Package ubic.gemma.core.loader.genome.gene.ncbi.model

Class NCBIGeneInfo

java.lang.Object
ubic.gemma.core.loader.genome.gene.ncbi.model.NCBIGeneInfo
public class NCBIGeneInfo extends Object

See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README 

   ===========================================================================
   gene_info
   ---------------------------------------------------------------------------
   This file can be considered as the logical equivalent of
   ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL.out
   tab-delimited
   one line per GeneID
   ---------------------------------------------------------------------------
   tax_id:
   the unique identifier provided by NCBI Taxonomy
   for the species or strain/isolate
   GeneID:
   the unique identifier for a gene
   ASN1:  geneid
   --note:  for genomes previously available from LocusLink,
   the identifiers are equivalent
   Symbol:
   the default symbol for the gene
   ASN1:  gene->locus
   LocusTag:
   the LocusTag value
   ASN1:  gene->locus-tag
   Synonyms:
   bar-delimited set of unoffical symbols for the gene
   dbXrefs:
   bar-delimited set of identifiers in other databases
   for this gene.  The unit of the set is database:value.
   chromosome:
   the chromosome on which this gene is placed
   map location:
   the map location for this gene
   description
   a descriptive name for this gene
   type of gene:
   the type assigned to the gene according to the list of options
   provided in http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
   Symbol from nomenclature authority:
   when not '-', indicates that this symbol is from a
   a nomenclature authority
   Full name from nomenclature authority:
   when not '-', indicates that this full name is from a
   a nomenclature authority
   Nomenclature status
   when not '-', indicates the status of the name from the
   nomenclature authority (O for official, I for interim)
Author:
pavlidis

  • Constructor Details

    • NCBIGeneInfo

      public NCBIGeneInfo()

  • Method Details

    • typeStringToGeneType

      public static NCBIGeneInfo.GeneType typeStringToGeneType(String typeString)
      Convert string to GeneType. See http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/objects/entrezgene/entrezgene.asn
      Parameters:
      typeString - type string
      Returns:
      gene type

    • addToDbXRefs

      public void addToDbXRefs(String dbName, String identifier)

    • addToSynonyms

      public void addToSynonyms(String synonym)

    • getChromosome

      public String getChromosome()
      Returns:
      Returns the chromosome.

    • setChromosome

      public void setChromosome(String chromosome)
      Parameters:
      chromosome - The chromosome to set.

    • getDbXrefs

      public Map<String,String> getDbXrefs()
      Returns:
      Returns the dbXrefs.

    • getDefaultSymbol

      public String getDefaultSymbol()
      Returns:
      Returns the defaultSymbol.

    • setDefaultSymbol

      public void setDefaultSymbol(String defaultSymbol)
      Parameters:
      defaultSymbol - The defaultSymbol to set.

    • getDescription

      public String getDescription()
      Returns:
      Returns the description.

    • setDescription

      public void setDescription(String description)
      Parameters:
      description - The description to set.

    • getDiscontinuedId

      public String getDiscontinuedId()
      Returns:
      The NCBI gene ID that was 'discontinued' for the gene that match this symbol and taxon. These correspond to the lines in gene_history that have a '-' in the second column. But because we are matching only on the symbol+taxon, we have to be a bit careful using it.

    • setDiscontinuedId

      public void setDiscontinuedId(String discontinuedIdForGene)

    • getEnsemblId

      public String getEnsemblId()

    • setEnsemblId

      public void setEnsemblId(String ensemblId)

    • getGeneId

      public String getGeneId()
      Returns:
      Returns the geneId.

    • setGeneId

      public void setGeneId(String geneId)
      Parameters:
      geneId - The geneId to set.

    • getGeneType

      public NCBIGeneInfo.GeneType getGeneType()
      Returns:
      Returns the geneType.

    • setGeneType

      public void setGeneType(NCBIGeneInfo.GeneType geneType)
      Parameters:
      geneType - The geneType to set.

    • getHistory

      public NcbiGeneHistory getHistory()
      Returns:
      the history

    • setHistory

      public void setHistory(NcbiGeneHistory history)
      Parameters:
      history - the history to set

    • getLocusTag

      public String getLocusTag()
      Returns:
      Returns the locusTag.

    • setLocusTag

      public void setLocusTag(String locusTag)
      Parameters:
      locusTag - The locusTag to set.

    • getMapLocation

      public String getMapLocation()
      Returns:
      Returns the mapLocation.

    • setMapLocation

      public void setMapLocation(String mapLocation)
      Parameters:
      mapLocation - The mapLocation to set.

    • getNomenclatureStatus

      public NCBIGeneInfo.NomenclatureStatus getNomenclatureStatus()
      Returns:
      Returns the nomenclatureStatus.

    • setNomenclatureStatus

      public void setNomenclatureStatus(NCBIGeneInfo.NomenclatureStatus nomenclatureStatus)
      Parameters:
      nomenclatureStatus - The nomenclatureStatus to set.

    • getSynonyms

      public Collection<String> getSynonyms()
      Returns:
      Returns the synonyms.

    • getTaxId

      public int getTaxId()
      Returns:
      Returns the taxId.

    • setTaxId

      public void setTaxId(int taxId)
      Parameters:
      taxId - The taxId to set.

    • isNameIsFromAuthority

      public boolean isNameIsFromAuthority()
      Returns:
      Returns the nameIsFromAuthority.

    • setNameIsFromAuthority

      public void setNameIsFromAuthority(boolean nameIsFromAuthority)
      Parameters:
      nameIsFromAuthority - The nameIsFromAuthority to set.

    • isSymbolIsFromAuthority

      public boolean isSymbolIsFromAuthority()
      Returns:
      Returns the symbolIsFromAuthority.

    • setSymbolIsFromAuthority

      public void setSymbolIsFromAuthority(boolean symbolIsFromAuthority)
      Parameters:
      symbolIsFromAuthority - The symbolIsFromAuthority to set.