
{
"id": "TTO:1049346",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus mexicanus"
},
{
"id": "TTO:1004550",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus meridionalis"
},
{
"id": "TTO:1005781",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus balsanus"
},
{
"id": "TTO:1045587",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus australis"
},
{
"id": "TTO:1005768",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus pricei"
},
{
"id": "TTO:1039419",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus ochoterenai"
},
{
"id": "TTO:1004547",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus furcatus"
},
{
"id": "TTO:1054206",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus punctatus"
},
{
"id": "TTO:10000228",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus sp. (Mo 1991)"
},
{
"id": "TTO:10000044",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus sp. (Fink and Fink 1981)"
},
{
"id": "TTO:1046960",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Ictalurus dugesii"
}]
} </javascript>
Error
If there is no term with the given ID, the service should return “404 Not Found”.
URI
/term/publication/{term_id}
This is a specialized term info service which returns data in a format customized for publications.
Returns
JSON:
"id": "PSPUB:0000042",
"name": "Lundberg 1982",
"abstract": "The skeletal and soft anatomy of Trogloglanis pattersoni Eigenmann are described and compared to other ictalurids.
Trogloglanis is shown to possess a distinctive mosaic of relatively primitive and highly derived character states. Many of its features are paralleled in rother troglobitic catfishes, some of its features are paedomorphic. Phylogenetic analysis leads to the following
hypothesis of inter-relationships. Pylodictis and Satan are sister groups, Noturus is monophyletic and is the sister group of Prietella,
the subgenus Amiurus of Ictalurus is monophyletic and is the sister group of Noturus + Prietella + Pylodictis + Satan. In turn this large lineage is the sister group of Trogloglanis. The subgenus Ictalurus is monophyletic and is the sister group of all other living ictalurids. Geological and paleontological data suggest that Trogloglanis could not have evolved in situ before middle Eocene, but that its immediate repigean ancestors evolved by middle Oligocene.”,
"citation": "Lundberg, J. G. 1982. The comparative anatomy of the toothless blindcat, Trogloglanis pattersoni Eigenmann, with a phylogenetic analysis of the ictalurid catfishes.",
"source": {
"id": "phenoscape_pub",
"name": "Phenoscape-annotated publications"
},
"doi":"some doi" //may not be present
} </javascript>
Error
If there is no term with the given ID, the service should return “404 Not Found”.
/term/publication/{term_id}/matrix
Returns a data matrix containing all characters and OTUs loaded from a published dataset.
Returns
JSON:
"matrix": {
"2875e05f-9479-4456-91fb-81b8709a7b44": {
"6d6adec7-a220-4629-883c-b65346beba25": {
"label": "absent"
},
"92087cf1-a738-4315-be78-58a0bc28079d": {
"label": "absent"
},
"c34ce73c-fc2e-4919-886a-68200eb19704": {
"label": "passing through these bones"
},
"c306421f-9fcc-4dee-90b1-ea96428cf672": {
"label": "fused with articular"
}},
“dc038812-e6e7-47ed-9656-576cd46f8da5”: {
"6d6adec7-a220-4629-883c-b65346beba25": {
"label": "absent"
},
"92087cf1-a738-4315-be78-58a0bc28079d": {
"label": "present"
},
"c34ce73c-fc2e-4919-886a-68200eb19704": {
"label": "passing through these bones"
},
"8b710077-4b7c-433c-81eb-cc20ce920bfa": {
"label": "present"
},
"c306421f-9fcc-4dee-90b1-ea96428cf672": {
"label": "fused with articular"
}},
“otus”: [{
"id": "2875e05f-9479-4456-91fb-81b8709a7b44",
"label": "Armigatus brevissimus",
"taxon": {
"id": "TTO:10000250",
"extinct": true,
"rank": {
"id": "TAXRANK:0000006",
"label": "species"
},
"label": "Armigatus brevissimus"
}
},
{
"id": "99c913d0-f84c-4340-afac-cd0ad3ba0f0a",
"label": "Clupea harengus",
"taxon": {
"id": "TTO:1001154",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"label": "species"
},
"label": "Clupea harengus"
}
}],
“characters”: [{
"id": "92087cf1-a738-4315-be78-58a0bc28079d",
"num": "1",
"label": "Recessus lateralis"
},
{
"id": "4b6e04bd-affa-47cc-95a2-b314cc17c20d",
"num": "2",
"label": "Otophysic connection involving a diverticulum of the swimbladder that penetraates the exoccipital and extends into the prootic within the lateral wall of the braincase"
},
{
"id": "597b3b2b-10f2-4b4a-a8ce-07bd84b8e261",
"num": "3",
"label": "Preepiotic fossa"
},
{
"id": "b71d0cb7-f67c-4100-9325-6e0450ea21b3",
"num": "4",
"label": "Parietals "
}]
} </javascript>
Error
If there is no publication with the given ID, the service should return “404 Not Found”.
