Difference between revisions of "Molecule model build"
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///////////////////////////small molecule/chemical/drug //////////////////////////// | ///////////////////////////small molecule/chemical/drug //////////////////////////// | ||
// | // | ||
| − | // ?Sm_molecule | + | // ?Sm_molecule (taken from the WB grant, this model is supposed to represent the proposed small_molecule class, but that name alone is a bit long given the latest feedback of other model names, so if you can propose something shorter and still meaningful, feel free, or let the group decide. |
// | // | ||
//////////////////////////////////////////////////////////////////////////////////// | //////////////////////////////////////////////////////////////////////////////////// | ||
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sm_molecule_phenotype_interaction | sm_molecule_phenotype_interaction | ||
/////////////////////////////////////////////////////////////////////////////////// | /////////////////////////////////////////////////////////////////////////////////// | ||
| + | ---- | ||
| + | ==Model elements== | ||
| + | Name-> do we want a WBID for this class<br> | ||
| + | Synonym -> public/common names<br> | ||
| + | DB_info links to other databases and database ID's <br> | ||
| + | * ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do | ||
| + | * KEGG COMPOUND ''used in Reactome/ nemapath'' http://www.genome.jp/kegg/ | ||
| + | * PubChem ''used in Reactome'' hhtp://www.pubchem.ncbi.nlm.nih.gov/ | ||
| + | * Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html | ||
| + | |||
| + | |||
| + | |||
| + | ===Possible model elements=== | ||
| + | KEGG ID (enzyme classification) , Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now. <br> | ||
| + | Vendors/Sources //This information should be linked to a particular experiment and therefore paper.<br> | ||
| + | * Sigma-Aldrich | ||
| + | * MP Biochemicals | ||
| + | * Calbiochem | ||
| + | * ZINC | ||
| + | |||
| + | Other databases | ||
| + | * Enzyme database? http://ca.expasy.org/enzyme/enzyme-bycompound.html | ||
| + | * DrugBank ''found in pubchem'' http://www.drugbank.ca/ | ||
| + | * LeadScope ''found in pubchem'' http://www.leadscope.com/ | ||
| + | * EPA ''found in pubchem'' http://www.epa.gov/ncct/dsstox/ | ||
| + | * NIH Small molecule repository ''found in pubchem'' http://mlsmr.glpg.com/MLSMR_HomePage/ | ||
| + | * Nature chemical biology ''found in pubchem'' http://www.nature.com/nchembio/index.html | ||
| + | * NIH chemical genomics center ''found in pubchem'' http://ncgc.nih.gov/db/ | ||
| + | * see pubchem compounds for more | ||
| + | |||
---- | ---- | ||
Revision as of 21:32, 2 March 2010
links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages
Contents
Proposed starting model
///////////////////////////small molecule/chemical/drug ////////////////////////////
//
// ?Sm_molecule (taken from the WB grant, this model is supposed to represent the proposed small_molecule class, but that name alone is a bit long given the latest feedback of other model names, so if you can propose something shorter and still meaningful, feel free, or let the group decide.
//
////////////////////////////////////////////////////////////////////////////////////
?Sm_molecule Name ?Text
Synonym ?Text
DB_info Database ?Database ?Database_field ?Accession_number
Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence
sm_molecule_phenotype_interaction
///////////////////////////////////////////////////////////////////////////////////
Model elements
Name-> do we want a WBID for this class
Synonym -> public/common names
DB_info links to other databases and database ID's
- ChEBI used in Reactome http://www.ebi.ac.uk/chebi/init.do
- KEGG COMPOUND used in Reactome/ nemapath http://www.genome.jp/kegg/
- PubChem used in Reactome hhtp://www.pubchem.ncbi.nlm.nih.gov/
- Klotho (?)used for BioCyc http://www.biocheminfo.org/klotho/accession_table.html
Possible model elements
KEGG ID (enzyme classification) , Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now.
Vendors/Sources //This information should be linked to a particular experiment and therefore paper.
- Sigma-Aldrich
- MP Biochemicals
- Calbiochem
- ZINC
Other databases
- Enzyme database? http://ca.expasy.org/enzyme/enzyme-bycompound.html
- DrugBank found in pubchem http://www.drugbank.ca/
- LeadScope found in pubchem http://www.leadscope.com/
- EPA found in pubchem http://www.epa.gov/ncct/dsstox/
- NIH Small molecule repository found in pubchem http://mlsmr.glpg.com/MLSMR_HomePage/
- Nature chemical biology found in pubchem http://www.nature.com/nchembio/index.html
- NIH chemical genomics center found in pubchem http://ncgc.nih.gov/db/
- see pubchem compounds for more
