Difference between revisions of "Molecule model build"
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///////////////////////////small molecule/chemical/drug //////////////////////////// | ///////////////////////////small molecule/chemical/drug //////////////////////////// | ||
// | // | ||
| − | // ? | + | // ?Molecule |
// * metabolites: precursors, intermediates, or end products of a metabolic pathway | // * 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?? | // * monomeric or very small oligomeric nucleic acids (not RNAi primers), e.g. ATP, ADP, cAMP, GTP, trinucleotide repeats?? | ||
| Line 30: | Line 30: | ||
// | // | ||
//////////////////////////////////////////////////////////////////////////////////// | //////////////////////////////////////////////////////////////////////////////////// | ||
| − | ? | + | ?Molecule Name ?Text |
| + | Public_name ?Text | ||
Synonym ?Text | Synonym ?Text | ||
DB_info Database ?Database ?Database_field ?Accession_number | DB_info Database ?Database ?Database_field ?Accession_number | ||
| Line 40: | Line 41: | ||
==Model elements== | ==Model elements== | ||
| − | * Name-> | + | * Name-> WBMolID |
| − | * Public name -> | + | * Public name -> common name in elegans literature |
* Synonym -> other names, how do we mine these from other DBs? | * 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 | * DB_info -> links to entity in other database add following databases to database.ace | ||
| Line 52: | Line 53: | ||
** KDR http://www.kdr.co.kr | ** KDR http://www.kdr.co.kr | ||
*** for daumone http://www.kdr.co.kr/Daumone/main.asp | *** for daumone http://www.kdr.co.kr/Daumone/main.asp | ||
| − | If a | + | If a Molecule tag is added to the following classes, do we need a XREF in the Sm_molecule model? |
* Phenotype Phenotype_assay ?Phenotype_info | * Phenotype Phenotype_assay ?Phenotype_info | ||
* Gene_regulation --to annotate chemicals as regulators of gene activity | * Gene_regulation --to annotate chemicals as regulators of gene activity | ||
| Line 77: | Line 78: | ||
---- | ---- | ||
| + | ==Anthony's notes== | ||
==Chris's notes== | ==Chris's notes== | ||
Revision as of 07:56, 16 March 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.
///////////////////////////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 Sm_molecule #Phenotype_info #Evidence -- Add Sm_molecule to Phenotype Assay? If so, do we need a XREF here?
Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator #Evidence
//Microarray_experiment -- can this be done by adding Sm_molecule to ?Condition?
Reference ?Paper XREF Sm_molecule
///////////////////////////////////////////////////////////////////////////////////
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
If a Molecule tag is added to the following classes, do we need a XREF in the Sm_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
- 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
