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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 addresses the 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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− | This is the original model proposed by Anthony so that small molecules can be included on process pages<br>
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− | //<br>
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− | // ?Molecule<br>
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− | // Name ?Text<br>
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− | // Public_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 model, so the following model omits the WBProcess XREF.<br>
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− | ?Molecule Name ?Text
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− | ...
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− | Variation ?Variation XREF Molecule
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− | Strain ?Strain XREF Molecule
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− | ...
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− | Phenotype ?Phenotype XREF Molecule
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− |
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− | ?Variation
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− | Phenotype ?Phenotype XREF Variation
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− | Molecule ?Molecule XREF Variation
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− |
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− | ?Phenotype
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− | Molecule ?Molecule XREF Phenotype
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− | Variation ?Variation XREF Phenotype
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− | Strain ?Strain XREF Phenotype
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− | ...
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− | Mol1 - Var1 - Phe1
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− | Mol1 - Var1 - Phe3
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− | Mol1 - Var2 - Phe1
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− | Mol1 - Var2 - Phe3
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− | Mol2 - Var1 - Phe2
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− |
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− | Mol1 - Var1
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− | Mol1 - Var2
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− | Mol2 - Var1
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− | Mol1 - Phe1
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− | Mol1 - Phe3
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− | Mol1 - Phe3
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− | Mol2 - Phe2
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− | Var1 - Phe1
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− | Var2 - Phe2
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− | Var1 - Phe3
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− | Var2 - Phe1
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− | Var2 - Phe3
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− |
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− | ?Triplet_text
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− | Variation_comma_delimited Text
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− | ?Triple Some_Id
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− | Variation_comma_delimited<tab>"molecule_name, variation_name, phenotype_name"
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− |
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− |
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− | ///////////////////////////small molecule/chemical/drug ////////////////////////////
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− | //
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− | // ?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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− | ?Molecule Name ?Text
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− | Public_name ?Text
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− | Synonym ?Text
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− | DB_info Database ?Database ?Database_field ?Accession_number
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− | Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator
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− | Effects_phenotype_of Variation ?Variation XREF Variation #Phenotype_hash
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− | Strain ?Strain #Evidence
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− | Transgene ?Transgene #Evidence
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− | RNAi ?RNAi #Evidence
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− | Reference ?Paper XREF Molecule #Evidence
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− | ///////////////////////////////////////////////////////////////////////////////////
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− |
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− | ?Phenotype_hash Phenotype ?Phenotype
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− |
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− | ?Phenotype_info
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− | Molecule ?Molecule #Evidence
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− |
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− | Molecule "Molecule_id"
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− | Variation "Variation_id" Phenotype "Phenotype_id"
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− |
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− | Variation "Variation_id"
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− | Phenotype "Phenotype_id" Molecule "Molecule_id"
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− |
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− | Corresponding changes in touched models
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− | /////
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− | ?Phenotype_info Regulated_by Molecule ?Molecule #Evidence
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− | /////
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− |
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− | /////
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− | ?Gene_regulation Regulator Molecule_regulator ?Molecule XREF Gene_regulator #Boolean
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− | /////
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− |
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− | /////
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− | ?Paper Refers_to Molecule ?Molecule XREF Reference
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− | /////
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− |
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− | ==Model elements==
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− | * Name-> WBMolID
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− | * Public name -> common name in elegans literature
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− | * Synonym -> other names, how do we mine these from other DBs?
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− | * DB_info -> links to entity in other database add following databases to database.ace
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− | ** ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do
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− | ***does not have daumone, ascarosides
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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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− | *** has ascarosides but might not be the ones purified from elegans
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− | ** Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html
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− | ** KDR http://www.kdr.co.kr
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− | *** for daumone http://www.kdr.co.kr/Daumone/main.asp
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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.
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− | * Vendors/Sources //This information should be linked to a particular experiment and therefore paper?
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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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− | ==Anthony's notes==
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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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