Difference between revisions of "Data Services"

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{{StatusBox|This page documents data services for version 1 of the Phenoscape KB, available as a legacy resource at http://fish.phenoscape.org. The web-services API for the current version of the KB is documented at http://docs.phenoscapekb.apiary.io/.}}
 +
 
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 <code>?media=json</code> or similar to the request URL.  URI specifications are defined (loosely) using [http://bitworking.org/projects/URI-Templates/draft-gregorio-uritemplate-00.html URI Templates].
 
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 <code>?media=json</code> or similar to the request URL.  URI specifications are defined (loosely) using [http://bitworking.org/projects/URI-Templates/draft-gregorio-uritemplate-00.html URI Templates].
  
−
=Phenoscape Knowledgebase data services (under development)=
+
=Phenoscape Knowledgebase data services=
−
These are currently only available at http://kb-dev.phenoscape.org/OBD-WS/
+
These are available at the base URI http://fish.phenoscape.org/OBD-WS.
  
 
==Timestamp==
 
==Timestamp==
Line 321: Line 323:
  
 
If there is no term with the given ID, the service should return "404 Not Found".
 
If there is no term with the given ID, the service should return "404 Not Found".
 +
 +
==Publication term info==
 +
'''URI'''
 +
 +
<BASE URI>/term/publication/{term_id}
 +
 +
This is a specialized term info service which returns data in a format customized for publications.
 +
 +
'''Returns'''
 +
 +
JSON:
 +
<javascript>
 +
{
 +
    "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".
 +
 +
==Publication data matrix==
 +
 +
<BASE URI>/term/publication/{term_id}/matrix
 +
 +
Returns a data matrix containing all characters and OTUs loaded from a published dataset.
 +
 +
'''Returns'''
 +
 +
JSON:
 +
<javascript>
 +
{
 +
    "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".
 +
 +
==Publication OTUs list==
 +
 +
<BASE URI>/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:
 +
<javascript>
 +
{
 +
    "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".
  
 
==Bulk term name mapper==
 
==Bulk term name mapper==
Line 390: Line 632:
  
 
If there are no terms matching the given input, a document should still be returned, containing an empty results list.
 
If there are no terms matching the given input, a document should still be returned, containing an empty results list.
 +
 +
==Attribute qualities==
 +
'''URI'''
 +
 +
<BASE 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:
 +
<javascript>
 +
{
 +
    "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>
  
 
==Gene annotations==
 
==Gene annotations==
Line 770: Line 1,093:
 
     ],
 
     ],
 
     "match_all_phenotypes": false,
 
     "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>
 +
 +
==Phenotypes==
 +
 +
'''URI'''
 +
 +
<BASE 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 <code>limit</code> parameter limits the number of results to the given integer count. This must be a positive integer. The <code>index</code> parameter can be used for pagination under a given sorting and limit regime. It should be greater than or equal to zero (the default). <code>desc</code> can be used to return the results in descending order (it is false by default). If a value is not provided for <code>sortby</code>, the sort order, limit, and start index are not very useful.
 +
 +
'''Phenotype query specification'''
 +
 +
The value of the <code>query</code> 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"
 +
    }
 +
    ],
 +
    "gene_class": [
 +
    {
 +
        "id": "GO:XXXX"
 +
    },
 +
    {
 +
        "id": "GO:YYYY"
 +
    }
 +
    ],
 +
    "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_taxa": false,
 
     "match_all_publications": false,
 
     "match_all_publications": false,
 
     "include_inferred": false
 
     "include_inferred": false
Line 848: Line 1,254:
 
