UniProt Paper - Gene - Data Type

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Revision as of 18:32, 19 May 2015 by Vanaukenk (talk | contribs)
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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

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

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


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


    ?GO_annotation -> Gene
                   -> Reference

PPI: ?Interaction -> Interaction_type Physical

            -> Interactor_overlapping_gene

-> Paper

Phenotype: ?RNAi -> Inhibits

     -> Phenotype
     -> Reference

?Variation -> Affects

          -> Phenotype
          -> Reference

Disease: ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence

     -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence

Expression: ?Expr_pattern -> Expression_of -> Gene

             -> Reference

Sequence: ?Variation -> Affects

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