Difference between revisions of "WormBase Model:Molecule"

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[[Molecule#mop_tables|postgres molecule tables]]
 
[[Molecule#mop_tables|postgres molecule tables]]
  
== Model ==
+
== Models==
<pre>
 
//////////////////////////////////////////////////
 
//
 
// Molecule class Model - Proposed by Karen Yook WS217
 
// Connects to: #Phenotype_info
 
//              ?Gene_regulation
 
//
 
//////////////////////////////////////////////////     
 
  
?Molecule  Name ?Text
+
===WS251 (proposed)===
          Public_name ?Text
 
          Synonym ?Text
 
          DB_info Database ?Database ?Database_field ?Accession_number
 
          Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator
 
          Affects_phenotype_of    Variation ?Variation ?Phenotype #Evidence
 
                                    Strain    ?Strain    ?Phenotype #Evidence
 
                                    Transgene ?Transgene ?Phenotype #Evidence
 
                                    RNAi      ?RNAi      ?Phenotype #Evidence
 
          Molecule_use  ?Text  #Evidence
 
          Remark ?Text #Evidence
 
 
 
</pre>
 
 
 
== Proposed Changes ==
 
===WS251===
 
 
Based on conversations with Michael Witting to bring in metabolites for C. elegans<br>
 
Based on conversations with Michael Witting to bring in metabolites for C. elegans<br>
 
These model changes add tags for curating molecules that are predicted or determined to be metabolites as well as more identifiers for all molecules
 
These model changes add tags for curating molecules that are predicted or determined to be metabolites as well as more identifiers for all molecules
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</pre>
 
</pre>
  
== Approved Changes ==
 
 
===WS235===
 
===WS235===
 
  Reference ?Paper XREF Molecule //Added ability to cite molecules used in a published study
 
  Reference ?Paper XREF Molecule //Added ability to cite molecules used in a published study
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===WS227===
 
===WS227===
 
  Rearrangement  ?Rearrangement  ?Phenotype  #Evidence  //KY [110602 pad]
 
  Rearrangement  ?Rearrangement  ?Phenotype  #Evidence  //KY [110602 pad]
 +
 +
===WS217(original)===
 +
<pre>
 +
//////////////////////////////////////////////////
 +
//
 +
// Molecule class Model - Proposed by Karen Yook WS217
 +
// Connects to: #Phenotype_info
 +
//              ?Gene_regulation
 +
//
 +
//////////////////////////////////////////////////     
 +
 +
?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
 +
          Affects_phenotype_of    Variation ?Variation ?Phenotype #Evidence
 +
                                    Strain    ?Strain    ?Phenotype #Evidence
 +
                                    Transgene ?Transgene ?Phenotype #Evidence
 +
                                    RNAi      ?RNAi      ?Phenotype #Evidence
 +
          Molecule_use  ?Text  #Evidence
 +
          Remark ?Text #Evidence
 +
 +
</pre>
  
 
==Unused tags==
 
==Unused tags==
  
WS219 is the 1st data release that this will be included in.
+
WS219 is the 1st data release that included data

Revision as of 00:15, 27 August 2015

WormBase Models

Curator Comments/Description

Molecule wiki
postgres molecule tables

Models

WS251 (proposed)

Based on conversations with Michael Witting to bring in metabolites for C. elegans
These model changes add tags for curating molecules that are predicted or determined to be metabolites as well as more identifiers for all molecules

?Molecule	
	Public_name	?Text
	Formula UNIQUE ?Text
	Monoisotopic_mass UNIQUE ?Text
	IUPAC UNIQUE ?Text
	SMILES ?Text  //not unique, there may be many SMILES strings for a given molecule
	InChi UNIQUE?Text
    InChi_key UNIQUE ?Text
	Synonym	?Text
	DB_info	Database	?Database	?Database_field	?Text
	Status 	Detected	#Evidence
			Predicted #Evidence
	Classified_as	?Database	?Database_field	?Text //for ChEBI or other database classification system
	Source	Endogenous ?Species #Evidence //produced within animal
			Exogenous #Evidence //produced by other living being
			Pharmaceutical #Evidence  //e.g., synthetic drug
                        Industrial #Evidence // e.g., inorganic substance
	Ligand_for Gene_product_receptor ?Gene Receptor_for_molecule #Evidence 
			Molecule_receptor ?Molecule XREF Receptor_for_molecule #Evidence 
	Pathway_database	?Database ?Database_field ?Text  //for importing KEGG pathways, for example

WS235

Reference ?Paper XREF Molecule //Added ability to cite molecules used in a published study

WS228

 Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Added for molecule regulation of gene expression

WS227

Rearrangement  ?Rearrangement  ?Phenotype  #Evidence  //KY [110602 pad]

WS217(original)

//////////////////////////////////////////////////
//
// Molecule class Model - Proposed by Karen Yook WS217
// Connects to: #Phenotype_info
//              ?Gene_regulation 
//
//////////////////////////////////////////////////      

?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
           Affects_phenotype_of     Variation ?Variation ?Phenotype #Evidence
                                    Strain    ?Strain    ?Phenotype #Evidence
                                    Transgene ?Transgene ?Phenotype #Evidence
                                    RNAi      ?RNAi      ?Phenotype #Evidence 
           Molecule_use  ?Text  #Evidence
           Remark ?Text #Evidence

Unused tags

WS219 is the 1st data release that included data