Package ubic.gemma.core.loader.association

Class NCBIGene2GOAssociationParser

java.lang.Object
ubic.gemma.core.loader.util.parser.BasicLineParser<Gene2GOAssociation>
ubic.gemma.core.loader.association.NCBIGene2GOAssociationParser
All Implemented Interfaces:
LineParser<Gene2GOAssociation>, Parser<Gene2GOAssociation>, QueuingParser<Gene2GOAssociation>
public class NCBIGene2GOAssociationParser extends BasicLineParser<Gene2GOAssociation> implements QueuingParser<Gene2GOAssociation>
This parses GO annotations from NCBI. See readme. 
 tax_id:
 the unique identifier provided by NCBI Taxonomy
 for the species or strain/isolate
 GeneID:
 the unique identifier for a gene
 --note:  for genomes previously available from LocusLink,
 the identifiers are equivalent
 GO ID:
 the GO ID, formatted as GO:0000000
 Evidence:
 the evidence code in the gene_association file
 Qualifier:
 a qualifier for the relationship between the gene
 and the GO term
 GO term:
 the term indicated by the GO ID
 PubMed:
 pipe-delimited set of PubMed uids reported as evidence
 for the association
 Category:
 the GO category (Function, Process, or Component)
Author:
keshav, pavlidis