Topic (WBProcess) Model build

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Links to other relevant pages:
Caltech documentation
Topic pages

Molecule model build

Project Model

Proposed structure for the Biological topic (WB biological processes) model

Fixed by Paul for WS233:

  • the Database line is a broken model issue, I have fixed it for WS233 models.
  • renamed the Name -> Public_name

--kjy 22:29, 13 July 2012 (UTC)

///////////////////////////////////////////////////////////////////////
//
//?WBProcess Model - renamed Biological topics for website and curation
//
///////////////////////////////////////////////////////////////////////
 
 ?WBProcess      
        Public_name UNIQUE ?Text 
        Process_term (isn't necessary)         
        Summary ?Text   #Evidence       
        Other_name      ?Text
        Related_process ?WBProcess      XREF    Related_process
        Taxon   NCBITaxonomyID  ?Text
        Involved_entity Gene    ?Gene   XREF    WBProcess       #Evidence
                Expression_cluster      ?Expression_cluster     XREF    WBProcess       #Evidence
                Interaction     ?Interaction    XREF    WBProcess       #Evidence
                Anatomy_term    ?Anatomy_term   XREF    WBProcess       #Evidence
                Life_stage      ?Life_stage     XREF    WBProcess       #Evidence
                Molecule        ?Molecule       XREF    WBProcess       #Evidence
        Associated_with Phenotype       ?Phenotype      XREF    WBProcess       #Evidence
                GO_term ?GO_term        #Evidence
        Picture ?Picture        #Evidence
        Movie   ?Movie  #Evidence
        Pathway DB_info Database  ?Database ?Database_field ?Accession_number
        Remark  ?Text   #Evidence
        Reference       ?Paper  XREF    WBProcess


Definition and use of classes and tags

  • WBbioprID An ID space for the process (e.g., WBbiopr:0000001) <We can get rid of a few of the zeros>
  • Public_name
  • Process_term ->should be removed if not gone already
  • Summary -> A definition of the process with reference evidence (will it be enough to have the reference listed here, or do we also need a separate reference in the model?)
  • Other_name -> Synonyms
  • Related_process -> Relationships between different WB defined biological processes
  • Involved_entity-> XREF to objects in other classes that will be annotated with a process term. Process annotations for genes and papers that have not yet been attached to genes and papers through any other tag or annotation. Direct gene and paper annotations can be filtered out during .ace file dumps for those cases where the gene and paper have been connected to the process through other tags, i.e. GO mappings, phenotype mappings, microarray, anatomy.
  • Associated_with -> Mappings to terms in GO and Phenotype classes
  • Remark -> A remark field to capture things that don't quite fit anywhere else yet. Also to be used to make comments about papers that should be connected to the process, if it has not been through other means, possibly review papers? Could also make a separate paper XREF.
  • Reference -> Associated papers. The evidence hash for this tag is for remarks to record why the paper is associated with the process, this is especially useful for those papers that are associated with the process directly rather than through any of the other tags. Ideally I would like the papers sorted by type for display on the website, that is it would be good to have papers that are reviews separate from papers that are primary research.

test .ace data

Current wspec model file

This will have all the other model corrections in place