Molecule model build

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links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages


Proposed starting model

///////////////////////////small molecule/chemical/drug ////////////////////////////
// 
// ?Sm_molecule
//  
// This model is supposed to represent the proposed small_molecule class that was discussed in WB 
// 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.
// // This model is also only taking into account metabolites and exogenous chemical/drug treatment, not gene products that play enzymatic // roles, gene or gene product regulation, or interactions. // //////////////////////////////////////////////////////////////////////////////////// ?Sm_molecule Name ?Text Synonym ?Text DB_info Database ?Database ?Database_field ?Accession_number Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule #Evidence Gene_regulation Regulator_chemical ?Gene_regulation XREF Microarray_experiment ?Condition Paper ///////////////////////////////////////////////////////////////////////////////////

Name = WBSMa ID Common name = most prevalent name in elegans literature Synonym = other names mined from other databases, literature, etc. DB_info = mappings chemical databases Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here.


Model elements

Name-> do we want a WBID for this class
Synonym -> public/common names
DB_info links to other databases and database ID's


Possible model elements

KEGG ID (enzyme classification) , Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now.
Vendors/Sources //This information should be linked to a particular experiment and therefore paper.

  • Sigma-Aldrich
  • MP Biochemicals
  • Calbiochem
  • ZINC

Other databases


Chris's notes

Jolene's notes

Raymond's notes

Karen's notes

General concerns and comments