/term/publication/{term_id}/otus
Returns a list of all OTUs in the data matrix for the given publication. For each OTU, the valid taxon TTO identifier and a list of specimens is provided.
Returns
JSON:
"otus": [{
"label": "Glyptothorax sp.",
"specimens": [{
"catalog_number": "288474",
"collection": {
"id": "COLLECTION:0000417",
"name": "USNM"
}
},
{
"catalog_number": "288474",
"collection": {
"id": "COLLECTION:0000417",
"name": "USNM"
}
},
{
"catalog_number": "288474",
"collection": {
"id": "COLLECTION:0000417",
"name": "USNM"
}
}],
"taxon": {
"id": "TTO:10000098",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Glyptothorax sp. (de Pinna 1996)"
}
},
{
"label": "Glyptothorax telchitta",
"specimens": [{
"catalog_number": "208876",
"collection": {
"id": "COLLECTION:0000403",
"name": "UMMZ"
}
},
{
"catalog_number": "208876",
"collection": {
"id": "COLLECTION:0000403",
"name": "UMMZ"
}
}],
"taxon": {
"id": "TTO:1051772",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Glyptothorax telchitta"
}
},
{
"label": "Breitensteinia insignis",
"specimens": [{
"catalog_number": "58378",
"collection": {
"id": "COLLECTION:0000009",
"name": "AMNH"
}
},
{
"catalog_number": "58378",
"collection": {
"id": "COLLECTION:0000009",
"name": "AMNH"
}
},
{
"catalog_number": "58378",
"collection": {
"id": "COLLECTION:0000009",
"name": "AMNH"
}
}],
"taxon": {
"id": "TTO:1005733",
"extinct": false,
"rank": {
"id": "TAXRANK:0000006",
"name": "species"
},
"name": "Breitensteinia insignis"
}
}
]
} </javascript>
Error
If there is no publication with the given ID, the service should return “404 Not Found”.
URI
/term/names
This service accepts a list of term IDs and returns a JSON mapping of
IDs to names. Rank and extinct status are included in the output for
taxon terms. The render_postcompositions key is optional, and can take
the values “none” (the default), “structure”, “semantic_label”, or
“simple_label”.
Accepts via POST
JSON:
Returns
JSON:
URI
/term/search?text=[input]&name=[true|false]&syn=[true|false]&ontology=[ont1,ont2,...]&type=[type1,type2,...]&limit=[count]
All URI parameters are optional except for text. Default values are
name=true, syn=false. The ontology parameter should be a
comma-separated list of ontology prefixes to search within (any of
tao, go, pato, tto, zfin, pspub). The type parameter should be any
of: entity, quality, taxon, gene, pub. If no ontology or type is
given, the default is to search all ontologies. The limit parameter
limits the number of results to the given integer count.
Returns
JSON:
"matches": [{
"match_text": "Brachydanio rerio",
"id": "TTO:1001979",
"match_type": "syn",
"name": "Danio rerio",
"source": "teleost-taxonomy"
},
{
"match_text": "Cyprinus rerio",
"id": "TTO:1001979",
"match_type": "syn",
"name": "Danio rerio",
"source": "teleost-taxonomy"
},
{
"match_text": "Danio rerio",
"id": "TTO:1001979",
"match_type": "name",
"name": "Danio rerio",
"source": "teleost-taxonomy"
}],
"search_term": "rerio"
} </javascript>
Error
If there are no terms matching the given input, a document should still be returned, containing an empty results list.
URI
/term/attributes
This service returns the quality terms which have been marked as “attributes”, commonly used to categorize phenotype data for display.
