Data Services
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.
Phenoscape Knowledgebase data services (under development)
These are currently only available at http://kb-dev.phenoscape.org/OBD-WS/
Timestamp
URI
<BASE URI>/timestamp
This service returns the date on which the Knowledgebase content was refreshed.
Returns
JSON: <javascript> { "refresh_date":"2010-01-09" }
</javascript>
Term info
URI
<BASE 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: <javascript> {
"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".
Path to root term info
URI
<BASE URI>/term/{term_id}/path
This returns an array of term info objects from the ontology root to the given term.
Returns
JSON: <javascript> {
"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".
Taxon term info
URI
<BASE URI>/term/taxon/{term_id}
This is a specialized term info service which returns data in a format customized for taxa.
Returns
JSON: <javascript> {
"id": "TTO:101020",
"extinct": false,
"rank": {
"id": "TAXRANK:0000005",
"name": "genus"
},
"name": "Ictalurus",
"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".
Bulk term name mapper
URI
<BASE 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: <javascript> { "ids":["TAO:0000620", "TTO:1380", "TTO:11021", "ZFIN:ZDB-GENE-061116-1"], "render_postcompositions": "none" } </javascript>
Returns
JSON: <javascript> {"terms":[ {"id":"TAO:0000620","name":"autopalatine"}, {"id":"TTO:1380","extinct":false,"rank":{"id":"TAXRANK:0000003","name":"order"},"name":"Siluriformes"}, {"id":"TTO:11021","extinct":false,"rank":{"id":"TAXRANK:0000004","name":"family"},"name":"Erethistidae"}, {"id":"ZFIN:ZDB-GENE-061116-1","name":"foxe1"}]} </javascript>
Autocomplete
URI
<BASE 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: <javascript> {
"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.
Gene annotations
URI
<BASE 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):
<javascript> {
"gene": [
{
"id": "ZFIN:XXXX"
},
{
"id": "ZFIN:YYYY"
}
],
"phenotype": [
{
"entity": {
"id": "TAO:XXXX",
"including_parts": false
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
],
"include_inferred": false
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON: <javascript> {
"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>
Gene annotation sources
URI
<BASE 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):
<javascript> {
"gene": [
{
"id": "ZFIN:XXXX"
}
],
"phenotype": [
{
"entity": {
"id": "TAO:XXXX"
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
]
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON: <javascript> {"annotations":[ {"gene":{"id":"ZFIN:ZDB-GENE-040426-731","name":"brpf1"}, "entity":{"id":"TAO:0000316","name":"basihyal bone"}, "quality":{"id":"PATO:0000587","name":"decreased size"}, "genotype":{"id":"ZFIN:ZDB-GENO-080925-12","name":"brpf1b943/b943<\/sup>","type":{"id":"SO:0001027","name":"genotype"}}, "publication":{"id":"ZFIN:ZDB-PUB-080515-4","name":"Laue, K., Daujat, S., Crump, J.G., Plaster, N., Roehl, H.H.; Tübingen 2000 Screen Consortium, Kimmel, C.B., Schneider, R., and Hammerschmidt, M.. 2008. The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development 135(11):1935-1946."}}, {"gene":{"id":"ZFIN:ZDB-GENE-040426-731","name":"brpf1"}, "entity":{"id":"TAO:0000316","name":"basihyal bone"}, "quality":{"id":"PATO:0000587","name":"decreased size"}, "genotype":{"id":"ZFIN:ZDB-GENO-080925-13","name":"brpf1t20002/t20002<\/sup>","type":{"id":"SO:0001027","name":"genotype"}}, "publication":{"id":"ZFIN:ZDB-PUB-080515-4","name":"Laue, K., Daujat, S., Crump, J.G., Plaster, N., Roehl, H.H.; Tübingen 2000 Screen Consortium, Kimmel, C.B., Schneider, R., and Hammerschmidt, M.. 2008. The multidomain protein Brpf1 binds histones and is required for Hox gene expression and segmental identity. Development 135(11):1935-1946."}} ]} </javascript>
Genes
URI
<BASE 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):
<javascript> {
