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
−
        //need to add in numeric (float) fields to capture concentrations or ranges
+
          Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics
−
Classified_as ?Database ?Database_field ?Text //for ChEBI or other database classification system; may be too complicated, any given molecule can be classified as many things within any given database, need to capture all classifications? also if classified through an ontology, what level do we take?  
+
          Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid
−
Source Endogenous ?Species #Evidence //produced within animal
+
          Nonspecies_source ?Text //xenobiotic, antibiotic, drug, chemical synthesis, toxin, pollutant, food additive, food, hydrocarbon, pesticide, antihelmintic
−
Exogenous #Evidence //produced by other living being
+
          Endogenous_in ?Species #Evidence
−
Pharmaceutical #Evidence //e.g., synthetic drug
+
          Biofunction_role Metabolite ?Text #Evidence
−
                        Industrial #Evidence // e.g., inorganic substance
+
                          Regulator ?Text #Evidence
−
Ligand_for Gene_product_receptor ?Gene Receptor_for_molecule #Evidence  
+
                          Structural_component ?Text #Evidence
−
Molecule_receptor ?Molecule XREF Receptor_for_molecule #Evidence  
+
                          Cofactor ?Text #Evidence
−
        Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator
+
                          Activator ?Text #Evidence
−
        Affects_phenotype_of     Variation ?Variation ?Phenotype #Evidence //Change to Causes_phenotype ?Phenotype_info XREF Caused_by_molecule #Evidence for PATO?
+
                          Inhibitor ?Text #Evidence
−
                                    Strain   ?Strain   ?Phenotype #Evidence
+
                          Product ?Text #Evidence
−
                                    Transgene ?Transgene ?Phenotype #Evidence
+
                          Substrate ?Text #Evidence
−
                                    RNAi     ?RNAi     ?Phenotype #Evidence  
+
                          Ligand ?Text #Evidence
−
        Affected_by_genetics ?Phenotype_info XREF Molecule_affected #Evidence //added by Chris for PATO constructions
+
                          Receptor ?Text #Evidence
−
        Molecule_use ?Text #Evidence
+
          Essential_for ?Species #Evidence
−
        Remark ?Text #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 46: 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>
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==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

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