Difference between revisions of "Molecule model build"
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///////////////////////////small molecule/chemical/drug //////////////////////////// | ///////////////////////////small molecule/chemical/drug //////////////////////////// | ||
// | // | ||
− | // ?Sm_molecule | + | // ?Sm_molecule |
+ | // | ||
+ | // This model is supposed to represent the proposed small_molecule class that was discussed in WB <br> | ||
+ | // but that name alone is a bit long given the latest feedback of other model names, so please propose something shorter if you care to.<br> | ||
+ | // | ||
+ | // This model is also only taking into account metabolites and exogenous chemical/drug treatment, not gene products that play enzymatic | ||
+ | // roles, gene or gene product regulation, or interactions. | ||
// | // | ||
//////////////////////////////////////////////////////////////////////////////////// | //////////////////////////////////////////////////////////////////////////////////// | ||
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DB_info Database ?Database ?Database_field ?Accession_number | DB_info Database ?Database ?Database_field ?Accession_number | ||
Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence | Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence | ||
− | + | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule #Evidence | |
+ | Gene_regulation Regulator_chemical ?Gene_regulation XREF | ||
+ | Microarray_experiment ?Condition | ||
+ | Paper | ||
/////////////////////////////////////////////////////////////////////////////////// | /////////////////////////////////////////////////////////////////////////////////// | ||
+ | |||
+ | Name = WBSMa ID | ||
+ | Common name = most prevalent name in elegans literature | ||
+ | Synonym = other names mined from other databases, literature, etc. | ||
+ | DB_info = mappings chemical databases | ||
+ | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule | ||
+ | Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation | ||
+ | Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies | ||
+ | Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here. | ||
---- | ---- | ||
+ | |||
==Model elements== | ==Model elements== | ||
Name-> do we want a WBID for this class<br> | Name-> do we want a WBID for this class<br> |
Revision as of 20:08, 10 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 // // This model is supposed to represent the proposed small_molecule class that was discussed in WB
// but that name alone is a bit long given the latest feedback of other model names, so please propose something shorter if you care to.
// // This model is also only taking into account metabolites and exogenous chemical/drug treatment, not gene products that play enzymatic // roles, gene or gene product regulation, or interactions. // //////////////////////////////////////////////////////////////////////////////////// ?Sm_molecule Name ?Text Synonym ?Text DB_info Database ?Database ?Database_field ?Accession_number Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule #Evidence Gene_regulation Regulator_chemical ?Gene_regulation XREF Microarray_experiment ?Condition Paper ///////////////////////////////////////////////////////////////////////////////////
Name = WBSMa ID Common name = most prevalent name in elegans literature Synonym = other names mined from other databases, literature, etc. DB_info = mappings chemical databases Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here.
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