{"id":"PSPUB:0000018","name":"Chen 1994"}]}
 
{"id":"PSPUB:0000018","name":"Chen 1994"}]}
 
</javascript>
 
</javascript>
 +
 +
==Phenotype facet counts==
 +
 +
'''URI'''
 +
 +
<BASE 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
 +
<javascript>
 +
{
 +
    "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>
 +
 +
==Phenotypic profile match service==
 +
 +
'''URI'''
 +
 +
<BASE 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 <code>include_inferred</code> option. The <code>taxon</code> 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 <code>query</code> 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"
 +
        }
 +
    }
 +
    ],
 +
    "include_inferred": false
 +
}
 +
</javascript>
 +
It should be URL-encoded to include in the request.
 +
 +
'''Returns'''
 +
 +
JSON
 +
<javascript>
 +
{
 +
    "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>
 +
 +
==Phenotypic variation sets service==
 +
 +
'''URI'''
 +
 +
<BASE 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 <code>taxon</code> 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 <code>exclude_unannotated</code> is true, no child taxa without annotations to the given phenotype will be returned. If <code>exclude_attribute</code> is true, annotations to the queried attribute (and no more specific quality) will not be returned.
 +
 +
'''Alternative usage:''' if the <code>taxon</code> 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 <code>query</code> 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"
 +
        },
 +
        "quality": {
 +
            "id": "PATO:XXXX"
 +
        },
 +
        "related_entity": {
 +
            "id": "TAO:YYYYY"
 +
        }
 +
    }
 +
    ]
 +
}
 +
</javascript>
 +
It should be URL-encoded to include in the request.
 +
 +
'''Returns'''
 +
 +
JSON
 +
<javascript>
 +
{
 +
    "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
 +
<javascript>
 +
</javascript>
 +
 +
=Other ontology service definitions (for comparison)=
 +
 +
* [http://www.ebi.ac.uk/ontology-lookup/ Ontology Lookup Service (OLS)] at the EBI. <cite>cote2006</cite> According to the website, the OLS can integrate any ontology available in OBO format. OLS is implemented as a web-service. The website has documentation on
 +
**  [http://www.ebi.ac.uk/ontology-lookup/WSDLDocumentation.do web-service API] (representing the WSDL) with [http://www.ebi.ac.uk/ontology-lookup/api/uk/ac/ebi/ook/web/interfaces/QueryImpl.html JavaDoc for the interface contract], and
 +
** [http://www.ebi.ac.uk/ontology-lookup/implementationOverview.do implementation overview] (architecture)
 +
**  OLS also provides 3 ReST-style services, similar to some of the lookups described above.  These queries return a simple key-value XML format.
 +
*** Term info: http://www.ebi.ac.uk/ontology-lookup/ajax.view?q=termmetadata&termid=ID&ontologyname=LABEL
 +
*** Completion list: http://www.ebi.ac.uk/ontology-lookup/ajax.view?q=termautocomplete&termname=NAME&ontologyname=LABEL
 +
***  Term name for ID: http://www.ebi.ac.uk/ontology-lookup/ajax.view?q=termname&termid=ID&ontologyname=LABEL
 +
* The NCBO [http://www.bioontology.org/ncbo/faces/index.xhtml BioPortal] supports a [http://www.bioontology.org/docs/bioportal/development/web_services.html SOAP-based web-service API]:
 +
** WSDL: http://www.bioontology.org/ncboservicebeans/NCBOWebserviceBean?wsdl
 +
** Java JUnit test: [http://smi-protege.stanford.edu/repos/cbio/ncbo/trunk/test/webservice/NCBOServiceTest.java test.webservice.NCBOServiceTest]
 +
* The [http://zthes.z3950.org/srw/zthes-srw-1.0.html Zthes profile for SRU] is a specification for navigating and querying remote thesauri
 +
** [http://www.loc.gov/sru/ SRU] is a Library of Congress-sponsored standard for query interoperability between digital repositories
 +
** The Zthes profile for SRU is based on an [http://zthes.z3950.org/model/zthes-model-1.0.html abstract model for thesaurus representation], which is also available as an XML Schema implementation.
  
 
[[Category:Informatics]]
 
[[Category:Informatics]]
 
[[Category:API]]
 
[[Category:API]]

Latest revision as of 19:11, 29 June 2016

Status: This page documents data services for version 1 of the Phenoscape KB, available as a legacy resource at http://fish.phenoscape.org. The web-services API for the current version of the KB is documented at http://docs.phenoscapekb.apiary.io/.

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

These are available at the base URI http://fish.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",
   "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".

Publication term info

URI 

<BASE URI>/term/publication/{term_id}

This is a specialized term info service which returns data in a format customized for publications.

Returns

JSON: <javascript> { 

   "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".

Publication data matrix

<BASE URI>/term/publication/{term_id}/matrix

Returns a data matrix containing all characters and OTUs loaded from a published dataset.

Returns

JSON: <javascript> { 

   "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".

Publication OTUs list

<BASE URI>/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: <javascript> { 

   "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".

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.

Attribute qualities

URI 

<BASE 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: <javascript> { 

   "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>

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>

Phenotypes

URI 

<BASE 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):

<javascript> { 

   "gene": [
   {
       "id": "ZFIN:XXXX"
   },
   {
       "id": "ZFIN:YYYY"
   }
   ],
   "gene_class": [
   {
       "id": "GO:XXXX"
   },
   {
       "id": "GO:YYYY"
   }
   ],
   "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_taxa": 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>

Phenotype facet counts

URI 

<BASE 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 <javascript> { 

   "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>

Phenotypic profile match service

URI 

<BASE 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):

<javascript> { 

   "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> { 

   "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>

Phenotypic variation sets service

URI 

<BASE 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):

<javascript> { 

   "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> { 

   "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 <javascript> </javascript>

Other ontology service definitions (for comparison)

Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Data_Services&oldid=11837"