Ontology Data Service API

Goal and motivation

A common API implemented by ontology data services enables clients such as EQ editors that heavily rely on such a service to plug into different data providers, local or remote, at their choice.

Service definitions

Ontology Data Service

1. Ontology listing lookup
   • Function: lookup the ontologies being served by the data service
   • Input: none, or a particular name, and/or the name of the ontology category
   • Output: a record of name, version, identifier, meta-data (e.g., retired? in production? purpose?) for each ontology being served
2. Look up term
   • Function: Obtain the full term information for a given ID
   • Input: a term ID, or the combination of a term name and ontology ID
   • Output: the matching term in OBO or RDF/OWL format
   • Notes: do we need neighborhood here too (e.g., with IDs only); OBO only has parents, not children.
3. Completion list
   • 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, search obsoletes or not, search definition or not)
   • Output: matches as records of term name, term ID, ontology ID, synonym that was hit, how the term was hit (name, synonym, or definition)
4. Neighborhood graph
   • Function: Obtain parents, children, descendants, or ancestors for a given term
   • Input: term ID, list of relationships to include or exclude, number of levels (path length) up and down to include
   • Output: list of terms in OBO or RDF format
   • Note: Is it sensible to return a graph as OBO format? Do we need to mandate the semantics of matching mixed-type paths (e.g., is-a and part-of)?
5. Downloading ontology
   • Function: Obtain all terms and relationships comprising an ontology
   • Input: ontology ID, optionally name of the slim
   • Output: the ontology as an OBO or OWL stream of text
   • Notes: do we need a parameter for specifying the desired format? do we need parameter for including obsoletes or not
6. SPARQL endpoint
   • Function: Issue SPARQL queries and obtain the results in RDF
   • Input:
   • Output:

Notes applicable to all:

• Do we need to add search parameter to specify the 'slim' for each service that involves specifying an ontoloy?
• Should we have a protocol for client and server negotiating the desired return format, or should this be a parameter (in which case we also need a method to obtain all supported formats from the server)?

Phenotype Data Service

1. Login
   • Function: Given a username and secret, obtain an authentication token
   • Input:
   • Output:
2. Save EQ statements
   • Function: Save an array of EQ statements to the data store
   • Input: a list of EQ statements on OBD-xml or pheno-xml format
   • Output: success/failure indicator
3. Load EQ statements
   • Function: Load an array of EQ statements from the data store
   • Input: author, or list of taxa,
   • Output: matching EQ statements in pheno-xml or pheno-syntax format
   • Notes: do we need parameter of list of entities to obtain EQs for?

Query languages

• SPARQL

Data exchange formats

• Plain text over HTTP:
  • OBO format
  • YAML
  • JSON

• XML over HTTP:
  • OBO-XML format
  • OBD-XML format

• RDF over HTTP:
  • RDF/XML
  • RDF/N-triples

Other ontology service definitions

• A team at the EBI created the Ontology Lookup Service (OLS).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)
• This service 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

Next Steps

1. Finalize list of services for the ontology data service API.
   • This will be an initial revision 1.0 - we'll surely have iterations later down the road.
   • We'll need an acronym - anyone had a flash of creativity? What about OBODS
2. Define which services are mandatory, and which are optional.
3. Decide on protocol and query syntax.
   • What about using REST, e.g., http://onto.myorg.edu/obods?q=list_ontology&category=anatomy, or using paths http://onto.myorg.edu/obods/ontology/list?category=anatomy)
4. Create a reference implementation for the server.
   • A very generic reference implementation would be a wrapper over a SPARQL endpoint, i.e., translating API calls into SPARQL queries and transforming returned RDF into the required format.
5. Create a reference implementation for a web-application client (using JavaScript) and for, e.g., a Java client (for servlets or Java stand-alone apps).

References

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1. cote2006 pmid=16507094

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