Closed Mar 30, 2015
Due by December 31, 2012
•Closed Switch to identifiers.org URIs and xml:base
Goal
Modify cpath2 and the BioPAX validator/normalizer to generate/normalize-to standard identifiers.org URIs (but it's not for Xrefs, except for PublicationXref, types), where possible; also use own (configured) xml:base to consistently generate resolvable (URL) URIs for Xrefs. Stop encoding information and imposing a particular style into xref URIs (i.e., don't make urn:biopax:RelationshipXref:... things)
Tasks
| ID | NAME | DESCRIPTION | Estimated time | OWNER | |
|---|---|---|---|---|---|
| 1 | identifiers.org | update the biopax-validator and cpath2 (import pipeline and services) | 3 weeks | Igor | Done |
| 2 | xml:base | update the biopax-validator, and cpath2 (respect xml:base) | 2 weeks | Igor | Done |
| 3 | uniprot isoforms | ACs like P04150-3 are now valid IDs in the uniprot.isoform MIRIAM/identifiers.org namespace; make changes that appreciate this (in the validator); but keep merging (modify the cpath2 Merger) isoform PRs into corr. canonical one (P04150) | 1 week | Igor | Done |
Done.
Dates
- Start - November 2012
- End - December, 2012
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