Difference between revisions of "Topic (WBProcess) Model build"
From WormBaseWikiJump to navigationJump to search
|Line 65:||Line 65:|
Revision as of 00:51, 7 November 2013
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
- WBbioprID An ID space for the process (e.g., WBbiopr:0000001) <We can get rid of a few of the zeros>
- 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