Difference between revisions of "WormBase Model:Molecule"

From WormBaseWiki
Jump to navigationJump to search
Line 10: Line 10:
  
 
===WS251 (proposed)===
 
===WS251 (proposed)===
−
Based on conversations with Michael Witting to bring in metabolites for C. elegans<br>
+
see [[Molecule#Changes_for_WS251 | Molecule wiki]]
−
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>
 
−
?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
 
−
        //need to add in numeric (float) fields to capture concentrations or ranges
 
−
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?
 
−
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
 
−
        Gene_regulation Gene_regulator ?Gene_regulation XREF Molecule_regulator
 
−
        Affects_phenotype_of    Variation ?Variation ?Phenotype #Evidence //Change to Causes_phenotype ?Phenotype_info XREF Caused_by_molecule #Evidence for PATO?
 
−
                                    Strain    ?Strain    ?Phenotype #Evidence
 
−
                                    Transgene ?Transgene ?Phenotype #Evidence
 
−
                                    RNAi      ?RNAi      ?Phenotype #Evidence
 
−
        Affected_by_genetics ?Phenotype_info XREF Molecule_affected #Evidence //added by Chris for PATO constructions
 
−
        Molecule_use  ?Text  #Evidence
 
−
        Remark ?Text #Evidence
 
−
</pre>
 
  
 
===WS235===
 
===WS235===

Revision as of 22:47, 27 August 2015

WormBase Models

Curator Comments/Description

Molecule wiki
postgres molecule tables

Models

WS251 (proposed)

see Molecule wiki

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

Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase_Model:Molecule&oldid=27591"