Data Repository and Data Services
Contents
Data loader
A data loader application to refresh the data in the Phenoscape database on a daily basis is under development. The application is being developed as a Perl module which:
- Downloads curated NeXML files from the Phenoscape SVN repositories
Ichthyologists curate scientific publications using the Phenex character matrix annotator and these curations are stored in an SVN repository. The data loader downloads these data files on a daily basis for subsequent uploading into the relational database
- Drops and recreates the database
- Loads the requisite ontologies into the database
The annotations of character matrices use terms that are defined in life science ontologies. These ontologies include the Teleost Taxonomy Ontology (TTO) that contains definitions of taxa, the Teleost Anatomy Ontology (TAO) that contains definitions of teleost specific anatomical characteristics, and the Phenotype and Trait Ontology (PATO) that contains definitions of phenotypic qualities. The data loader loads these definitions into the relational database
- Loads the data from the curated NeXML files into the database, and
- Invokes the OBD reasoner to elicit implicit information from the data and adds them to the database
Web services
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.
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."
"parents" :
[
{
"relation" : "OBO_REL:is_a",
"id" : "TAO:0001514",
"name" : "bone"
},
{
"relation" : "OBO_REL:part_of",
"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}?name=[true|false]&syn=[true|false]&def=[true|false]&ontology=[ont1;ont2;...]
All URI parameters are optional. Default values are name=true, syn=false, def=false. The "ontology" parameter should be a semicolon-separated list of ontology prefixes to search within. If not given, the default is to search all ontologies.
Returns
JSON: <javascript> [
{ // 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."
}
] </javascript>
I'm not sure if an array can be the outer-most object in JSON (need to check). If not, this should be wrapped in an object with a single "matches" key.
Error
If there are no terms matching the given input, a document should still be returned, containing an empty results list.
