Difference between revisions of "Molecule model build"
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//////////////////////////////////////////////////////////////////////////////////// | //////////////////////////////////////////////////////////////////////////////////// | ||
− | ?Sm_molecule Name ?Text | + | ?Sm_molecule Name ?Text <br> |
− | Synonym ?Text | + | Synonym ?Text <br> |
− | DB_info Database ?Database ?Database_field ?Accession_number | + | DB_info Database ?Database ?Database_field ?Accession_number |
− | Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence | + | Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence |
− | Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Following example from other Phenotype_info Phenotype_assay tags | + | Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Following example from other Phenotype_info Phenotype_assay tags |
− | Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Following example of other objects in Regulator sub-class of gene regulation | + | Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Following example of other objects in Regulator sub-class of gene regulation |
//we need to also link sm_molecule to Microarray_experiment. can this be done through ?Condition? | //we need to also link sm_molecule to Microarray_experiment. can this be done through ?Condition? | ||
Reference ?Paper XREF Sm_molecule #Evidence //This is to attach a sm_molecule to a paper in a similar way to attaching a gene to a paper, not to make a reference to this sm_molecule itself. | Reference ?Paper XREF Sm_molecule #Evidence //This is to attach a sm_molecule to a paper in a similar way to attaching a gene to a paper, not to make a reference to this sm_molecule itself. | ||
/////////////////////////////////////////////////////////////////////////////////// | /////////////////////////////////////////////////////////////////////////////////// | ||
− | Name = WBSMa ID | + | Name = WBSMa ID <br> |
− | Common name = most prevalent name in elegans literature | + | Common name = most prevalent name in elegans literature <br> |
− | Synonym = other names mined from other databases, literature, etc. | + | Synonym = other names mined from other databases, literature, etc. <br> |
− | DB_info = mappings chemical databases | + | DB_info = mappings chemical databases <br> |
− | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule | + | Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule <br> |
− | Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation | + | Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation<br> |
− | Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies? | + | Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies?<br> |
− | Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here. | + | Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here.<br> |
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Revision as of 16:44, 11 March 2010
links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages
Contents
Proposed starting model
///////////////////////////small molecule/chemical/drug //////////////////////////// // // ?Sm_molecule // // This model is supposed to represent the proposed small_molecule class that was discussed in WB // but that name alone is a bit long given the latest feedback of other model names, so please propose something shorter if you care to. // // This model is also only taking into account metabolites and exogenous chemical/drug treatment, not gene products that play enzymatic // roles, gene or gene product regulation, or interactions. // //////////////////////////////////////////////////////////////////////////////////// ?Sm_molecule Name ?Text
Synonym ?Text
DB_info Database ?Database ?Database_field ?Accession_number Involved_in_process WBProcess ?WBProcess XREF Molecule #Evidence Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Following example from other Phenotype_info Phenotype_assay tags Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Following example of other objects in Regulator sub-class of gene regulation //we need to also link sm_molecule to Microarray_experiment. can this be done through ?Condition? Reference ?Paper XREF Sm_molecule #Evidence //This is to attach a sm_molecule to a paper in a similar way to attaching a gene to a paper, not to make a reference to this sm_molecule itself. ///////////////////////////////////////////////////////////////////////////////////
Name = WBSMa ID
Common name = most prevalent name in elegans literature
Synonym = other names mined from other databases, literature, etc.
DB_info = mappings chemical databases
Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule
Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation
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.
Model elements
Name-> do we want a WBID for this class
Synonym -> public/common names
DB_info links to other databases and database ID's
- ChEBI used in Reactome http://www.ebi.ac.uk/chebi/init.do
- KEGG COMPOUND used in Reactome/ nemapath http://www.genome.jp/kegg/
- PubChem used in Reactome hhtp://www.pubchem.ncbi.nlm.nih.gov/
- Klotho (?)used for BioCyc http://www.biocheminfo.org/klotho/accession_table.html
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