Difference between revisions of "Data Repository and Data Services"

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==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>
 
{
 
    "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."
 
        }
 
    ]
 
}
 
</javascript>
 
 
 
'''Error'''
 
 
 
If there are no terms matching the given input, a document should still be returned, containing an empty results list.
 

Latest revision as of 00:44, 9 January 2009