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>
 
  
 
?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
 
      Affects_phenotype_of Variation ?Variation ?Phenotype #Phenotype_info
 
Strain ?Strain ?Phenotype #Phenotype_info
 
Transgene ?Transgene ?Phenotype #Phenotype_info
 
RNAi ?RNAi ?Phenotype #Phenotype_info
 
///////////////////////////////////////////////////////////////////////////////////
 
 
 
 
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->  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
 
**Comparative Toxicogenomic Database http://ctd.mdibl.org/
 
***downloads from http://ctd.mdibl.org/downloads/ 
 
***MeSH UIDs
 
 
===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
 
** 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
 
* 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
 
 
----
 
 
==Anthony's notes==
 
 
==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