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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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| | | | |
| − | ///////////////////////////small molecule/chemical/drug ////////////////////////////
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| − | //
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| − | // ?Sm_molecule
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| − | //
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| − | // This model is supposed to represent the proposed small_molecule class that was discussed in WB
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| − | // 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.
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| − | //
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| − | // This model is also only taking into account metabolites and exogenous chemical/drug treatment, not gene products that play enzymatic
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| − | // roles, gene or gene product regulation, or interactions.
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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 //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.
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| − | Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Following example from other Phenotype_info Phenotype_assay tags
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| − | Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Following example of other objects in Regulator sub-class of gene regulation
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| − | //we need to also link sm_molecule to 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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| − | Name = WBSMa 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. <br>
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| − | DB_info = mappings chemical databases <br>
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| − | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule <br>
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| − | Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation<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.<br>
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| − | ----
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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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| − | 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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