Molecule model build

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

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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.

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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.

?Molecule Name ?Text ... Variation ?Variation XREF Molecule Strain ?Strain XREF Molecule ... Phenotype ?Phenotype XREF Molecule

?Variation Phenotype ?Phenotype XREF Variation Molecule ?Molecule XREF Variation

?Phenotype Molecule ?Molecule XREF Phenotype Variation ?Variation XREF Phenotype Strain ?Strain XREF Phenotype ...

Mol1 - Var1 - Phe1 Mol1 - Var1 - Phe3 Mol1 - Var2 - Phe1 Mol1 - Var2 - Phe3 Mol2 - Var1 - Phe2

Mol1 - Var1 Mol1 - Var2 Mol2 - Var1 Mol1 - Phe1 Mol1 - Phe3 Mol1 - Phe3 Mol2 - Phe2 Var1 - Phe1 Var2 - Phe2 Var1 - Phe3 Var2 - Phe1 Var2 - Phe3

?Triplet_text Variation_comma_delimited Text

?Triple Some_Id Variation_comma_delimited<tab>"molecule_name, variation_name, phenotype_name"

///////////////////////////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 
	       Effects_phenotype_of 	Variation ?Variation XREF Variation #Phenotype_hash
					Strain	?Strain	#Evidence
					Transgene ?Transgene #Evidence 
					RNAi ?RNAi #Evidence 
               Reference ?Paper XREF Molecule #Evidence
///////////////////////////////////////////////////////////////////////////////////

?Phenotype_hash Phenotype ?Phenotype

?Phenotype_info Molecule ?Molecule #Evidence

Molecule "Molecule_id" Variation "Variation_id" Phenotype "Phenotype_id"

Variation "Variation_id" Phenotype "Phenotype_id" Molecule "Molecule_id"

Corresponding changes in touched models

/////
?Phenotype_info    Regulated_by  Molecule  ?Molecule    #Evidence
/////

/////
?Gene_regulation  Regulator Molecule_regulator   ?Molecule  XREF  Gene_regulator  #Boolean 
/////

/////
?Paper   Refers_to  Molecule ?Molecule XREF Reference 
/////

Model elements

• Name-> WBMolID
• 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
  • 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

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

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