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Abbreviation Plus Pseudo-Precision (Ab3P)

Ab3P is an abbreviation definition detector. A set of rules recognizes simple patterns such as Alpha Beta (AB) as well as more involved cases. The precision of each rule is estimated by applying to randomized data (psuedo-precision). The algorithm is described in the paper:

Abbreviation definition identification based on automatic precision estimates. Sohn S, Comeau DC, Kim W, Wilbur WJ. BMC Bioinformatics. 2008 Sep 25;9:402. PubMed ID: 18817555

The text of the paper can be read at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2576267/

Public Domain Notice

This work is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the authors' official duties as a United States Government employee and thus cannot be copyrighted within the United States. The data is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.

Although all reasonable efforts have been taken to ensure the accuracy and reliability of the data and its source code, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using it. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose.

Setup

This abbreviation identification package is provided as a C++ library. The sample program can be used to identify abbreviations in plain text.

  1. Install the NCBITextLib library (https://github.com/ncbi-nlp/NCBITextLib)

  2. Define the NCBITEXTLIB variable in the file Makefile, in the main directory and the Library directory, to point to where NCBITextLib is located.

  3. The command make builds the library, builds the program, and creates the data files.

  4. The command make test runs the abbreviation identification program on our gold standard and compares your results to our results. They should be identical.

Usage

To identify SF-LF pairs from free text use the command
./identify_abbr text_file_name
It processes the input one line at a time and prints out:

input line
  sf|lf|P-precision

To run this program in a directory other than where it was originally built, include a file called path_Ab3P in the directory that gives the path to the WordData directory. Include the final slash (/).

The program identify_abbr.C also provides an example of using the Ab3P library in a program. Documentation on the routines can be found in Library/Ab3P.h.

Information Ab3P needs to work appears in the WordData directory. This includes information about words and abbreviation strategies and their estimated precision in Ab3P_prec.dat. Stop words are in the file stop. Long forms for 1-character short forms are in the file Lf1chSf. Defined words, for subword matching, are in SingTermFreq.dat.

Before this information can be used by the program, it needs to be in a form the program can efficiently access. The command make data creates these files.

We provide 1250 random MEDLINE records annotated manually (MED1250_labeled) and the original unlabeled version (MED1250_unlabeled). The format of the labeled data is:

PubMed ID
Title
Abstract
  sf|lf (skip two space in the beginning)

Double slashes indicate comments. Certain comments have a particular meaning as follows:

//*  sf|lf
  skip two spaces after //*) for synonyms.   Synonyms are
  identified but not included in the gold standard.

//!syn
  If there is no matching character for technical terms, including
  element symbols, for example MeHg|methyl mercury.

//!out
  If the long form does not appear earlier in the same sentence.

//!ord
  If the matching characters are not in the same order.  For example,
  Y73SV|Sarcoma Virus Y73

//!num
  If a number matches a word.  For example, 2D|two dimension

//!nch
  If we find a long form, but some characters do not match.  For
  example, Bet|Bel-1 plus Bel-2

//!cnj
  Conjunction complicates long form determination.  For example, alpha
  beta (ABG) and coal delta (DDG) gamma.

//
  any other comments (not starting with '!')

Previous, non-GitHub versions

v1.5 Easier to run identify_abbr from a directory other than where built.

v1.1 API clarified

v1 Original public release