GO client interface

[alberskib]

@bio4j/dynamograph Actually we have talks about scarph model, table layout etc but we do not talk about requirements from client perspective(functional requirements). This project should (I strongly believe that someone will use it) deliver easy in use interface for clients. I take a look into neo4db/titandb implementations and see that there were method that enables finding GO by Id. My question is: Is there any other ways in which clients will query db for given GOTerm:

• by name?
• by description?
• by some words that are in description Because if client will have GOTerm that he want he will be able to get relations(in, out of all types etc.)

Generally how clients will use dynamoGraph? Could you provide some usecases?

[eparejatobes]

Full-text search on definitions is certainly something that could be of some use in some circumstances. It is anyway something that could be easily added on top afterwards; also we don't have a finished model for indexing in general (we will).

In general, GO data is accessed through external rels that point to them from other datasources; one exampleis RefSeq elements (genes etc) which are annotated with GO terms:

• refseq ftp - gene2go.gz