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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
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− | Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence
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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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− | Name = WBSMa ID
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− | Common name = most prevalent name in elegans literature
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− | Synonym = other names mined from other databases, literature, etc.
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− | DB_info = mappings chemical databases
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− | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule
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− | Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation
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− | Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies?
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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.
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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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− | ===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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− | ==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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