Returns
JSON:
"attributes": [
{
"id": "PATO:0000150",
"name": "texture"
},
{
"id": "PATO:0000141",
"name": "structure"
},
{
"id": "PATO:0000117",
"name": "size"
},
{
"id": "PATO:0002281",
"name": "Shape+Size"
},
{
"id": "PATO:0000052",
"name": "shape"
},
{
"id": "PATO:0001546",
"name": "quality of a solid"
},
{
"id": "PATO:0000140",
"name": "position"
},
{
"id": "PATO:0002062",
"name": "physical quality of a process"
},
{
"id": "PATO:0000004",
"name": "mobility"
},
{
"id": "PATO:0000125",
"name": "mass"
},
{
"id": "PATO:0000070",
"name": "count"
},
{
"id": "PATO:0000025",
"name": "composition"
},
{
"id": "PATO:0002282",
"name": "Closure+Structure"
},
{
"id": "PATO:0000136",
"name": "closure"
},
{
"id": "PATO:0001396",
"name": "cellular quality"
},
{
"id": "PATO:0000186",
"name": "behavioral quality"
}
]
} </javascript>
URI
/annotation/gene?query=[url-encoded-json]&sortby=[gene|entity|quality|relatedentity]&limit=[count]&index=[start_index]&desc=[true|false]&postcompositions=[none|structure|simple|semantic]
All URI parameters are optional. If no JSON-formatted query
specification is provided, all gene annotations will be returned. The
limit parameter limits the number of results to the given integer
count. This must be a positive integer. The index parameter can be
used for pagination under a given sorting and limit regime. It should be
greater than or equal to zero (the default). desc can be used to
return the results in descending order (it is false by default). If a
value is not provided for sortby, the sort order, limit, and start
index are not very useful. The postcompositions parameter is optional,
and is “none” by default. Rendering postcompositions should only be
requested for a limited number of returned results.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON:
"total": 5478,
"annotations": [
{
"gene": {
"id": "TAO0001514",
"name": "brph1"
},
"entity": {
"id": "TAO0001516",
"name": "basihyal bone"
},
"quality": {
"id": "TAO0001517",
"name": "fused with"
},
"related_entity": {
"id": "TAO0001518",
"name": "posterior ceratohyal"
}
},
{
"gene": {
"id": "TAO0001522",
"name": "brph2"
},
"entity": {
"id": "TAO0001524",
"name": "fossa of basihyal bone"
},
"quality": {
"id": "TAO0001525",
"name": "decreased width"
},
"related_entity": null
}
]
} </javascript>
URI
/annotation/gene/source?query=[url-encoded-json]&postcompositions=[none|structure|simple|semantic]
A JSON-formatted query specification must be provided. It must contain
entries for one annotation, including gene, entity, quality, and
optional related entity. While the gene and phenotype entries are lists,
this is just for consistency with the query format used in other
services - each list should contain only one entry. The
postcompositions parameter is optional, and is “none” by default.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON:
URI
/gene/annotated?query=[url-encoded-json]&sortby=[gene|fullname]&limit=[count]&index=[start_index]&desc=[true|false]
All URI parameters are optional. If no JSON-formatted query
specification is provided, all annotated genes will be returned. The
limit parameter limits the number of results to the given integer
count. This must be a positive integer. The index parameter can be
used for pagination under a given sorting and limit regime. It should be
greater than or equal to zero (the default). desc can be used to
return the results in descending order (it is false by default). If a
value is not provided for sortby, the sort order, limit, and start
index are not very useful.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
URI
/annotation/taxon/distinct?query=[url-encoded-json]&sortby=[taxon|entity|quality|relatedentity]&limit=[count]&index=[start_index]&desc=[true|false]&postcompositions=[none|structure|simple|semantic]
All URI parameters are optional. If no JSON-formatted query
specification is provided, all taxon annotations will be returned. The
limit parameter limits the number of results to the given integer
count. This must be a positive integer. The index parameter can be
used for pagination under a given sorting and limit regime. It should be
greater than or equal to zero (the default). desc can be used to
return the results in descending order (it is false by default). If a
value is not provided for sortby, the sort order, limit, and start
index are not very useful. The postcompositions parameter is optional,
