Difference between revisions of "Molecule model build"
Line 19: | Line 19: | ||
If molecules can be attached to phenotypes, microarray, gene regulation, and papers, it does not need to <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> | 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" | ||
Line 35: | Line 78: | ||
DB_info Database ?Database ?Database_field ?Accession_number | DB_info Database ?Database ?Database_field ?Accession_number | ||
Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator | Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator | ||
− | Effects_phenotype_of Variation ?Variation # | + | Effects_phenotype_of Variation ?Variation XREF Variation #Phenotype_hash |
Strain ?Strain #Evidence | Strain ?Strain #Evidence | ||
Transgene ?Transgene #Evidence | Transgene ?Transgene #Evidence | ||
Line 41: | Line 84: | ||
Reference ?Paper XREF Molecule #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 | Corresponding changes in touched models |
Revision as of 21:04, 7 April 2010
links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages
Contents
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.
?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
- ChEBI used in Reactome http://www.ebi.ac.uk/chebi/init.do
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