Topic pages

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Revision as of 14:06, 6 September 2011 by Jchan (talk | contribs) (→‎WBProcess OA)
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back to' Caltech documentation
Other process related pages

Goals of the process pages

  • Portal for larger biomedical community into C. elegans gene function.
  • Context for data that fits within a larger biological picture such as microarray results, and responses to chemical/drugs, i.e. orphaned data
  • On the fly update addendum to WormBook chapters
    • process pages will dissect the chapters and link them to entities in WormBase,
    • process pages will link summaries of processed with the most recent acedb data
  • Home for pathway views of data from Reactome, BioCyc, and Nemapath

Summary

A general summary of the process term. Can be extracted from WormBook if possible.

Genes

Genes related to the process with references.

  • Mined from GO
  • Mined from Phenotype
  • Assigned manually: coordinate with GO and Phenotype curators?

Cells / Anatomy

  • Mined from gene function?
  • Assigned manually from paper/reviews
  • Display should be embedded anatomy ontology window pointing to relevant cells/tissue objects.
  • Eventually, this should be the whole worm image or cell image (Neurobrowse where appropriate?)

Cell component

  • GO:CC associated with process with references.
  • Mined through gene GO assignments

GO biological processes

  • Embedded gene ontology window pointing to relevant GO biological process and genes.
  • Each process term will be manually mapped to a GO term, following the hierarchy of the GO ontology when useful

Phenotypes

  • Phenotypes from RNAi experiments, variations in major genes, discussed in reviews, with references.
  • Process terms will be associated with a phenotype through the GO2Phenotype mapping (curator validation will be needed)
  • For those phenotypes that are not associated through the GO2Phenotype mapping, a curator will do this manually, with feedback to GO and Phenotype curators for coordination of efforts.

Chemicals/small molecules

  • Drug/chemical/small molecule, CHEBI_ID, with references.

Genetic interactions

  • Manually associated
  • With the process with references.
  • Gene interaction networks (N-browse view?)

Microarray experiments

  • Expression clusters only (all microarray experiments should have these cluster views of the results)
  • link to SPELL page for microarray data

Related human disease

  • OMIM assignments based on process-associated genes, ranked by most evidence supported.

Subprocesses and pathways

  • List of processes based on WormBook and other reviews. Mined through GO hierarchy

Pathway/Reaction

  • Metabolic pathways: BioCyc, Reactome, NemaPath (KEGG)
  • Other pathways: Reactome

Resources

  • WormBook (Viewed as WormBook chapter title and author (WBPerson/Author page))
  • WormAtlas (WormAtlas page(s) link, display page title)


WBProcess OA

TAB1
WBProcessID -- name -- auto-incremental based on new record dump as WBProcess : "WBbiopr:00000x" is this padding to 5 or 6 digits ? if we could do 8 or 10 that would be slightly easier -- J
Process_term -- processterm --  text
Summary -- summary --  big text
Other_name -- othername -- big text, values will be pipe separated
Related_process -- relprocess -- XREF to WBProcess -multi-ontology field, autocomplete on Process_term not on other_name ? -- J
Taxon -- taxon -- multi-ontology of NCBITaxonomy ID, autocomplete on species name - doesn't exist yet text until your file is ready for obo_ table -- J
WBProcess -- wbprocess -- ontology autocomplete on process_term same as the related_process ontology ? -- J
Remark -- remark -- big text 

TAB2
WBPaper -- paper -- ontology autocomplete on WBPaperID; term info-WBProcess, Gene
Gene -- wbgene -- multi-ontology autocomplete on public_name; term info- name, WBGeneID, WBProcess
Expression_cluster -- exprcluster -- multi-ontology -doesn't exist yet text until your file is ready for obo_ table -- J
Interaction -- interaction -- multi-ontology, autocomplete on gene, term info- WBPaperID, all interactors,  and  interaction type. already exists in interaction OA, talk to the interaction curator to change autocomplete or what-not (and tell them to email me or sign this wiki) -- J
Anatomy_term -- anat_term --  multi-ontology autocomplete on name; term info- name
Life_stage -- lifestage -- multi-ontology autocomplete on name; term info- name
Molecule -- molecule -- multi-ontology  autocomplete on name and synonym; term info- molecule ID, name, synonym

TAB3
Phenotype -- phenotype -- multi-ontology  autocomplete on name and synonym; term info -description
GO_term -- goid -- multi-ontology autocomplete on name and synonym; term info -description
Human_disease -- humdisease --   multi-ontology autocomplete on name and synonym  (does one exist?) text until your file is ready for obo_ table -- J
Picture -- picture -- multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, Expression pattern
Movie -- movie -- multi-ontology  autocomplete on ID doesn't exist yet text until your file is ready for obo_ table -- J
Pathway Database --pathwaydb -- ontology  autocomplete on name  text until your file is ready for obo_ table -- J
Pathway accession -- pathwayacc -- text
Curator -- curator -- dropdown missing from specs, added here -- J