Difference between revisions of "WormBase Model:Molecule"
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Jump to navigationJump to search| Line 20: | Line 20: | ||
SMILES ?Text //not unique, there may be many SMILES strings for a given molecule | SMILES ?Text //not unique, there may be many SMILES strings for a given molecule | ||
InChi UNIQUE?Text | InChi UNIQUE?Text | ||
| − | + | InChi_key UNIQUE ?Text | |
Synonym ?Text | Synonym ?Text | ||
DB_info Database ?Database ?Database_field ?Text | DB_info Database ?Database ?Database_field ?Text | ||
Status Detected #Evidence | Status Detected #Evidence | ||
Predicted #Evidence | Predicted #Evidence | ||
| − | Classified_as ?Database ?Database_field ?Text //for ChEBI or other database classification system | + | //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 //this will be way too complicated, any given molecule is 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 | Source Endogenous ?Species #Evidence //produced within animal | ||
Exogenous #Evidence //produced by other living being | Exogenous #Evidence //produced by other living being | ||
| Line 32: | Line 33: | ||
Ligand_for Gene_product_receptor ?Gene Receptor_for_molecule #Evidence | Ligand_for Gene_product_receptor ?Gene Receptor_for_molecule #Evidence | ||
Molecule_receptor ?Molecule XREF Receptor_for_molecule #Evidence | Molecule_receptor ?Molecule XREF Receptor_for_molecule #Evidence | ||
| − | Causes_phenotype ?Phenotype_info XREF Caused_by_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 | Affected_by_genetics ?Phenotype_info XREF Molecule_affected #Evidence //added by Chris for PATO constructions | ||
| − | + | Molecule_use ?Text #Evidence | |
| + | Remark ?Text #Evidence | ||
</pre> | </pre> | ||
Revision as of 00:26, 27 August 2015
Contents
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
//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 //this will be way too complicated, any given molecule is 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
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
