Package org.biopax.paxtools.util

Class HGNC

java.lang.Object
org.biopax.paxtools.util.HGNC
public class HGNC extends Object
This class provides a mapping between HGNC IDs and Symbols. If JVM option paxtools.core.use-latest-genenames=ture, then it downloads the custom mapping data from genenames.org; otherwise will use previously downloaded built-in mapping file.
Author:
Ozgun Babur, Igor Rodchenkov

  • Field Details

  • Constructor Details

    • HGNC

      public HGNC()

  • Method Details

    • getSymbolByHgncIdOrSym

      public static String getSymbolByHgncIdOrSym(String idOrSymbol)
      Find HGNC Symbol by HGNC id or name (do not use NCBI/Entrez gene id as the input to avoid mistakes).
      Parameters:
      idOrSymbol - HGNC ID (with or without "HGNC:" banana) or gene symbol (e.g. previous version)
      Returns:
      primary HGNC gene symbol (if it's already the one, return the same)

    • getHgncId

      public static String getHgncId(String symbol)

    • getGeneId

      public static String getGeneId(String symbol)
      Provides NCBI (Entrez) Gene ID of the given gene symbol.
      Parameters:
      symbol - gene symbol
      Returns:
      EG ID

    • getSymbolByGeneId

      public static String getSymbolByGeneId(String id)

    • containsGeneId

      public static boolean containsGeneId(String id)