Molecule model build

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


Approved model

This model addresses the small_molecule class, or part of it, that was discussed in the 2007 WB grant.



///////////////////////////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 
               Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator 
	      Affects_phenotype_of 	Variation ?Variation  #Evidence
					Strain	?Strain	#Evidence
					Transgene ?Transgene #Evidence
					RNAi ?RNAi #Evidence
///////////////////////////////////////////////////////////////////////////////////

Corresponding changes in touched models

/////
?Phenotype_info    Affected_by  Molecule  ?Molecule    #Evidence
/////
/////
?Gene_regulation  Regulator Molecule_regulator   ?Molecule  XREF  Gene_regulator  #Boolean 
/////

Model elements

  • Name-> MeSH UID
  • Public name -> common name in elegans literature
  • 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