|
|
| (47 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| − | ==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 [http://bioportal.bioontology.org/ontologies/38703 Teleost Taxonomy Ontology (TTO)] that contains definitions of taxa, the [https://www.nescent.org/phenoscape/Teleost_Anatomy_Ontology Teleost Anatomy Ontology (TAO)] that contains definitions of teleost specific anatomical characteristics, and the [http://bioontology.org/wiki/index.php/PATO:Main_Page 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''',
| |
| − | **The data loader transforms the curated data from NeXML syntax to a set of relational tuples (records), which are then sequentially inserted into the database
| |
| − | *'''Invokes the OBD reasoner to elicit implicit information from the data and adds them to the database'''
| |
| − | **The OBD reasoner uses definitions of transitive relations, relation hierarchies, and relation compositions to infer implicit information. These inferences are added to the relational database in the final step
| |
| | | | |
| − | ==Web services==
| |
| − | 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].
| |
| − | ===Term info===
| |
| − | '''URI'''
| |
| | | | |
| − | <BASE URI>/term/{term_id}
| + | [[Category:Informatics]] |
| − | | |
| − | '''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.
| |
