Difference between revisions of "WormBase Model:Molecule"

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== Models==
 
== Models==
  
−
===WS252 (proposed)===
+
===WS254===
−
see [[Molecule#Changes_for_WS252 |  Molecule wiki]]
+
<pre>
 +
?Molecule Name ?Text //WBMoleculeID
 +
          Public_name ?Text
 +
          Formula ?Text //imported from ChEBI
 +
          Monoisotopic_mass ?Float //need to set up automated calculation based on formula
 +
          IUPAC ?Text //imported from ChEBI
 +
          SMILES ?Text //imported from ChEBI
 +
          InChi ?Text //imported from ChEBI
 +
          InChiKey ?Text //imported from ChEBI
 +
          Synonym ?Text //mainly from CTD, but also from papers and ChEBI
 +
          DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, UniProt
 +
          Status Detected #Evidence
 +
                Predicted #Evidence
 +
          Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics
 +
          Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid
 +
          Nonspecies_source ?Text //xenobiotic, antibiotic, drug, chemical synthesis, toxin, pollutant, food additive, food, hydrocarbon, pesticide, antihelmintic
 +
          Endogenous_in ?Species #Evidence
 +
          Biofunction_role Metabolite ?Text #Evidence
 +
                          Regulator ?Text #Evidence
 +
                          Structural_component ?Text #Evidence
 +
                          Cofactor ?Text #Evidence
 +
                          Activator ?Text #Evidence
 +
                          Inhibitor ?Text #Evidence
 +
                          Product ?Text #Evidence
 +
                          Substrate ?Text #Evidence
 +
                          Ligand ?Text #Evidence
 +
                          Receptor ?Text #Evidence
 +
          Essential_for ?Species #Evidence
 +
          WBProcess ?WBProcess XREF Molecule
 +
          Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule    // Wen WS228
 +
          Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence
 +
                              Strain ?Strain ?Phenotype #Evidence
 +
                              Transgene ?Transgene ?Phenotype #Evidence
 +
                              RNAi ?RNAi ?Phenotype #Evidence
 +
                              Rearrangement ?Rearrangement ?Phenotype #Evidence
 +
          Interaction ?Interaction XREF Molecule_interactor // Chris WS244
 +
          Molecule_use ?Text #Evidence
 +
          Reference ?Paper XREF Molecule
 +
          Remark
 +
</pre>
 +
 
 +
===WS252===
 +
<pre>
 +
?Molecule Name ?Text //WBMoleculeID
 +
          Public_name ?Text
 +
          Formula ?Text //imported from ChEBI
 +
          Monoisotopic_mass ?Float //need to set up automated calculation based on formula
 +
          IUPAC ?Text //imported from ChEBI
 +
          SMILES ?Text //imported from ChEBI
 +
          InChi ?Text //imported from ChEBI
 +
          InChiKey ?Text //imported from ChEBI
 +
          Synonym ?Text //mainly from CTD, but also from papers and ChEBI
 +
          DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, etc
 +
          Status Detected #Evidence
 +
                Predicted #Evidence
 +
          Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics
 +
          Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid
 +
          Nonspecies_source ?Text
 +
          Chemical_synthesis #Evidence
 +
          Endogenous_in ?Species #Evidence
 +
          Biofunction_role Metabolite ?Text #Evidence
 +
                          Regulator ?Text #Evidence
 +
                          Structural_component ?Text #Evidence
 +
                          Cofactor ?Text #Evidence
 +
                          Activator ?Text #Evidence
 +
                          Inhibitor ?Text #Evidence
 +
                          Product ?Text #Evidence
 +
                          Substrate ?Text #Evidence
 +
                          Ligand ?Text #Evidence
 +
                          Receptor ?Text #Evidence
 +
          Essential_for ?Species #Evidence
 +
          WBProcess ?WBProcess XREF Molecule
 +
          Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule    // Wen WS228
 +
          Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence
 +
                              Strain ?Strain ?Phenotype #Evidence
 +
                              Transgene ?Transgene ?Phenotype #Evidence
 +
                              RNAi ?RNAi ?Phenotype #Evidence
 +
                              Rearrangement ?Rearrangement ?Phenotype #Evidence
 +
          Interaction ?Interaction XREF Molecule_interactor // Chris WS244
 +
          Molecule_use ?Text #Evidence
 +
          Reference ?Paper XREF Molecule
 +
          Remark
 +
</pre>
  
