Difference between revisions of "Topic pages"

From WormBaseWiki
Jump to navigationJump to search
Line 71: Line 71:
  
 
TAB1
 
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'' '''8 to 10 total digits is fine--k'''
+
* '''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'' '''8 to 10 total digits is fine--k'''
'''Process_term''' -- processterm --  text
+
*'''Process_term''' -- processterm --  text
'''Summary''' -- summary --  big text
+
*'''Summary''' -- summary --  big text
'''Other_name''' -- othername -- big text, values will be pipe separated
+
*'''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'' no, on process_term--k'' so it works ok ? -- J''
+
*'''Related_process''' -- relprocess -- XREF to WBProcess -multi-ontology field, autocomplete on Process_term ''not on other_name ? -- J'' no, on process_term--k'' so it works ok ? -- 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'' sent the file to you today, --k ''please let me know where the file is on tazendra or mangolassi, also some columns don't have a value for col2. we just store column 2 in postgres ? -- 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'' sent the file to you today, --k ''please let me know where the file is on tazendra or mangolassi, also some columns don't have a value for col2. we just store column 2 in postgres ? -- J''
'''WBProcess''' -- wbprocess -- ontology autocomplete on process_term ''same as the related_process ontology ? -- J'' '''remove this table,  it is not necessary --k'''
+
*'''WBProcess''' -- wbprocess -- ontology autocomplete on process_term ''same as the related_process ontology ? -- J'' '''remove this table,  it is not necessary --k'''
'''Remark''' -- remark -- big text  
+
*'''Remark''' -- remark -- big text  
 
   
 
   
 
TAB2
 
TAB2
'''WBPaper''' -- paper -- ontology autocomplete on WBPaperID; term info-WBProcess, Gene
+
*'''WBPaper''' -- paper -- ontology autocomplete on WBPaperID; term info-WBProcess, Gene
'''Gene''' -- wbgene -- multi-ontology autocomplete on public_name; term info- name, WBGeneID, WBProcess
+
*'''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'' ok--k
+
*'''''Expression_cluster''' -- exprcluster -- multi-ontology -doesn't exist yet'' ''text until your file is ready for obo_ table -- J'' ok--k
'''Interaction''' -- interaction -- multi-ontology, autocomplete on interactionID, 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'' '''changed from autocomplete on gene to autocomplete on interaction, does this still need me to talk to the interaction curator?--k'''
+
*'''Interaction''' -- interaction -- multi-ontology, autocomplete on interactionID, 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'' '''changed from autocomplete on gene to autocomplete on interaction, does this still need me to talk to the interaction curator?--k'''
'''Anatomy_term''' -- anat_term --  multi-ontology autocomplete on name; term info- name
+
*'''Anatomy_term''' -- anat_term --  multi-ontology autocomplete on name; term info- name
'''Life_stage''' -- lifestage -- 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
+
*'''Molecule''' -- molecule -- multi-ontology  autocomplete on name and synonym; term info- molecule ID, name, synonym
 
   
 
   
 
TAB3
 
TAB3
'''Phenotype''' -- phenotype -- multi-ontology  autocomplete on name and synonym; term info -description
+
*'''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
+
*'''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''
+
*'''''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
+
*'''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''
+
*'''''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 Database''' --pathwaydb -- ontology  autocomplete on name  ''text until your file is ready for obo_ table -- J''
'''Pathway accession''' -- pathwayacc -- text
+
*'''Pathway accession''' -- pathwayacc -- text
'''Curator''' -- curator -- dropdown ''missing from specs, added here -- J''
+
*'''Curator''' -- curator -- dropdown ''missing from specs, added here -- J''
 
   
 
   
 
[[Category: Process page]]
 
[[Category: Process page]]

Revision as of 23:14, 19 September 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 -- 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 8 to 10 total digits is fine--k
  • 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 no, on process_term--k so it works ok ? -- 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 sent the file to you today, --k please let me know where the file is on tazendra or mangolassi, also some columns don't have a value for col2. we just store column 2 in postgres ? -- J
  • WBProcess -- wbprocess -- ontology autocomplete on process_term same as the related_process ontology ? -- J remove this table, it is not necessary --k
  • 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 ok--k
  • Interaction -- interaction -- multi-ontology, autocomplete on interactionID, 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 changed from autocomplete on gene to autocomplete on interaction, does this still need me to talk to the interaction curator?--k
  • 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