Molecule model build

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

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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 //need to figure out how this link works,  ideally we would like to link to the actual entity page in the other database, not the front page of the data base. 
               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.

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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

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