[Lexical/terminological resource] A Spanish Medical Abbreviation DataBase.
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README.md

README.md

AbreMES-DB: Base de datos de Abreviaturas Médicas en Español (Spanish Medical Abbreviation DataBase)

Digital Object Identifier (DOI) and access to dataset files

https://doi.org/10.5281/zenodo.2207130

Introduction

This repository contains the Spanish Medical Abbreviation DataBase (base de datos de Abreviaturas Médicas en Español, AbreMES-DB). This database is based on the "Allie Search Service for Abbreviation / Long Form", developed by Yamamoto et al.[1], but it contains Spanish abbreviations and their definitions instead of English ones. The database is created automatically by detecting abbreviations and their potential definitions explicitly mentioned in the same sentence. These abbreviations are extracted from the metadata of different biomedical publications written in Spanish, which contain the titles and abstracts. The sources of these publications are SciELO[2], IBECS[3] and Pubmed[4]. The chosen schema is Dublin Core (http://dublincore.org/). We use the official ones from SciELO, and customized adaptations of the XML files to Dublin Core from IBECS and Pubmed metadata. The source code used to generate this resource is available here: https://github.com/PlanTL/AbreMES-X

Directory structure

abbreviations.tsv
This file gathers all abbreviations in the database and displays information about them. Each column is 
structured in the following way:
  - Abbreviation ID.
  - Frequency: the number of times the abbreviation has been detected in the corpora, together with 
  the definition in the same sentence.
  - Abbreviation: the abbreviation in string format.
  - Definitions: definition IDs where the abbreviation has been associated to.
  - Appears on: publication IDs where the abbreviation is mentioned.

definitions.tsv
This file gathers all definitions in the database and displays information about them. Each column is 
structured in the following way:
  - Definition ID.
  - Frequency: the number of times the definition has been detected in the corpora, together with 
  the abbreviation in the same sentence.
  - Definition: the definition in string format.
  - Abbreviations: abbreviation IDs where the definition has been associated to.
  - Appears on: publication IDs where the definition is mentioned.

pairs.tsv
This file gathers all abbreviation-definition pairs found in the corpora and displays information 
about them. Each column is structured in the following way:
  - Pair ID.
  - Abbreviation ID.
  - Definition ID.
  - Frequency: the number of times this abbreviation-definition pair has been detected in the corpora.
  - Abbreviation: abbreviation in string format.
  - Definition: definition in string format.
  - Appears on: publication IDs where the pair is mentioned.

CoAbbreviations.tsv
This file gathers all abbreviations found in the corpora and those abbreviations with whom 
they share publications. Each column is structured in the following way:
  - Abbreviation ID.
  - Abbreviation: the abbreviation in string format.
  - Co-Abbr frequency: the number of times other detected abbreviations appear in the same 
  publication with the current abbreviation.
  - Pub. frequency: the number of publications the abbreviation appears in the analyzed corpora, 
  together with the definition explicitly mentioned in the same sentence.
  - Co-abbreviations: abbreviation IDs that appear in the same publication.
  - Appears on: publication IDs where we this abbreviation is mentioned.

publications.tsv
This file gathers all analyzed publications in the corpora and those abbreviation-definition 
pairs that have been detected in each publications. Each column is structured in the following way:
  - ID: the publications's official ID.
  - Source: the name of the source where the publication can be found.
  - Date: the day the publications was published.
  - Publisher: publisher of the article.
  - ISSN: ISSN of the journal where the article was published.
  - Journal Subject Term: research field of the article.
  - Abbreviations: all abbreviation IDs of the abbreviations that have been detected in the publications.
  - Definitions: all definition IDs of the definitions that have been detected in the publications.
  - Pairs: abbreviation-definition pair IDs that appear in the article.

preprocessed.tsv
This is a file created after gathering all abbreviation-definition pairs detected in all the 
publication of the corpora. We use this file as a base to organize all the information specified 
in the previous files. In each line we can find:
  - Line num.: an ID for each line.
  - Pub. ID: official ID of each publication.
  - The name of the source where the publication can be found.
  - The year the article was published.
  - Abbreviation ID present in the article.
  - Definition ID of the abbreviation, mentioned explicitly in the document in the same sentence.
  - Abbreviation in string format.
  - Definition in string format.

Contact

Ander Intxaurrondo (ander.intxaurrondo@bsc.es)

License

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Copyright (c) 2018 Secretaría de Estado para el Avance Digital (SEAD)

References

[1] Y. Yamamoto, A. Yamaguchi, H. Bono and T. Takagi, "Allie: a database and a search service of abbreviations and long forms." http://allie.dbcls.jp/

[2] Scientific Electronic Library Online (SciELO Spain) is an electronic virtual library covering a collection of Spanish health scientific journals selected following preestablished quality criteria. Developed and maintained by the Spanish National Library of Health Sciences. http://scielo.isciii.es

[3] Bibliographical database for health articles, contains abstracts and references of different articles written in Spanish. Developed and maintained by the Carlos III Health Institute in Madrid, Spain. http://ibecs.isciii.es

[4] PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval. https://www.ncbi.nlm.nih.gov/pubmed/