Difference between revisions of "Topic pages"
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Jump to navigationJump to searchm (New page: =Goals of the process pages= * Portal for larger biomedical community into C. elegans gene function.<br> * Context for experimental data such as microarray results * On the fly update adde...) |
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| + | ''back to''' [[Caltech documentation]]<br> | ||
| + | ''Other process related pages''<br> | ||
| + | *[[Example process pages]] | ||
| + | *[[WBProcess Model build]] | ||
| + | |||
=Goals of the process pages= | =Goals of the process pages= | ||
* Portal for larger biomedical community into C. elegans gene function.<br> | * Portal for larger biomedical community into C. elegans gene function.<br> | ||
| − | * Context for | + | * 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 <br> | * On the fly update addendum to WormBook chapters <br> | ||
**process pages will dissect the chapters and link them to entities in WormBase, | **process pages will dissect the chapters and link them to entities in WormBase, | ||
| − | **process pages will | + | **process pages will link summaries of processed with the most recent acedb data |
| − | |||
* Home for pathway views of data from Reactome, BioCyc, and Nemapath | * Home for pathway views of data from Reactome, BioCyc, and Nemapath | ||
| Line 11: | Line 15: | ||
===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. | ||
| − | |||
===Genes=== | ===Genes=== | ||
| Line 29: | Line 32: | ||
* Mined through gene GO assignments | * Mined through gene GO assignments | ||
| − | + | ===GO biological processes=== | |
* Embedded gene ontology window pointing to relevant GO biological process and genes. | * 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 | * 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. | * 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) | * 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. | * 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. | * Drug/chemical/small molecule, CHEBI_ID, with references. | ||
* [[Molecule model build]] | * [[Molecule model build]] | ||
| − | + | ===Genetic interactions=== | |
| − | |||
| − | |||
* Manually associated | * Manually associated | ||
* With the process with references. | * 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) | * Expression clusters only (all microarray experiments should have these cluster views of the results) | ||
* link to SPELL page for microarray data | * link to SPELL page for microarray data | ||
| Line 61: | Line 64: | ||
* Other pathways: Reactome | * Other pathways: Reactome | ||
| − | + | ===Resources=== | |
* WormBook (Viewed as WormBook chapter title and author (WBPerson/Author page)) | * WormBook (Viewed as WormBook chapter title and author (WBPerson/Author page)) | ||
* WormAtlas (WormAtlas page(s) link, display page title) | * WormAtlas (WormAtlas page(s) link, display page title) | ||
Revision as of 19:51, 26 February 2010
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 of page elements
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.
- Molecule model build
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)
