Difference between revisions of "Topic pages"

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* Home for pathway views of data from Reactome, BioCyc, and Nemapath
 
* Home for pathway views of data from Reactome, BioCyc, and Nemapath
  
=WBProcess OA=
+
=Summary=
 
 
TAB1
 
'''WBProcessID''' auto-incremental based on new record dump as WBProcess : "WBbiopr:00000x"
 
'''Process_term'''  text
 
'''Summary''' big text
 
'''Other_name''' big text, values will be pipe separated
 
'''Related_process''' XREF to WBProcess -multi-ontology field, autocomplete on Process_term
 
'''Taxon''' multi-ontology of NCBITaxonomy ID, autocomplete on
 
'''WBProcess''' ontology autocomplete on process_term
 
'''Remark''' big text
 
 
TAB2
 
'''WBPaper''' ontology autocomplete on WBPaperID
 
'''Gene''' multi-ontology autocomplete on public_name
 
'''Expression_cluster'''  multi-ontology (will need to query for this an add to OA ontology file with rest  of it)
 
'''Interaction''' multi-ontology, autocomplete on gene, term info must have WBPaperID, all interactors,  and  interaction type.
 
'''Anatomy_term''' multi-ontology autocomplete on name
 
'''Life_stage''' multi-ontology autocomplete on name
 
'''Molecule''' multi-ontology  autocomplete on name and synonym
 
'''Phenotype''' multi-ontology  autocomplete on name and synonym
 
'''GO_term''' multi-ontology autocomplete on name and synonym
 
 
TAB3
 
'''Picture''' multi-ontology autocomplete on ID
 
'''Movie''' multi-ontology  autocomplete on ID
 
'''Pathway Database''' ontology  autocomplete on name
 
'''Pathway accession''' text
 
 
 
'''
 
 
 
 
 
 
 
 
 
 
 
===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.
 
 
 
===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)
 
 
 
==Process OA==
 
 
 
===Summary===
 
 
A general summary of the process term.  Can be extracted from WormBook if possible.
 
A general summary of the process term.  Can be extracted from WormBook if possible.
  
Line 146: Line 67:
  
  
 +
 +
=WBProcess OA=
 +
 +
TAB1
 +
'''WBProcessID''' auto-incremental based on new record dump as WBProcess : "WBbiopr:00000x"
 +
'''Process_term'''  text
 +
'''Summary''' big text
 +
'''Other_name''' big text, values will be pipe separated
 +
'''Related_process''' XREF to WBProcess -multi-ontology field, autocomplete on Process_term
 +
'''''Taxon''' multi-ontology of NCBITaxonomy ID, autocomplete on species name - doesn't exist yet''
 +
'''WBProcess''' ontology autocomplete on process_term
 +
'''Remark''' big text
 +
 +
TAB2
 +
'''WBPaper''' ontology autocomplete on WBPaperID; term info-WBProcess, Gene
 +
'''Gene''' multi-ontology autocomplete on public_name; term info- name, WBGeneID, WBProcess
 +
'''''Expression_cluster'''  multi-ontology -doesn't exist yet''
 +
'''Interaction''' multi-ontology, autocomplete on gene, term info- WBPaperID, all interactors,  and  interaction type.
 +
'''Anatomy_term''' multi-ontology autocomplete on name; term info- name
 +
'''Life_stage''' multi-ontology autocomplete on name; term info- name
 +
'''Molecule''' multi-ontology  autocomplete on name and synonym; term info- molecule ID, name, synonym
 +
 +
TAB3
 +
'''Phenotype''' multi-ontology  autocomplete on name and synonym; term info -description
 +
'''GO_term''' multi-ontology autocomplete on name and synonym; term info -description
 +
'''''Human_disease'''  multi-ontology autocomplete on name and synonym  (does one exist?)''
 +
'''Picture''' multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, Expression pattern
 +
'''''Movie''' multi-ontology  autocomplete on ID doesn't exist yet''
 +
'''Pathway Database''' ontology  autocomplete on name
 +
'''Pathway accession''' text
 +
 
[[Category: Process page]]
 
[[Category: Process page]]

Revision as of 23:39, 30 August 2011

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 auto-incremental based on new record dump as WBProcess : "WBbiopr:00000x"
Process_term  text
Summary big text
Other_name big text, values will be pipe separated
Related_process XREF to WBProcess -multi-ontology field, autocomplete on Process_term
Taxon multi-ontology of NCBITaxonomy ID, autocomplete on species name - doesn't exist yet
WBProcess ontology autocomplete on process_term
Remark big text 

TAB2
WBPaper ontology autocomplete on WBPaperID; term info-WBProcess, Gene
Gene multi-ontology autocomplete on public_name; term info- name, WBGeneID, WBProcess
Expression_cluster  multi-ontology -doesn't exist yet
Interaction multi-ontology, autocomplete on gene, term info- WBPaperID, all interactors,  and  interaction type.
Anatomy_term multi-ontology autocomplete on name; term info- name
Life_stage multi-ontology autocomplete on name; term info- name
Molecule multi-ontology  autocomplete on name and synonym; term info- molecule ID, name, synonym

TAB3
Phenotype multi-ontology  autocomplete on name and synonym; term info -description
GO_term multi-ontology autocomplete on name and synonym; term info -description
Human_disease  multi-ontology autocomplete on name and synonym  (does one exist?)
Picture multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, Expression pattern
Movie multi-ontology  autocomplete on ID doesn't exist yet
Pathway Database ontology  autocomplete on name 
Pathway accession text