Ontology Data Service API

Overview

Data services have been implemented as part of the Phenoscape application to retrieve data about evolutionary and model organism phenotypes. Ancillary services function in the auto completion of partially entered search terms by retrieving matching terms from the database, query relevant summary information on search terms, and retrieve any stored homology information about the search terms. This page details the functioning of each of these services, which make up the very first implementation of the Phenoscape application.

Service definitions

Basic Data Services

1. Auto completion service
   • Function: Obtain matching term names for a partial term name string
   • Input: partial term name string, a list of ontology IDs, search parameters (search names only or synonyms only or both)
   • Output: matches as records of term name or synonym that was hit, and how the term was hit (name or synonym)
2. Term info service
   • Function: Obtain the full term information for a given term
   • Input: a term ID
   • Output: the definition and synonyms for the term. In addition, all the parent and child terms of this term are returned. For terms from the Teleost Taxonomy Ontology, their rank and extant/extinct information are returned as well.
3. Homology information service
   • Function: Obtain homology information for the given anatomical entity. This is applicable only for anatomical entities
   • Input: term ID for the anatomical entity
   • Output: homology information for the given entity, with references and evidence codes

Phenotype Data Service

1. Phenotype summary service
   • Function: For a given anatomical entity, taxon, or gene, retrieve a summary of all annotated phenotypes involving the search term
   • Input: A UID for an anatomical entity, taxon, or gene
   • Output: A summary of all the phenotypes the given anatomical entity, taxon, or gene is involved in. Phenotypes are categorized by anatomical entity-character (EC) combinations. For each EC combination, the numbers of taxa and genes associated with it are returned
2. Phenotype details service
   • Function: For a given anatomical entity, gene, or taxon, retrieve the details of all the phenotypes it is involved in
   • Input: A UID for an anatomical entity, taxon, or gene
   • Output: A listing of all the Entities and Qualities (EQ) the search term in involved in. The output can be either a listing of genes, or a listing of taxa, or both. For taxa lists, the service creates a taxonomical hierarchy rooted at the Most Recent Common Ancestor (MRCA) of all the taxa, with corresponding listings of EQ combinations at each level and node of the tree. At the leaf level, where the EQ combinations are directly asserted, the service also provides citation information such as the paper from which the assertion was derived, along with character comments, text, and state comments and text

Data exchange formats

• Plain text over HTTP:
  • JSON

Other ontology service definitions

• Ontology Lookup Service (OLS) at the EBI. cote2006 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
  • web-service API (representing the WSDL) with JavaDoc for the interface contract, and
  • 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 BioPortal supports a SOAP-based web-service API:
  • WSDL: http://www.bioontology.org/ncboservicebeans/NCBOWebserviceBean?wsdl
  • Java JUnit test: test.webservice.NCBOServiceTest
• The Zthes profile for SRU is a specification for navigating and querying remote thesauri
  • SRU is a Library of Congress-sponsored standard for query interoperability between digital repositories
  • The Zthes profile for SRU is based on an abstract model for thesaurus representation, which is also available as an XML Schema implementation.

References

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1. cote2006 pmid=16507094

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