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


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


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


Chris's notes

Jolene's notes

Raymond's notes

Karen's notes

General concerns and comments