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

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Line 35: Line 35:
  
 
PPI:
 
PPI:
?Interaction -> Interaction_type Physical
+
    ?Interaction -> Interaction_type Physical
            -> Interactor_overlapping_gene
+
                  -> Interactor_overlapping_gene
    -> Paper
+
          -> Paper
  
  
 
Phenotype:
 
Phenotype:
?RNAi -> Inhibits
+
    ?RNAi -> Inhibits
      -> Phenotype
 
      -> Reference
 
 
 
?Variation -> Affects
 
 
           -> Phenotype
 
           -> Phenotype
 
           -> Reference
 
           -> Reference
 +
 +
    ?Variation -> Affects
 +
                -> Phenotype
 +
                -> Reference
  
  
 
Disease:
 
Disease:
?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence
+
    ?Gene -> Disease_info -> Experimental -> Evidence -> Paper_evidence
      -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence
+
          -> Disease_info -> Disease_relevance -> Evidence -> Paper_evidence
  
 
Expression:
 
Expression:
?Expr_pattern -> Expression_of -> Gene
+
    ?Expr_pattern -> Expression_of -> Gene
              -> Reference
+
                  -> Reference
  
  
 
Sequence:
 
Sequence:
?Variation -> Affects
+
    ?Variation -> Affects
                -> Nonsense
+
                -> Nonsense
                -> Missense
+
                -> Missense
                -> Silent Any one of these filled in
+
                -> Silent Any one of these filled in
                -> Splice_site
+
                -> Splice_site
                -> Frameshift
+
                -> Frameshift
                -> Readthrough
+
                -> Readthrough
                -> Reference
+
                -> Reference

Revision as of 18:34, 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