and is “none” by default. Rendering postcompositions should only be
requested for a limited number of returned results.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
"total": 5478,
"annotations": [
{
"taxon": {
"id": "TAO0001514",
"name": "Ictalurus punctatus",
"rank": {
"id": "TAXRANK:00000",
"name": "species"
},
"extinct": false
},
"entity": {
"id": "TAO0001516",
"name": "basihyal bone"
},
"quality": {
"id": "TAO0001517",
"name": "fused with"
},
"related_entity": {
"id": "TAO0001518",
"name": "posterior ceratohyal"
}
},
{
"taxon": {
"id": "TAO0001522",
"name": "Danio rerio",
"rank": {
"id": "TAXRANK:00000",
"name": "species"
},
"extinct": false
},
"entity": {
"id": "TAO0001524",
"name": "fossa of basihyal bone"
},
"quality": {
"id": "TAO0001525",
"name": "decreased width"
},
"related_entity": null
}
]
} </javascript>
URI
/annotation/taxon/source?query=[url-encoded-json]&postcompositions=[none|structure|simple|semantic]
A JSON-formatted query specification must be provided. It must contain
entries for one annotation, including taxon, entity, quality, and
optional related entity. While the taxon and phenotype entries are
lists, this is just for consistency with the query format used in other
services - each list should contain only one entry. The “publication”
list is optional, but may contain multiple publications within which to
constrain the results. The postcompositions parameter is optional, and
is “none” by default.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON:
URI
/taxon/annotated?query=[url-encoded-json]&sortby=[taxon|family|order]&limit=[count]&index=[start_index]&desc=[true|false]
All URI parameters are optional. If no JSON-formatted query
specification is provided, all annotated taxa will be returned. The
limit parameter limits the number of results to the given integer
count. This must be a positive integer. The index parameter can be
used for pagination under a given sorting and limit regime. It should be
greater than or equal to zero (the default). desc can be used to
return the results in descending order (it is false by default). If a
value is not provided for sortby, the sort order, limit, and start
index are not very useful.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
URI
/phenotype?query=[url-encoded-json]&sortby=[entity|quality|related_entity]&limit=[count]&index=[start_index]&desc=[true|false]
All URI parameters are optional. If no JSON-formatted query
specification is provided, all phenotypes will be returned. The limit
parameter limits the number of results to the given integer count. This
must be a positive integer. The index parameter can be used for
pagination under a given sorting and limit regime. It should be greater
than or equal to zero (the default). desc can be used to return the
results in descending order (it is false by default). If a value is not
provided for sortby, the sort order, limit, and start index are not
very useful.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
URI
/publication/annotated?query=[url-encoded-json]&sortby=[publication]&limit=[count]&index=[start_index]&desc=[true|false]
All URI parameters are optional. If no JSON-formatted query
specification is provided, all annotated publications will be returned.
The limit parameter limits the number of results to the given integer
count. This must be a positive integer. The index parameter can be
used for pagination under a given sorting and limit regime. It should be
greater than or equal to zero (the default). desc can be used to
return the results in descending order (it is false by default). If a
value is not provided for sortby, the sort order, limit, and start
index are not very useful.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
URI
/phenotype/facet/{facet}?path=[ids]entity=[entity-id]&quality=[quality-id]&related_entity=[related_entity-id]&taxon=[taxon-id]&gene=[gene-id]&part_of=[true|false]
A facet name of either “entity”, “quality”, “related_entity”, “taxon”, or “gene” must be substituted in the URI path. All URI parameters are optional. It is an error to supply query parameter matching the facet name, i.e. for ‘…/phenotype/facet/entity’, do not provide ‘?entity=xx’. The “path” parameter accepts a comma-separated list of IDs, ordered parent-to-child. The “part_of” parameter affects the entity traversal - the default is “false”.
