Difference between revisions of "Topic pages"
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'''Other_name''' big text, values will be pipe separated | '''Other_name''' big text, values will be pipe separated | ||
'''Related_process''' XREF to WBProcess -multi-ontology field, autocomplete on Process_term | '''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'' | + | '''''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''' ontology autocomplete on process_term | '''WBProcess''' ontology autocomplete on process_term | ||
'''Remark''' big text | '''Remark''' big text | ||
Line 83: | Line 83: | ||
'''WBPaper''' ontology autocomplete on WBPaperID; term info-WBProcess, Gene | '''WBPaper''' ontology autocomplete on WBPaperID; term info-WBProcess, Gene | ||
'''Gene''' multi-ontology autocomplete on public_name; term info- name, WBGeneID, WBProcess | '''Gene''' multi-ontology autocomplete on public_name; term info- name, WBGeneID, WBProcess | ||
− | '''''Expression_cluster''' multi-ontology -doesn't exist yet'' | + | '''''Expression_cluster''' multi-ontology -doesn't exist yet'' ''text until your file is ready for obo_ table -- J'' |
'''Interaction''' multi-ontology, autocomplete on gene, term info- WBPaperID, all interactors, and interaction type. | '''Interaction''' multi-ontology, autocomplete on gene, term info- WBPaperID, all interactors, and interaction type. | ||
'''Anatomy_term''' multi-ontology autocomplete on name; term info- name | '''Anatomy_term''' multi-ontology autocomplete on name; term info- name | ||
Line 92: | Line 92: | ||
'''Phenotype''' multi-ontology autocomplete on name and synonym; term info -description | '''Phenotype''' multi-ontology autocomplete on name and synonym; term info -description | ||
'''GO_term''' 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?)'' | + | '''''Human_disease''' multi-ontology autocomplete on name and synonym (does one exist?)'' ''text until your file is ready for obo_ table -- J'' |
'''Picture''' multi-ontology from picture OA table autocomplete on WBPaperID; term info -WBPicture, description, Expression pattern | '''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'' | + | '''''Movie''' multi-ontology autocomplete on ID doesn't exist yet'' ''text until your file is ready for obo_ table -- J'' |
− | '''Pathway Database''' ontology autocomplete on name | + | '''Pathway Database''' ontology autocomplete on name ''text until your file is ready for obo_ table -- J'' |
'''Pathway accession''' text | '''Pathway accession''' text | ||
[[Category: Process page]] | [[Category: Process page]] |
Revision as of 13:05, 6 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 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 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 text until your file is ready for obo_ table -- J 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 text until your file is ready for obo_ table -- J 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?) text until your file is ready for obo_ table -- J 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 text until your file is ready for obo_ table -- J Pathway Database ontology autocomplete on name text until your file is ready for obo_ table -- J Pathway accession text