 
===WS235===
 
===WS235===

Latest revision as of 23:29, 15 March 2016

WormBase Models

Curator Comments/Description

Molecule wiki
postgres molecule tables

Models

WS254

?Molecule Name ?Text //WBMoleculeID
          Public_name ?Text
          Formula ?Text //imported from ChEBI
          Monoisotopic_mass ?Float //need to set up automated calculation based on formula
          IUPAC ?Text //imported from ChEBI
          SMILES ?Text //imported from ChEBI
          InChi ?Text //imported from ChEBI
          InChiKey ?Text //imported from ChEBI
          Synonym ?Text //mainly from CTD, but also from papers and ChEBI
          DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, UniProt
          Status Detected #Evidence
                 Predicted #Evidence
          Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics
          Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid
          Nonspecies_source ?Text //xenobiotic, antibiotic, drug, chemical synthesis, toxin, pollutant, food additive, food, hydrocarbon, pesticide, antihelmintic
          Endogenous_in ?Species #Evidence
          Biofunction_role Metabolite ?Text #Evidence
                           Regulator ?Text #Evidence
                           Structural_component ?Text #Evidence
                           Cofactor ?Text #Evidence
                           Activator ?Text #Evidence
                           Inhibitor ?Text #Evidence
                           Product ?Text #Evidence
                           Substrate ?Text #Evidence
                           Ligand ?Text #Evidence
                           Receptor ?Text #Evidence
          Essential_for ?Species #Evidence
          WBProcess ?WBProcess XREF Molecule
          Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule    // Wen WS228
          Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence
                               Strain ?Strain ?Phenotype #Evidence
                               Transgene ?Transgene ?Phenotype #Evidence
                               RNAi ?RNAi ?Phenotype #Evidence
                               Rearrangement ?Rearrangement ?Phenotype #Evidence
          Interaction ?Interaction XREF Molecule_interactor // Chris WS244
          Molecule_use ?Text #Evidence
          Reference ?Paper XREF Molecule
          Remark

WS252

?Molecule Name ?Text //WBMoleculeID
          Public_name ?Text
          Formula ?Text //imported from ChEBI
          Monoisotopic_mass ?Float //need to set up automated calculation based on formula
          IUPAC ?Text //imported from ChEBI
          SMILES ?Text //imported from ChEBI
          InChi ?Text //imported from ChEBI
          InChiKey ?Text //imported from ChEBI
          Synonym ?Text //mainly from CTD, but also from papers and ChEBI
          DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, etc
          Status Detected #Evidence
                 Predicted #Evidence
          Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics
          Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid
          Nonspecies_source ?Text
          Chemical_synthesis #Evidence
          Endogenous_in ?Species #Evidence
          Biofunction_role Metabolite ?Text #Evidence
                           Regulator ?Text #Evidence
                           Structural_component ?Text #Evidence
                           Cofactor ?Text #Evidence
                           Activator ?Text #Evidence
                           Inhibitor ?Text #Evidence
                           Product ?Text #Evidence
                           Substrate ?Text #Evidence
                           Ligand ?Text #Evidence
                           Receptor ?Text #Evidence
          Essential_for ?Species #Evidence
          WBProcess ?WBProcess XREF Molecule
          Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule    // Wen WS228
          Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence
                               Strain ?Strain ?Phenotype #Evidence
                               Transgene ?Transgene ?Phenotype #Evidence
                               RNAi ?RNAi ?Phenotype #Evidence
                               Rearrangement ?Rearrangement ?Phenotype #Evidence
          Interaction ?Interaction XREF Molecule_interactor // Chris WS244
          Molecule_use ?Text #Evidence
          Reference ?Paper XREF Molecule
          Remark

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 by Wen


WS224

Interaction ?Interaction XREF Molecule_interactor       // Chris WS244

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 release that included data

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