Returns
JSON
"facet": [{
"count": 13892
},
{
"id": "TAO:0000037",
"count": 8841
},
{
"id": "TAO:0001477",
"count": 3841,
"children": [{
"id": "TAO:0007009",
"count": 51
},
{
"id": "TAO:0000393",
"count": 9
},
{
"id": "TAO:0001082",
"count": 2
},
{
"id": "TAO:0001821",
"count": 4
},
{
"id": "TAO:0002189",
"count": 1
},
{
"id": "TAO:0000190",
"count": 26
},
{
"id": "TAO:0000089",
"count": 11
},
{
"id": "TAO:0001122",
"count": 21
},
{
"id": "TAO:0001641",
"count": 3558
},
{
"id": "TAO:0002205",
"count": 1
},
{
"id": "TAO:0005125",
"count": 6
},
{
"id": "TAO:0002223",
"count": 10
},
{
"id": "TAO:0002215",
"count": 1
},
{
"id": "TAO:0005147",
"count": 13
},
{
"id": "TAO:0005145",
"count": 50
},
{
"id": "TAO:0002193",
"count": 1
},
{
"id": "TAO:0001486",
"count": 33
},
{
"id": "TAO:0000135",
"count": 43
}]
}]
} </javascript>
URI
/phenotype/profile?taxon=[taxonID]&query=[url-encoded-json]
The JSON-formatted query specification should contain only a list of
phenotypes, and a value for the include_inferred option. The taxon
parameter is optional. If included, the results will contain profile
match counts for each of the taxon’s children. If not provided, the
service will return data the highest taxon which has children with
different match counts (useful for starting the tree display).
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
"matches": [{
"taxon_id": "TTO:10000304",
"greatest_profile_match": 1
},
{
"taxon_id": "TTO:10000293",
"greatest_profile_match": 1
},
{
"taxon_id": "TTO:251",
"greatest_profile_match": 2
},
{
"taxon_id": "TTO:10000352",
"greatest_profile_match": 1
},
{
"taxon_id": "TTO:10000326",
"greatest_profile_match": 1
},
{
"taxon_id": "TTO:10000316",
"greatest_profile_match": 1
},
{
"taxon_id": "TTO:254",
"greatest_profile_match": 2
},
{
"taxon_id": "TTO:10000357",
"greatest_profile_match": 1
},
{
"taxon_id": "TTO:253",
"greatest_profile_match": 2
},
{
"taxon_id": "TTO:252",
"greatest_profile_match": 2
}]
} </javascript>
URI
/phenotype/variationsets?taxon=[taxonID]&exclude_unannotated=[true|false]&exclude_attribute=[true|false]&query=[url-encoded-json]
The JSON-formatted query specification should contain only a single
phenotype. The taxon parameter is optional. If included, the results
will contain variation sets for the taxon’s children. If not provided,
the service will return data for the highest taxon which has children in
more than one variation set (useful for starting the tree display). If
exclude_unannotated is true, no child taxa without annotations to the
given phenotype will be returned. If exclude_attribute is true,
annotations to the queried attribute (and no more specific quality) will
not be returned.
Alternative usage: if the taxon parameter has the value “suggest”,
a list of taxa are returned which represent suggested starting points
for browsing the taxonomic tree using this service.
Phenotype query specification
The value of the query parameter should be an annotation query
represented as JSON, following this structure (in practice it should be
collapsed as far as possible to shorten the URL):
It should be URL-encoded to include in the request.
Returns
JSON
"parent_taxon" : "TTO:1234",
"phenotype_sets": [{
"phenotypes": [{
"entity": {
"id": "TAO:0001058",
"name": "caudal fin"
},
"quality": {
"id": "PATO:0001784",
"name": "bifurcated"
}
}],
"taxa": ["TTO:11020", "TTO:103997", "TTO:109064", "TTO:10980", "TTO:10940", "TTO:107212", "TTO:11085", "TTO:11160", "TTO:10960", "TTO:102898", "TTO:10920", "TTO:101648", "TTO:102441", "TTO:101629", "TTO:10990", "TTO:11010", "TTO:11080", "TTO:11130", "TTO:107449", "TTO:10000017", "TTO:11110", "TTO:109385", "TTO:11180", "TTO:10000012", "TTO:10950", "TTO:10970", "TTO:10000015", "TTO:101263", "TTO:10000014"]
},
{
"phenotypes": [{
"entity": {
"id": "TAO:0001058",
"name": "caudal fin"
},
"quality": {
"id": "PATO:0001877",
"name": "lanceolate"
}
},
{
"entity": {
"id": "TAO:0001058",
"name": "caudal fin"
},
"quality": {
"id": "PATO:0000936",
"name": "truncated"
}
},
{
"entity": {
"id": "TAO:0001058",
"name": "caudal fin"
},
"quality": {
"id": "PATO:0000411",
"name": "round"
}
}],
"taxa": ["TTO:11050", "TTO:11090", "TTO:11040", "TTO:11190", "TTO:11181", "TTO:11030"]
}]
} </javascript>
or
JSON