Difference between revisions of "UniProt Paper - Gene - Data Type"

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An example:
An example:
     WBGene00003508  WBPaper00003680  pmid10517638  GO;Phenotype;Disease;Expression;Sequence
     WBGene00003508  WBPaper00003680  pmid10517638  GO;Phenotype;Disease;Expression  

Revision as of 19:29, 19 May 2015

Original file generated for UniProt:


Updates to file will now include data types curated for a given gene.

What we currently supply:


Not sure how this is generated - before my time.

What we need to add:

WBGene WBPaperID PMID Category

The Categories would be gene-specific and we will supply information for:


An example:

    WBGene00003508  WBPaper00003680  pmid10517638  GO;Phenotype;Disease;Expression 

Strategy: Several possible strategies - not sure which is best.

Easiest to get everything from WS or a mixture of WS and postgres?

Some things, like GO, RNAi and Variation Phenotypes, need to be from WS

1) Start with Paper object and then trace the data types in the Refers_to tag - this works for everything but Disease

2) Look at each object in each relevant class - this seems computationally very intensive

How to map this onto our data types from each WS release:


    ?GO_annotation -> Gene
                   -> Reference


    ?Interaction -> Interaction_type Physical
                 -> Interactor_overlapping_gene
                 -> Paper


    ?RNAi -> Inhibits
          -> Phenotype
          -> Reference
    ?Variation -> Affects
                -> Phenotype
                -> Reference


    ?Expr_pattern -> Expression_of -> Gene
                  -> Reference


    ?Variation -> Affects
               -> Nonsense
               -> Missense
               -> Silent			Any one of these filled in
               -> Splice_site
               -> Frameshift
               -> Readthrough
               -> Reference


    ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence
          -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence