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Karen Yook edited this page Sep 23, 2013 · 2 revisions

Process pages

https://sites.google.com/site/wbprocesses/home (google site)

WS233 process model 

 ?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

 ?Gene     WBProcess ?WBProcess XREF Gene #Evidence \\
 ?Expression_cluster	 WBProcess ?WBProcess XREF Expression_cluster #Evidence \\
 ?Interaction 	WBProcess ?WBProcess XREF Interaction\\
 ?Anatomy_term	WBProcess ?WBProcess XREF Anatomy_term\\
 ?Life_stage	WBProcess ?WBProcess XREF Life_stage \\
 ?Molecule       WBProcess ?WBProcess XREF Molecule\\
 ?Phenotype	Associated_with WBProcess ?WBProcess XREF Phenotype \\
 ?Picture        WBProcess ?WBProcess XREF Picture\\
 ?Movie          WBProcess ?WBProcess XREF ?Movie\\
 ?Paper	Refers_to  WBProcess ?WBProcess XREF Reference \\

Definition and use of classes and tags

  • WBbioprID An ID space for the process (e.g., WBbiopr:0000001)
  • 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.
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