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

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(Created page with "Original file generated for UniProt: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/uniprot.cgi Updates to file will now include data types curated for a given gene.")
 
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Updates to file will now include data types curated for a given gene.
 
Updates to file will now include data types curated for a given gene.
 +
 +
 +
What we currently supply:
 +
 +
WBGene WBPaperID PMID
 +
 +
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:
 +
 +
GO:PPI;Phenotype;Disease;Expression;Sequence
 +
 +
 +
How to map this onto our data types from each WS release:
 +
 +
 +
GO:
 +
?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

Revision as of 18:32, 19 May 2015

Original file generated for UniProt:

http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/uniprot.cgi

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


What we currently supply:

WBGene WBPaperID PMID

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:

GO:PPI;Phenotype;Disease;Expression;Sequence


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


GO: ?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
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