Molecule model build

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

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Proposed starting model

This model the addresses small_molecule class, or part of it, that was discussed in the 2007 WB grant.
Propose a shorter name if you care to.

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Original model proposed by Anthony so that small molecules can be included on process pages
// ?Molecule
// Name ?Text
// Synonym ?Text
// DB_info Database ?Database ?Database_field ?Accession_number
// Involved_in_process ?WBProcess XREF Molecule
// -----
If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to
be attached directly to the process pages, so the following model omits the process page XREF.

///////////////////////////small molecule/chemical/drug ////////////////////////////
// 
// ?Sm_molecule
//  
//
////////////////////////////////////////////////////////////////////////////////////
?Sm_molecule	Name ?Text 
		Synonym ?Text 
		DB_info Database ?Database ?Database_field ?Accession_number // link to the actual entity page in the DB  
               Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Follows example from other Phenotype_info Phenotype_assay tags 
               Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Follows example of other objects in Regulator sub-class of gene regulation 
               //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.    
///////////////////////////////////////////////////////////////////////////////////

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Small Molecule:

• metabolites: precursors, intermediates, or end products of a metabolic pathway
• monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
• chemicals/drugs
• minerals, ions, salts

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Name = WBSMol ID
Common name = most prevalent name in elegans literature
Synonym = other names mined from other databases, literature, etc. :: how to mine these names in bulk?
DB_info = mappings to chemical databases, see databases to add via database.ace file below, no XREF needed?
Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule :: no XREF needed in Phenotype_info
Gene_regulation Regulator_chemical ?Gene_regulation :: to annotate chemical based gene regulation :: XREF needed
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 :: XREF needed

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Databases

• ChEBI
  • does not have daumone, ascarosides
• PubChem
  • has ascarosides but might not be the ones purified from elegans
• KDR
  • for daumone http://www.kdr.co.kr/Daumone/main.asp

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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