Topic (WBProcess) Model build

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Project Model

Proposed structure for the WB biological processes model

last updated 26 Feb, 2010

////////////////////////////////// ?WBProcess Model ///////////////////////////////////////////////


                              Summary           ?Text #Evidence
                              Process_term ?Text
                              Other_name ?Text
                              Related_process ?WBProcess XREF Related_process
                              Involved_entity      Gene ?Gene XREF WBProcess     #Evidence  
                                                               Anatomy_term ?Anatomy_term XREF WBProcess #Evidence
                                                               Expression_cluster ?Expression_cluster XREF WBProcess #Evidence
                              Associated_with         Phenotype ?Phenotype XREF WBProcess
                                                                   GO_term ?GO_term XREF WBProcess
                              Remark ?Text #Evidence 
                              Reference ?Paper XREF WBProcess  #Evidence //For remarks about the paper.

Definition of tags and use of classes

  • Name -> An ID space for the process (e.g., WBbiopr:0000001) <We can get rid of a few of the zeros>
  • 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?)
  • Process_term -> Public name
  • 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.

test .ace data

Current wspec model file

This will have all the other model corrections in place