K. NCBI Collaboration

With Brian Smith-White (NCBI) and Mau Ramil (IRRI) - Follow up of PAG XX

What is NCBI? The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

Guidelines and requirements for submitting genotype and phenotype association data to dbGaP.Brian's vision within 5 years is that NCBI users will need to have access to some Phenotypes data when they look at the sequenced (refSeq)

A 1st test case will be Rice to follow up on Susan McCouch discussion 

Brian realized there is not a single controlled vocabulary for phenotypes (Plant ontology, TRait Ontology, FAO descriptors) but several in use and then he is proposing that NCBI hosts a mapping table or translation table that would provide the links (1 to n) between traits lists. NCBI needs to look quickly at developing a feature like 'Get sequences' based on a trait request.  Brian wishes to understand  where the term can be used to cross reference data  and where. 

objective is to Produce a Root table of the most evident full matching for Rice trait as a proof of concept

March : The Rice ontology team will upload the updated Rice ontology and will produce a table with the traits and, in columns, all the matching trait IDs in other ontology. Fine tune the mapping and list with Breeders. See with Luca how to get the table extracted.

End of May: Send to the Rice table to Brian in XML 

June: Brian will test it and identified fields to associate to a sequence to get the phenotype info. produce a root table.

September: the ontology API will be adapted to provide what is necessary to NCBI if they wish to use more terms from CO. 

B. Example of a possible output: Synergizer


The Synergizer is a service for translating between sets of biological identifiers.

The Synergizer project consists of two main components: 1) a backend database of "synonym relationships" gleaned from various authorities; and 2) a web service with a very simple API, which allows programmers to write client applications to access the data in the backend database. These applications can range from one-time programs written by researchers for their individual use to interactive applications for wide research community.

The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access).