GENE INDEXING

Janice Ward

Indexer/Reviser

Index Section, NLM

LocusLink

http://www.ncbi.nlm.nih.gov/LocusLink/

• Developed by NCBI

• Provides single query interface about genetic loci

• Includes links to/from PubMed/MEDLINE citations

LocusLink Content

• LocusLink presents information on:– Official nomenclature & aliases– Sequence accessions– Phenotypes– EC & MIM numbers– UniGene clusters– Homology– Map locations– Related web sites

Organisms Included in LocusLink

• Current scope of LocusLink is five organisms– Fruit fly– Human– Mouse– Rat– Zebrafish

Gene Indexing

• MEDLINE indexers assist creation of LocusLink by performing gene indexing

• Gene indexing - Creating annotated links between records in LocusLink and MEDLINE citations which contain information about a gene or protein

Selection of Articles for Linking Restrictions

• Restricted to the five organisms currently in LocusLink

• Restricted to genes or proteins in which an unambiguous link can be made

Selection of Articles for LinkingCriteria

• Articles in which the basic biology of a gene or protein is a primary point

StructureIsolationFunction

• Most articles linked come from the preclinical literature -- few from the clinical

Gene Indexing Process

• Perform subject analysis of journal article• Recognize articles that report information about a

gene or protein appropriate for linking to LocusLink

• Search LocusLink for the gene or protein and create a link between LocusLink record and MEDLINE citation

• Provide short statement describing new information about gene or protein that is reported in article

Article to be linked

Gene Tab in DCMS

DCMS Gene Indexing Panel

DCMS LocusLink Query

LocusLink Record in DCMS

Full LocusLink Record

Gene Record added to DCMS

Completed Link

PubMed Link

LinkOut from PubMed

LinkOut from PubMed

LocusLink Record

Gene Indexing

• In-house indexers trained at beginning of December 2001

• 417 items gene indexed in December 2001

• 438 items indexed in January 2002

• Total of 1230 items gene indexed since start of pilot project in summer 2001