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 | ||
| − | =Summary of page | + | =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 | ||
| + | '''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=== | ===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. | ||
Revision as of 23:17, 30 August 2011
back to' Caltech documentation
Other process related pages
Contents
- 1 Goals of the process pages
- 2 WBProcess OA
- 2.1 Cells / Anatomy
- 2.2 GO biological processes
- 2.3 Phenotypes
- 2.4 Chemicals/small molecules
- 2.5 Genetic interactions
- 2.6 Microarray experiments
- 2.7 Related human disease
- 2.8 Pathway/Reaction
- 2.9 Resources
- 2.10 Process OA
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
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 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.
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)
