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

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Line 24: Line 24:
  
 
GO:PPI;Phenotype;Disease;Expression;Sequence
 
GO:PPI;Phenotype;Disease;Expression;Sequence
 +
 +
 +
Strategy: Several possible strategies - not sure which is best.
 +
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
  
  
Line 49: Line 54:
 
                 -> Reference
 
                 -> Reference
  
 
Disease:
 
    ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence
 
          -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence
 
  
 
Expression:
 
Expression:
Line 70: Line 71:
  
 
                 -> Reference
 
                 -> Reference
 +
 +
Disease:
 +
    ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence
 +
          -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence

Revision as of 19:11, 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


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

    ?GO_annotation -> Gene
                   -> Reference


PPI:

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


Phenotype:

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


Expression:

    ?Expr_pattern -> Expression_of -> Gene
                  -> Reference


Sequence:

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

Disease:

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