Difference between revisions of "Data Services"

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This section details of the data services that query the OBD Phenoscape 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 section details of the data services that query the OBD Phenoscape 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].
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==Timestamp==
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'''URI'''
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<BASE URI>/term/{term_id}
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'''Returns'''
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JSON:
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<javascript>
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{
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"timestamp":"2010-01-09"
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}
 +
 +
</javascript>
  
 
==Term info==
 
==Term info==

Revision as of 16:44, 12 January 2010

This section details of the data services that query the OBD Phenoscape 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.

Timestamp

URI 

<BASE URI>/term/{term_id}

Returns

JSON: <javascript> { "timestamp":"2010-01-09" }

</javascript>

Term info

URI 

<BASE URI>/term/{term_id}

Returns

JSON: <javascript> { 

   "id" : "TAO:0001700",
   "name" : "caudal-fin stay",
   "definition" : "Bone that is located anterior to the caudal procurrent rays. Caudal fin stays are unpaired bone.",
   "comment" : "Some comment text that may be in there."
   "parents" :
   [
       {
           "relation" : {
               "id" : "OBO_REL:is_a",
               "name" : "is_a"
           },
           "target" : {
               "id" : "TAO:0001514",
               "name" : "bone"
           }

       },
       {
           "relation" : {
               "id" : "OBO_REL:part_of",
               "name" : "part_of"
           },
           "target" : {
               "id" : "TAO:0000862",
               "name" : "caudal fin skeleton"
           }
       }
   ],
   "children" : [] // if there are children, this content should be in the same format as the parents list

} // how should xrefs, etc. be represented, property_value definitions? </javascript>

OWL-RDF: 

Todo...

Error

If there is no term with the given ID, the service should return "404 Not Found".

Handling of anonymous post-compositions

Autocomplete

URI 

<BASE URI>/term/search?text=[input]&name=[true|false]&syn=[true|false]&def=[true|false]&ontology=[ont1,ont2,...]&limit=[count]

All URI parameters are optional except for text. Default values are name=true, syn=false, def=false. The "ontology" parameter should be a comma-separated list of ontology prefixes to search within. If not given, the default is to search all ontologies. Specifying "ZFIN" for the ontology should be a search for gene nodes, by gene name. The "limit" parameter limits the number of results to the given integer.

Returns

JSON: <javascript> { 

   "matches" : [
       {   // overall format
           "id" : "TAO:0001514",
           "name" : "bone",
           "match_type" : "name" | "syn" | "def",
           "match_text" : "this is the term name, synonym name, or definition that matched"
       },
       {   // a name example
           "id" : "TAO:0001514",
           "name" : "bone",
           "match_type" : "name",
           "match_text" : "bone"
       },
       {   // a synonym example
           "id" : "TAO:0001795",
           "name" : "ceratohyal foramen",
           "match_type" : "syn",
           "match_text" : "bericiform foramen"
       },
       {   // a definition example
           "id" : "TAO:0000488",
           "name" : "ceratobranchial bone",
           "match_type" : "def",
           "match_text" : "Ceratobranchials are bilaterally paired cartilage bones that form part of the ventral branchial arches. They articulate medially with the hypobranchials and laterally and dorsally with the epibranchials.  Ceratobranchials 1-5 ossify in the ceratobranchial cartilages."
       }
   ],
   "search_term" : "bone",
   "total" : 1859

} </javascript>

Error

If there are no terms matching the given input, a document should still be returned, containing an empty results list.

Annotations summary

URI 

<BASE URI>/phenotypes/summary?subject={subject_id}&entity={entity_id}&quality={quality_id}&pub={publication_id]&examples={examples_count}

This service returns a summary of the phenotype annotations involving the given terms. The annotations are grouped by "character", which a unique combination of an entity and the "character quality" to which the quality in the annotation corresponds.

All parameters are optional. If no parameters are specified, the service should return a summary of all the phenotype annotations in the database. Otherwise, any term ID given for the various parameters restricts the annotations to only those concerning those terms (where "concerning" is defined for each type of parameter).

  • subject - an ID for a taxon or gene - the summarized characters are only those which this term exhibits
  • entity - an ID for an anatomical term - the summarized characters are only those whose phenotype inheres_in this entity (note - maybe we should add another parameter to include phenotypes which inhere_in_part_of the entity)
  • quality - an ID for a quality term - the summarized characters are only those whose phenotype is_a type of this term
  • pub - an ID for a publication - the summarized characters are only those contributed by the given publication
  • examples - the number of example terms to include in the output - default is zero

For each character, find all taxa and genes which exhibit phenotypes corresponding to that character. If "subject" is a taxon, limit the included taxa to those within the given subject taxon. If "pub" is specified, limit the included taxa to those within the given publication.

