Difference between revisions of "WormBase Model:Molecule"

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== Models==
 
== Models==
  
===WS251 (proposed)===
+
===WS254===
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
 
 
<pre>
 
<pre>
?Molecule
+
?Molecule Name ?Text //WBMoleculeID
Public_name ?Text
+
          Public_name ?Text
Formula UNIQUE ?Text
+
          Formula ?Text //imported from ChEBI
Monoisotopic_mass UNIQUE ?Text
+
          Monoisotopic_mass ?Float //need to set up automated calculation based on formula
IUPAC UNIQUE ?Text
+
          IUPAC ?Text //imported from ChEBI
SMILES ?Text //not unique, there may be many SMILES strings for a given molecule
+
          SMILES ?Text //imported from ChEBI
InChi UNIQUE?Text
+
          InChi ?Text //imported from ChEBI
    InChi_key UNIQUE ?Text
+
          InChiKey ?Text //imported from ChEBI
Synonym ?Text
+
          Synonym ?Text //mainly from CTD, but also from papers and ChEBI
DB_info Database ?Database ?Database_field ?Text
+
          DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, UniProt
Status Detected #Evidence
+
          Status Detected #Evidence
Predicted #Evidence
+
                Predicted #Evidence
Classified_as ?Database ?Database_field ?Text //for ChEBI or other database classification system
+
          Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics
Source Endogenous ?Species #Evidence //produced within animal
+
          Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid
Exogenous #Evidence //produced by other living being
+
          Nonspecies_source ?Text //xenobiotic, antibiotic, drug, chemical synthesis, toxin, pollutant, food additive, food, hydrocarbon, pesticide, antihelmintic
Pharmaceutical #Evidence //e.g., synthetic drug
+
          Endogenous_in ?Species #Evidence
                        Industrial #Evidence // e.g., inorganic substance
+
          Biofunction_role Metabolite ?Text #Evidence
Ligand_for Gene_product_receptor ?Gene Receptor_for_molecule #Evidence  
+
                          Regulator ?Text #Evidence
Molecule_receptor ?Molecule XREF Receptor_for_molecule #Evidence  
+
                          Structural_component ?Text #Evidence
        Causes_phenotype ?Phenotype_info XREF Caused_by_molecule #Evidence //added by Chris for PATO constructions
+
                          Cofactor ?Text #Evidence
        Affected_by_genetics ?Phenotype_info XREF Molecule_affected #Evidence //added by Chris for PATO constructions
+
                          Activator ?Text #Evidence
Pathway_database ?Database ?Database_field ?Text  //for importing KEGG pathways, for example
+
                          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>
 
</pre>
  
Line 40: Line 97:
 
  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
 
===WS228===
 
===WS228===
<pre style="white-space: pre-wrap;
+
  Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Added for molecule regulation of gene expression by Wen
white-space: -moz-pre-wrap;
+
 
white-space: -pre-wrap;
 
white-space: -o-pre-wrap;
 
word-wrap: break-word;">
 
Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule //Added for molecule regulation of gene expression
 
</pre>
 
===WS227===
 
Rearrangement  ?Rearrangement  ?Phenotype  #Evidence  //KY [110602 pad]
 
  
 +
===WS224===
 +
Interaction ?Interaction XREF Molecule_interactor      // Chris WS244
 
===WS217(original)===
 
===WS217(original)===
 
<pre>
 
<pre>
Line 76: Line 128:
 
==Unused tags==
 
==Unused tags==
  
WS219 is the 1st data release that included data
+
WS219 is the 1st release that included data

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