"phenotype": [
{
"entity": {
"id": "TAO:XXXX",
"including_parts": false
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
],
"match_all_phenotypes": false
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON <javascript> {"total":1690, "genes":[ {"id":"ZFIN:ZDB-GENE-040426-1995","name":"abce1","fullname":"ATP-binding cassette, sub-family E (OABP), member 1"}, {"id":"ZFIN:ZDB-GENE-070117-775","name":"abf","fullname":"about face"}, {"id":"ZFIN:ZDB-GENE-040909-1","name":"abhd11","fullname":"abhydrolase domain containing 11"}, {"id":"ZFIN:ZDB-GENE-030131-55","name":"acta1b","fullname":"actin, alpha 1b, skeletal muscle"}, {"id":"ZFIN:ZDB-GENE-020419-36","name":"actl6a","fullname":"actin-like 6A"}, {"id":"ZFIN:ZDB-GENE-990415-9","name":"acvr1l","fullname":"activin A receptor, type I like"}, {"id":"ZFIN:ZDB-GENE-021003-1","name":"acvrl1","fullname":"activin A receptor type II-like 1"}]} </javascript>
Taxon annotations
URI
<BASE 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):
<javascript> {
"taxon": [
{
"id": "TTO:XXXX"
},
{
"id": "TTO:YYYY"
}
],
"phenotype": [
{
"entity": {
"id": "TAO:XXXX",
"including_parts": false
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
],
"publication": [
{
"id": "PSPUB:1243"
}
],
"include_inferred": false
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON <javascript> {
"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>
Taxon annotation sources
URI
<BASE 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):
<javascript> {
"taxon": [
{
"id": "TTO:XXXX"
}
],
"phenotype": [
{
"entity": {
"id": "TAO:XXXX"
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
],
"publication": [
{
"id": "PSPUB:1243"
}
]
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON: <javascript> {"annotations":[{"otu":"Silurus glanis", "entity":{"id":"TAO:0000316","name":"basihyal bone"}, "state":{"text":"basihyal absent"}, "quality":{"id":"PATO:0000462","name":"absent"}, "taxon":{"id":"TTO:1005466","extinct":false,"rank":{"id":"TAXRANK:0000006","name":"species"},"name":"Silurus glanis"}, "character":{"text":"Basihyal","character_number":"240"}, "publication":{"id":"PSPUB:0000022","name":"de Pinna 1993"}}]} </javascript>
Taxa
URI
<BASE 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):
<javascript> {
"taxon": [
{
"id": "TTO:XXXX"
},
{
"id": "TTO:YYYY"
}
],
"phenotype": [
{
"entity": {
"id": "TAO:XXXX",
"including_parts": false
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
],
"publication": [
{
"id": "PSPUB:1243"
}
],
"match_all_phenotypes": false,
"match_all_publications": false,
"include_inferred": false
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON <javascript> {"total":2312, "taxa":[ {"id":"TTO:1068687","extinct":false, "rank":{"id":"TAXRANK:0000006","name":"species"}, "order":{"id":"TTO:1360","extinct":false,"name":"Cypriniformes"}, "family":{"id":"TTO:10760","extinct":false,"name":"Cyprinidae"}, "name":"Abbottina binhi"}, {"id":"TTO:1004289","extinct":false, "rank":{"id":"TAXRANK:0000006","name":"species"}, "order":{"id":"TTO:1370","extinct":false,"name":"Characiformes"}, "family":{"id":"TTO:10856","extinct":false,"name":"Anostomidae"}, "name":"Abramites hypselonotus"} ] } </javascript>
Publications
URI
<BASE 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):
<javascript> {
"taxon": [
{
"id": "TTO:XXXX"
},
{
"id": "TTO:YYYY"
}
],
"phenotype": [
{
"entity": {
"id": "TAO:XXXX",
"including_parts": false
},
"quality": {
"id": "PATO:XXXX"
},
"related_entity": {
"id": "TAO:YYYYY"
}
}
],
"match_all_phenotypes": false,
"match_all_taxa": false
} </javascript> It should be URL-encoded to include in the request.
Returns
JSON <javascript> {"total":19, "publications":[ {"id":"PSPUB:0000002","name":"Armbruster 2004"}, {"id":"PSPUB:0000006","name":"Bockmann 1998"}, {"id":"PSPUB:0000009","name":"Bornbusch 1995"}, {"id":"PSPUB:0000011","name":"Britto 2003"}, {"id":"PSPUB:0000018","name":"Chen 1994"}]} </javascript>
