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Current status of the LocusLink / Entrez Gene Transition Last updated March 8, 2005.

  1. Record Content
  2. FTP files

The purpose of this page is to provide a single site to check the current status of replacing LocusLink with Entrez Gene. The LocusLink interface was discontinued Tuesday, March 1, 2005. Only two ftp files continue to be refreshed: LL_tmpl and LocusID_history.

LocusID-specific queries of the format

  • http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=[LocusID]
    are now redirected to Entrez Gene as
  • http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=[LocusID].
    The last LocusLink ftp files generated March 1, 2005, were moved to the ARCHIVE subdirectory. The version of LL_tmpl for that date was renamed LL_tmpl_050301.gz

    We do have a category in our feedback/corrections form to allow you to register your suggestions about LocusLink/Entrez Gene, namely:

    item 2. What type of information are you submitting? ---> Comment on LocusLink/Entrez Gene

    We appreciate your suggestions and comments. We recognize that this transition may be difficult, but the staff of the LocusLink/Entrez Gene team is dedicated to maintaining the highest level of accuracy, completeness, and usability. By incorporating the data from LocusLink in an Entrez database with gene-specific data from other species, you now have a single point of lookup for gene-specific information for the taxa within the scope of the RefSeq project. You also have more immediate access to related data that was cumbersome to maintain independent of Entrez, and can harness the power of Entrez-based tools such as Entrez Programming Utilities (E-Utilities) and MyNCBI.

    Changes in Record Content back to top
    ElementLocusLinkEntrez Gene
    GeneRIF
    Gene References into Function    		 GeneRIF content was removed from LocusLink display but made available one click away via the Gene button. The GRIF content was removed from the LL_tmpl file November 4, 2004, and is no longer indexed to support retrieval of LocusLink records based on GeneRIF content. GeneRIFs can now be added to any record in Gene. More NEWENTRY records have been added to support submission of GeneRIFs for taxa in Gene's scope, but for which the Gene record does not exist.
    CDD
    Conserved Domain Database    		 CDD content removed from LocusLink display on September 9, 2004, but made available one click away via the Gene button. The CDD content is no longer reported in the LL_tmpl file which means that queries against LocusLink that depended on domain data will no longer return results. More.. Conserved Domain Data are available in Entrez Gene in several contexts:
    • As attributes of RefSeq proteins in the NCBI Reference Sequences section of the Gene record.
    • From the Links menu (Conserved Domains)
    • From the Protein Links menu attached to the RefSeq protein accession in the Transcripts and Products section of the Gene report.
    Scope of LL_tmpl Records for Drosophila melanogaster and Caenorhabiditis elegans were removed from the LL_tmpl report on March 7, 2005. The data in the archive file of LL_tmpl_050301.gz can be used to retrieve the data that are no longer being reported in LL_tmpl, because data for those genomes had not been updated in LocusLink recently. Gene-specific information for Drosophila melanogaster and Caenorhabiditis elegans is updated regularly in Entrez Gene.
    FTP Files Connect to the LocusLink or Gene directory. back to top
    LocusLink file nameEntrez Gene file nameComments
    LL_tmpl GeneRIF/generifs_basic.gz This file extracts the equivalent of the GRIF tag in the LL_tmpl file and reports text of the GeneRIF and the associated PubMed ids.
    DATA/ASN Files in this directory contain comprehensive extractions from Entrez Gene in ASN.1 format.
    LL.out_* gene_info GeneID, names, map locations, and database cross-reference.
    loc2acc gene2accession gene2accession includes the data in gene2refseq above. If you want to convert any accessions into GeneIDs, this one file should suffice.
    loc2cit gene2pubmed gene2pubmed includes the identifier for the species of the GeneID (i.e. the Taxonomy ID).
    loc2go gene2go GeneID / GO ID / Evidence Code
    Consolidated summary based on gene_association files from the GO Consortium and Entrez Gene's gene_info file. Differs from loc2go in supplying qualifiers of the GeneID/GO ID relationship, and the GO term itself.
    loc2ref gene2refseq The file in Entrez Gene does not include information about secondary accessions. This function is now provided from the RefSeq ftp site, as documented in the current release notes: ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release#.txt, where # is the value of the current release number.
    loc2sts gene2sts GeneID / UniSTS marker ID relationship
    loc2UG gene2unigene GeneID / UniGene cluster relationship
    mim2loc mim2gene GeneID / MIM number relationship