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

From WormBaseWiki
Jump to navigationJump to search
m
Line 22: Line 22:
 
New pipeline proposal is to retrieve information from WormBase ftp site, which will be updated with each release.
 
New pipeline proposal is to retrieve information from WormBase ftp site, which will be updated with each release.
  
ftp://ftp.wormbase.org/pub/wormbase/releases/WS270/ONTOLOGY/
+
ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release
 +
 
 +
 
 +
From: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY
 +
 
 +
General principles:
 +
# ignore lines with NOT qualifier (column 4 in GO, Phenotype
 +
# convert WB_REFs to PMIDs ??  will check with Ceci
  
  
 
GO:
 
GO:
    ?GO_annotation -> Gene
+
 
                    -> Reference
+
* File: gene_association.WSnnn.wb.c_elegans
 +
* Ignore lines with 'NOT' in column 4
 +
* Only use annotation lines that include a PMID, but ignore lines with WB_REF:WBPaper00046480|PMID:21873635
 +
* Relevant columns: 2 and 6
 +
 
 +
 
 +
Phenotype:
 +
 
 +
* File: phenotype_association.WSnnn.wb
 +
* Ignore lines with 'NOT' in column 4
 +
* Convert WBPaper ids into PMID
 +
* Relevant columns: 2 and 6
 +
 
 +
 
  
  
 
PPI:
 
PPI:
     ?Interaction -> Interaction_type Physical
+
      
                  -> Interactor_overlapping_gene
 
                  -> Paper
 
  
  
Phenotype:
 
    ?RNAi -> Inhibits -> Gene
 
          -> Phenotype (Only Phenotype Observed, doesn't matter what the Phenotype is)
 
          -> Reference
 
  
    ?Variation -> Affects -> Gene
 
                -> Phenotype (Only Phenotype Observed, doesn't matter what the Phenotype is)
 
                -> Reference
 
  
  
Line 63: Line 74:
 
                                       Disease relevance and Paper for Disease Rel
 
                                       Disease relevance and Paper for Disease Rel
 
     Will need to get OA table names
 
     Will need to get OA table names
 
 
 
 
  
 
= 2015 Pipeline =
 
= 2015 Pipeline =

Revision as of 20:28, 20 May 2019

2019 Pipeline

Objective: supply a regularly updated file to UniProt that lists:

WBGene WBPaperID PMID Category


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

GO

PPI (Protein-Protein Interaction)

Phenotype

Disease

Expression

Sequence

New pipeline proposal is to retrieve information from WormBase ftp site, which will be updated with each release.

ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release


From: ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/ONTOLOGY

General principles:

  1. ignore lines with NOT qualifier (column 4 in GO, Phenotype
  2. convert WB_REFs to PMIDs ?? will check with Ceci


GO:

  • File: gene_association.WSnnn.wb.c_elegans
  • Ignore lines with 'NOT' in column 4
  • Only use annotation lines that include a PMID, but ignore lines with WB_REF:WBPaper00046480|PMID:21873635
  • Relevant columns: 2 and 6


Phenotype:

  • File: phenotype_association.WSnnn.wb
  • Ignore lines with 'NOT' in column 4
  • Convert WBPaper ids into PMID
  • Relevant columns: 2 and 6



PPI:




Expression:

    ?Expr_pattern -> Expression_of -> Gene
                  -> Reference


Sequence:

    ?Variation -> Affects -> Gene
               -> Type_of_mutation -> Paper_evidence
            

Disease:

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

Disease:

    Alternatively, use OA tables for Experimental Model For and Paper for Exp Mod
                                     Disease relevance and Paper for Disease Rel
    Will need to get OA table names

2015 Pipeline

Original file generated for UniProt:

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

What we currently supply:

WBGene WBPaperID PMID

Not sure how this is generated; I believe this was done before my time as paper curator.


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

We would need to add:

WBGene WBPaperID PMID Category


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

GO

PPI (Protein-Protein Interaction)

Phenotype

Disease

Expression

Sequence


An example:

    WBGene00003508  WBPaper00003680  pmid10517638  GO;Phenotype;Disease;Expression 



Strategy: Several possible strategies, perhaps - 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

Possibilities:

1) Start with Paper object and then trace the information in the objects xref'ed 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


Relevant tags in the different object models:


GO:

    ?GO_annotation -> Gene
                   -> Reference


PPI:

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


Phenotype:

    ?RNAi -> Inhibits -> Gene
          -> Phenotype (Only Phenotype Observed, doesn't matter what the Phenotype is)
          -> Reference
    ?Variation -> Affects -> Gene
               -> Phenotype (Only Phenotype Observed, doesn't matter what the Phenotype is)
               -> Reference


Expression:

    ?Expr_pattern -> Expression_of -> Gene
                  -> Reference


Sequence:

    ?Variation -> Affects -> Gene
               -> Type_of_mutation -> Paper_evidence
            

Disease:

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

Disease:

    Alternatively, use OA tables for Experimental Model For and Paper for Exp Mod
                                     Disease relevance and Paper for Disease Rel
    Will need to get OA table names