Returns

JSON: <javascript> { 

   "characters" : [
       {
           "entity" : { "id" : "TAO:34242", "name" : "basihyal bone" },
           "character_quality" : { "id" : "PATO:34242", "name" : "texture" },
           "qualities" : {
               "count" : 14,
               "examples" : [
                   { "id" : "PATO:34242", "name" : "some quality" },
                   { "id" : "PATO:34242", "name" : "some quality" }
               ]
           },
           "taxa" : {
               "count" : 2,
               "examples" : [
                   { "id" : "TTO:34242", "name" : "some taxon" },
                   { "id" : "TTO:34246", "name" : "some taxon" }
               ]
           },
           "genes" : {
               "count" : 2,
               "examples" : [
                   { "id" : "ZDB:34242", "name" : "some gene" },
                   { "id" : "ZDB:34246", "name" : "some gene" }
               ]
           }
       },
       {
           "entity" : { "id" : "TAO:34242", "name" : "dorsal fin ray" },
           "character_quality" : { "id" : "PATO:34242", "name" : "shape" },
           "qualities" : {
               "count" : 9,
               "examples" : [
                   { "id" : "PATO:34242", "name" : "some quality" },
                   { "id" : "PATO:34242", "name" : "some quality" }
               ]
           },
           "taxa" : {
               "count" : 5,
               "examples" : [
                   { "id" : "TTO:34242", "name" : "some taxon" },
                   { "id" : "TTO:34246", "name" : "some taxon" }
               ]
           },
           "genes" : {
               "count" : 7,
               "examples" : [
                   { "id" : "ZDB:34242", "name" : "some gene" },
                   { "id" : "ZDB:34246", "name" : "some gene" }
               ]
           }
       }
   ]

} </javascript>

Annotations results

URI 

<BASE URI>/phenotypes?subject={subject_id}&entity={entity_id}&quality={quality_id}&pub={publication_id]&type=[evo|devo]&group=[root|{taxon_id}]

This service returns the phenotype annotations involving the given terms.

All parameters are optional. If no parameters are specified, the service should return all the phenotype annotations in the database. Otherwise, any term ID given for the various parameters restricts the annotations to only those concerning those terms (where "concerning" is defined for each type of parameter).

  • subject - an ID for a taxon or gene - the returned annotations are only those which this term exhibits
  • entity - an ID for an anatomical term - the returned annotations are only those whose phenotype inheres_in this entity (note - maybe we should add another parameter to include phenotypes which inhere_in_part_of the entity)
  • quality - an ID for a quality term - the returned annotations are only those whose phenotype is_a type of this term
  • pub - an ID for a publication - the returned annotations are only those contributed by the given publication
  • type - either "evo" or "devo" - return either evolutionary data (evo) or model organism data (devo) or both if not specified
  • group - if "root", return, as the subject, only the most recent common ancestor taxon for all taxa found in the query, along with the set of phenotypes found in the results. If a taxon id, return the results grouped into immediate children of that taxon (only those that have results). Only include the annotation ID if that phenotype-to-taxon link was actually asserted.

Returns

JSON: <javascript> { 

   "subjects" : [
   {   "id" : "TTO:34242",
       "name" : "some taxon",
       "leaf" : false, //whether it is useful to query for more specific sub-taxa
       "phenotypes" :  [
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : 22
           },
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           },
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           }
       ]
       },
       {   "id" : "TTO:34243",
       "name" : "some taxon",
       "phenotypes" :  [
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           },
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           },
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           }
       ]
       },
       {   "id" : "TTO:34244",
       "name" : "some taxon",
       "phenotypes" :  [
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           },
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           },
           {
               "id" : "internal annotation ID",
               "entity" : { "id" : "TAO:34242", "name" : "some entity" },
               "quality" : { "id" : "PATO:34242", "name" : "some quality" },
                "count" : ""
           }
       ]
       }
   ]

} </javascript>

Homology info

Return any homology statements which the given term participates in. Regardless of the direction of the homologous link in the database, the queried term should be returned as the "subject" in the returned data - the homologous term would be the "target".

URI 

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

Returns

JSON: <javascript> {"homologies" : [ 

   {
       "subject" : {
           "entity" : {"id" : "TAO:xxxx", "name" : "some anatomical thing"},
           "taxon" : {"id" : "TTO:xxxx", "name" : "some taxon"}
       },
       "target" : {
           "entity" : {"id" : "TAO:xxxx", "name" : "some anatomical thing"},
           "taxon" : {"id" : "TTO:xxxx", "name" : "some taxon"}
       },
       "source" : {

"publication" : "citation text", "evidence" : {"id" : "ECO:xxxx", "name" : "some evidence code"} } 

   },
   {
       "subject" : {
           "entity" : {"id" : "TAO:xxxx", "name" : "some anatomical thing"},
           "taxon" : {"id" : "TTO:xxxx", "name" : "some taxon"}
       },
       "target" : {
           "entity" : {"id" : "TAO:xxxx", "name" : "some anatomical thing"},
           "taxon" : {"id" : "TTO:xxxx", "name" : "some taxon"}
       },
       "source" : {

"publication" : "citation text", "evidence" : {"id" : "ECO:xxxx", "name" : "some evidence code"} } 

   }

] } </javascript>

Annotation source information

NOTE: URI spec has been changed because of Resolution problems on the Eryops server: Cartik

URI 

<BASE URI>/phenotypes/source/{annotation_id}

Returns

JSON: <javascript> { "phenotype" : { 

           "subject" : { "id" : "TTO:34242", "name" : "some taxon" },
           "entity" : { "id" : "TAO:34242", "name" : "some entity" },
           "quality" : { "id" : "PATO:34242", "name" : "some quality" }
       },

"sources" : [ 

   {
       "publication" : "citation text",
       "character_text" : "blah",
       "character_comment" : "blah",
       "state_text" : "blah",
       "curated_by" : "blah"
   }

] } </javascript>

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