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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 (taken from the WB grant, this model is supposed to represent the proposed small_molecule class, but that name alone is a bit long given the latest feedback of other model names, so if you can propose something shorter and still meaningful, feel free, or let the group decide.
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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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| − | sm_molecule_phenotype_interaction
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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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