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==
 
This model addresses the small_molecule class, or part of it, that was discussed in the 2007 WB grant.<br>
 
''Propose a shorter name if you care to.''<br>
 
-----<br>
 
This is the original model proposed by Anthony so that small molecules can be included on process pages<br>
 
//<br>
 
// ?Molecule<br>
 
//        Name ?Text<br>
 
//        Public_name ?Text<br>
 
//        Synonym ?Text<br>
 
//        DB_info Database ?Database ?Database_field ?Accession_number<br>
 
//        Involved_in_process ?WBProcess XREF Molecule<br>
 
//<br>
 
If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to <br>
 
be attached directly to the process model, so the following model omits the WBProcess XREF.<br>
 
  
 
///////////////////////////small molecule/chemical/drug ////////////////////////////
 
//
 
// ?Sm_molecule
 
//  * metabolites: precursors, intermediates, or end products of a metabolic pathway
 
//  * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats??
 
//  * chemicals/drugs
 
//  * minerals, ions, salts
 
//
 
////////////////////////////////////////////////////////////////////////////////////
 
?Sm_molecule Name ?Text
 
Synonym ?Text
 
DB_info Database ?Database ?Database_field ?Accession_number
 
                //Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence -- Add Sm_molecule to Phenotype Assay? If so, do we need a XREF here?
 
                Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator #Evidence
 
                //Microarray_experiment -- can this be done by adding Sm_molecule to  ?Condition?
 
                Reference ?Paper XREF Sm_molecule
 
///////////////////////////////////////////////////////////////////////////////////
 
 
==Model elements==
 
* Name->  WBSMolID, is this necessary?
 
* Public name -> prevalent name in elegans literature, or is this redundant with Synonym?
 
* Synonym -> other names, how do we mine these from other DBs?
 
* DB_info  -> links to entity in other database add following databases to database.ace
 
** ChEBI ''used in Reactome'' http://www.ebi.ac.uk/chebi/init.do
 
***does not have daumone, ascarosides
 
** KEGG COMPOUND ''used in Reactome/ nemapath'' http://www.genome.jp/kegg/
 
** PubChem  ''used in Reactome'' hhtp://www.pubchem.ncbi.nlm.nih.gov/
 
*** has ascarosides but might not be the ones purified from elegans
 
** Klotho (?)''used for BioCyc'' http://www.biocheminfo.org/klotho/accession_table.html
 
** KDR http://www.kdr.co.kr
 
*** for daumone http://www.kdr.co.kr/Daumone/main.asp
 
If a Sm_molecule tag is added to the following classes, do we need a XREF in the Sm_molecule model? 
 
* Phenotype Phenotype_assay ?Phenotype_info
 
* Gene_regulation  --to annotate chemicals as regulators of gene activity
 
* 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
 
 
===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
 
* 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