Difference between revisions of "Topic (WBProcess) Model build"

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[[Caltech documentation]]<br>
[[Caltech documentation]]<br>
[[Overview of process pages]]<br>
[[Overview of process pages]]<br>
*[[Example process pages]]<br>
[[Process page and model concerns]]<br>
[[Molecule model build]] <br>
[[Molecule model build]] <br>
=Project Model=
=Project Model=

Revision as of 00:44, 7 November 2013

Links to other relevant pages:
Caltech documentation
Overview of process pages

Molecule model build

Project Model

Proposed structure for the 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 ///////////////////////////////////////////////

       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