Molecule model build

links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages

---

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 XREF Sm_molecule #Phenotype_info #Evidence //Following example from other Phenotype_info Phenotype_assay tags
               Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Following example of other objects in Regulator sub-class of gene regulation
               //we need to also link sm_molecule to Microarray_experiment.  can this be done through ?Condition? 
               Reference ?Paper XREF Sm_molecule #Evidence //This is to attach a sm_molecule to a paper in a similar way to attaching a gene to a paper, not to make a reference to this sm_molecule itself.    
///////////////////////////////////////////////////////////////////////////////////

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

---