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| − | ''links to relevant pages''<br>
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| − | [[Caltech documentation]] <br>
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| − | [[Overview of molecule pages]]<br>
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| − | [[Example molecule pages]]<br>
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| − | ----
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| − | ==Proposed starting model==
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| − | This model the addresses small_molecule class, or part of it, that was discussed in the 2007 WB grant.<br>
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| − | ''Propose a shorter name if you care to.''<br>
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| − | -----<br>
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| − | Original model proposed by Anthony so that small molecules can be included on process pages<br>
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| − | // ?Molecule<br>
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| − | // Name ?Text<br>
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| − | // Synonym ?Text<br>
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| − | // DB_info Database ?Database ?Database_field ?Accession_number<br>
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| − | // Involved_in_process ?WBProcess XREF Molecule<br>
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| − | // -----<br>
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| − | If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to <br>
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| − | be attached directly to the process pages, so the following model omits the process page XREF.<br>
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| − |
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| − | ///////////////////////////small molecule/chemical/drug ////////////////////////////
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| − | //
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| − | // ?Sm_molecule
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| − | //
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| − | //
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| − | ////////////////////////////////////////////////////////////////////////////////////
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| − | ?Sm_molecule Name ?Text
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| − | Synonym ?Text
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| − | DB_info Database ?Database ?Database_field ?Accession_number // link to the actual entity page in the DB
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| − | Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Follows example from other Phenotype_info Phenotype_assay tags
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| − | Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Follows example of other objects in Regulator sub-class of gene regulation
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| − | //Microarray_experiment. can this be done through ?Condition?
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| − | 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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| − | ///////////////////////////////////////////////////////////////////////////////////
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| − |
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| − | ----
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| − |
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| − | Small Molecule:
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| − | * metabolites: precursors, intermediates, or end products of a metabolic pathway
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| − | * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
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| − | * chemicals/drugs
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| − | * minerals, ions, salts
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| − |
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| − | ----
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| − |
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| − | Name = WBSMol ID <br>
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| − | Common name = most prevalent name in elegans literature <br>
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| − | Synonym = other names mined from other databases, literature, etc. :: how to mine these names in bulk? <br>
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| − | DB_info = mappings to chemical databases, see databases to add via database.ace file below, no XREF needed? <br>
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| − | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule :: no XREF needed in Phenotype_info<br>
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| − | Gene_regulation Regulator_chemical ?Gene_regulation :: to annotate chemical based gene regulation :: XREF needed<br>
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| − | Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies?<br>
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| − | Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here :: XREF needed<br>
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| − | ----
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| − |
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| − | Databases
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| − |
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| − | * ChEBI
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| − | **does not have daumone, ascarosides
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| − | * PubChem
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| − | ** has ascarosides but might not be the ones purified from elegans
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| − | * KDR
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| − | ** for daumone http://www.kdr.co.kr/Daumone/main.asp
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| − |
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| − | ==Model elements==
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| − | Name-> do we want a WBID for this class<br>
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| − | Synonym -> public/common names<br>
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| − | DB_info links to other databases and database ID's <br>
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| − | * ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do
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| − | * KEGG COMPOUND ''used in Reactome/ nemapath'' http://www.genome.jp/kegg/
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| − | * PubChem ''used in Reactome'' hhtp://www.pubchem.ncbi.nlm.nih.gov/
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| − | * Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html
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| − |
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| − |
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| − |
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| − | ===Possible model elements===
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| − | KEGG ID (enzyme classification) , Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now. <br>
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| − | Vendors/Sources //This information should be linked to a particular experiment and therefore paper.<br>
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| − | * Sigma-Aldrich
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| − | * MP Biochemicals
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| − | * Calbiochem
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| − | * ZINC
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| − |
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| − | Other databases
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| − | * Enzyme database? http://ca.expasy.org/enzyme/enzyme-bycompound.html
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| − | * DrugBank ''found in pubchem'' http://www.drugbank.ca/
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| − | * LeadScope ''found in pubchem'' http://www.leadscope.com/
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| − | * EPA ''found in pubchem'' http://www.epa.gov/ncct/dsstox/
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| − | * NIH Small molecule repository ''found in pubchem'' http://mlsmr.glpg.com/MLSMR_HomePage/
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| − | * Nature chemical biology ''found in pubchem'' http://www.nature.com/nchembio/index.html
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| − | * NIH chemical genomics center ''found in pubchem'' http://ncgc.nih.gov/db/
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| − | * see pubchem compounds for more
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| − |
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| − | ----
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| − |
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| − | ==Chris's notes==
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| − |
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| − | ==Jolene's notes==
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| − |
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| − | ==Raymond's notes==
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| − |
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| − | ==Karen's notes==
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| − |
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| − | ==General concerns and comments==
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