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 addresses the 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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This is the original model proposed by Anthony so that small molecules can be included on process pages
//
// ?Molecule
// Name ?Text
// Public_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 model, so the following model omits the WBProcess XREF.

///////////////////////////small molecule/chemical/drug ////////////////////////////
// 
// ?Sm_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
//
////////////////////////////////////////////////////////////////////////////////////
?Sm_molecule	Name ?Text 
		Synonym ?Text 
		DB_info Database ?Database ?Database_field ?Accession_number 
               //Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence -- Add Sm_molecule to Phenotype Assay? If so, do we need a XREF here?
               Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator #Evidence
               //Microarray_experiment -- can this be done by adding Sm_molecule to  ?Condition? 
               Reference ?Paper XREF Sm_molecule
///////////////////////////////////////////////////////////////////////////////////

Model elements

• Name-> WBSMolID, is this necessary?
• Public name -> prevalent name in elegans literature, or is this redundant with Synonym?
• Synonym -> other names, how do we mine these from other DBs?
• DB_info -> links to entity in other database add following databases to database.ace
  • ChEBI used in Reactome http://www.ebi.ac.uk/chebi/init.do
    • does not have daumone, ascarosides
  • KEGG COMPOUND used in Reactome/ nemapath http://www.genome.jp/kegg/
  • PubChem used in Reactome hhtp://www.pubchem.ncbi.nlm.nih.gov/
    • has ascarosides but might not be the ones purified from elegans
  • Klotho (?)used for BioCyc http://www.biocheminfo.org/klotho/accession_table.html
  • KDR http://www.kdr.co.kr
    • for daumone http://www.kdr.co.kr/Daumone/main.asp

If a Sm_molecule tag is added to the following classes, do we need a XREF in the Sm_molecule model?

• Phenotype Phenotype_assay ?Phenotype_info
• Gene_regulation --to annotate chemicals as regulators of gene activity
• 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

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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