Difference between revisions of "Molecule model build"

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''links to relevant pages''<br>
 
[[Caltech documentation]] <br>
 
[[Overview of molecule pages]]<br>
 
[[Example molecule pages]]<br>
 
----
 
==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 <br>
 
Synonym ?Text <br>
 
DB_info Database ?Database ?Database_field ?Accession_number
 
Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence
 
                Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Following example from other Phenotype_info Phenotype_assay tags
 
                Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Following example of other objects in Regulator sub-class of gene regulation
 
                //we need to also link sm_molecule to Microarray_experiment.  can this be done through ?Condition?
 
                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.   
 
///////////////////////////////////////////////////////////////////////////////////
 
 
Name = WBSMa ID <br>
 
Common name = most prevalent name in elegans literature <br>
 
Synonym = other names mined from other databases, literature, etc. <br>
 
DB_info  = mappings chemical databases  <br>
 
Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule <br>
 
Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation<br>
 
Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies?<br>
 
Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here.<br>
 
----
 
 
==Model elements==
 
Name-> do we want a WBID for this class<br>
 
Synonym -> public/common names<br>
 
DB_info  links to other databases and database ID's  <br>
 
* ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do
 
* KEGG COMPOUND ''used in Reactome/ nemapath'' http://www.genome.jp/kegg/
 
* PubChem  ''used in Reactome'' hhtp://www.pubchem.ncbi.nlm.nih.gov/
 
* Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html
 
 
 
 
===Possible model elements===
 
KEGG ID  (enzyme classification) ,  Gene product KEGG enzyme assignments been supplied by Makedonka and is in the database now.  <br>
 
Vendors/Sources //This information should be linked to a particular experiment and therefore paper.<br>
 
* Sigma-Aldrich
 
* MP Biochemicals
 
* Calbiochem
 
* ZINC
 
 
Other databases
 
* Enzyme database?  http://ca.expasy.org/enzyme/enzyme-bycompound.html
 
* DrugBank ''found in pubchem'' http://www.drugbank.ca/
 
* LeadScope ''found in pubchem'' http://www.leadscope.com/
 
* EPA ''found in pubchem'' http://www.epa.gov/ncct/dsstox/
 
* NIH Small molecule repository ''found in pubchem'' http://mlsmr.glpg.com/MLSMR_HomePage/
 
* Nature chemical biology ''found in pubchem'' http://www.nature.com/nchembio/index.html
 
* NIH chemical genomics center ''found in pubchem'' http://ncgc.nih.gov/db/
 
* see pubchem compounds for more
 
 
----
 
 
==Chris's notes==
 
 
==Jolene's notes==
 
 
==Raymond's notes==
 
 
==Karen's notes==
 
 
==General concerns and comments==
 

Latest revision as of 23:38, 6 July 2010