Molecule model build

From WormBaseWiki
Jump to navigationJump to search

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


Proposed starting model

This model addresses the small_molecule class, or part of it, that was discussed in the 2007 WB grant.
Propose a shorter name if you care to.



This is the original model proposed by Anthony so that small molecules can be included on process pages
//
// ?Molecule
// Name ?Text
// Public_name ?Text
// Synonym ?Text
// DB_info Database ?Database ?Database_field ?Accession_number
// Involved_in_process ?WBProcess XREF Molecule
//
If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to
be attached directly to the process model, so the following model omits the WBProcess XREF.


///////////////////////////small molecule/chemical/drug ////////////////////////////
// 
// ?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
//
////////////////////////////////////////////////////////////////////////////////////
?Molecule	Name ?Text 
               Public_name ?Text
		Synonym ?Text 
		DB_info Database ?Database ?Database_field ?Accession_number 
               //Phenotype ?Phenotype XREF Molecule #Phenotype_info #Evidence 
               Gene_regulation gene_activity_regulator ?Gene_regulation XREF Molecule_regulator #Evidence
               //Microarray_experiment -- can this be done by adding Molecule to  ?Condition? 
               Reference ?Paper XREF Molecule
///////////////////////////////////////////////////////////////////////////////////

Model elements

If a Molecule tag is added to the following classes, do we need a XREF in the 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


Anthony's notes

Chris's notes

Jolene's notes

Raymond's notes

Karen's notes

General concerns and comments