Difference between revisions of "Molecule model build"

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----
 
----
 
==Proposed starting model==
 
==Proposed starting model==
 +
This model the addresses 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>
 +
Original model proposed by Anthony so that small molecules can be included on process pages<br>
 +
// ?Molecule<br>
 +
//        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 pages, so the following model omits the process page XREF.<br>
 +
  
 
  ///////////////////////////small molecule/chemical/drug ////////////////////////////
 
  ///////////////////////////small molecule/chemical/drug ////////////////////////////
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  // ?Sm_molecule
 
  // ?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  
 
  ?Sm_molecule Name ?Text  
 
  Synonym ?Text  
 
  Synonym ?Text  
−
  DB_info Database ?Database ?Database_field ?Accession_number //need to figure out how this link works,  ideally we would like to link to the actual entity page in the other database, not the front page of the data base.
+
  DB_info Database ?Database ?Database_field ?Accession_number // link to the actual entity page in the DB 
−
                 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 //Follows 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 //Follows 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?  
+
                 //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 <br>
+
----
 +
 
 +
Small 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
 +
 
 +
----
 +
 
 +
Name = WBSMol ID <br>
 
Common name = most prevalent name in elegans literature <br>
 
Common name = most prevalent name in elegans literature <br>
−
Synonym = other names mined from other databases, literature, etc. <br>
+
Synonym = other names mined from other databases, literature, etc. :: how to mine these names in bulk? <br>
−
DB_info  = mappings chemical databases <br>
+
DB_info  = mappings to chemical databases, see databases to add via database.ace file below, no XREF needed? <br>
−
Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule <br>
+
Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule ::  no XREF needed in Phenotype_info<br>
−
Gene_regulation Regulator_chemical ?Gene_regulation to annotate chemical based gene regulation<br>
+
Gene_regulation Regulator_chemical ?Gene_regulation :: to annotate chemical based gene regulation :: XREF needed<br>
 
Microarray_experiment ?Condition to capture chemical/drug treatment to large scale gene expression studies?<br>
 
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.<br>
+
Paper for referencing papers that contain metabolite, exogenous chemical/drug treatment that is not taken care of by any other tag here :: XREF needed<br>
 
----
 
----
 +
 +
Databases
 +
 +
* ChEBI
 +
**does not have daumone, ascarosides
 +
* PubChem
 +
** has ascarosides but might not be the ones purified from elegans
 +
* KDR
 +
** for daumone http://www.kdr.co.kr/Daumone/main.asp
  
 
==Model elements==
 
==Model elements==

Revision as of 15:50, 15 March 2010

links to relevant pages
Caltech documentation
Overview of molecule pages
Example molecule pages

Proposed starting model

This model the addresses small_molecule class, or part of it, that was discussed in the 2007 WB grant.
Propose a shorter name if you care to.


Original model proposed by Anthony so that small molecules can be included on process pages
// ?Molecule
// 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 pages, so the following model omits the process page XREF.


///////////////////////////small molecule/chemical/drug ////////////////////////////
// 
// ?Sm_molecule
//  
//
////////////////////////////////////////////////////////////////////////////////////
?Sm_molecule	Name ?Text 
		Synonym ?Text 
		DB_info Database ?Database ?Database_field ?Accession_number // link to the actual entity page in the DB  
               Phenotype ?Phenotype XREF Sm_molecule #Phenotype_info #Evidence //Follows example from other Phenotype_info Phenotype_assay tags 
               Gene_regulation gene_activity_regulator ?Gene_regulation XREF Sm_molecule_regulator //Follows example of other objects in Regulator sub-class of gene regulation 
               //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.    
///////////////////////////////////////////////////////////////////////////////////

Small 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

Name = WBSMol ID
Common name = most prevalent name in elegans literature
Synonym = other names mined from other databases, literature, etc. :: how to mine these names in bulk?
DB_info = mappings to chemical databases, see databases to add via database.ace file below, no XREF needed?
Phenotype Phenotype_assay ?Phenotype_info XREF Sm_molecule :: no XREF needed in Phenotype_info
Gene_regulation Regulator_chemical ?Gene_regulation :: to annotate chemical based gene regulation :: XREF needed
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 :: XREF needed

Databases

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

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