Format

Send to

Choose Destination
See comment in PubMed Commons below
J Am Med Inform Assoc. 2005 Sep-Oct;12(5):576-86. Epub 2005 May 19.

ALICE: an algorithm to extract abbreviations from MEDLINE.

Author information

  • 1Department of Computational Biology, University of Tokyo CB01, 5-1-5, Kashiwanoha, Kashiwa-shi, Chiba, 277-8561, Japan. aohiroko@hgc.jp

Abstract

OBJECTIVE:

To help biomedical researchers recognize dynamically introduced abbreviations in biomedical literature, such as gene and protein names, we have constructed a support system called ALICE (Abbreviation LIfter using Corpus-based Extraction). ALICE aims to extract all types of abbreviations with their expansions from a target paper on the fly.

METHODS:

ALICE extracts an abbreviation and its expansion from the literature by using heuristic pattern-matching rules. This system consists of three phases and potentially identifies valid 320 abbreviation-expansion patterns as combinations of the rules.

RESULTS:

It achieved 95% recall and 97% precision on randomly selected titles and abstracts from the MEDLINE database.

CONCLUSION:

ALICE extracted abbreviations and their expansions from the literature efficiently. The subtly compiled heuristics enabled it to extract abbreviations with high recall without significantly reducing precision. ALICE does not only facilitate recognition of an undefined abbreviation in a paper by constructing an abbreviation database or dictionary, but also makes biomedical literature retrieval more accurate. This system is freely available at http://uvdb3.hgc.jp/ALICE/ALICE_index.html.

PMID:
15905486
PMCID:
PMC1205607
DOI:
10.1197/jamia.M1757
[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Support Center