Molecule model build
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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
