Topic pages
From WormBaseWiki
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