Biomedical Abbreviation Recognition and Resolution 2nd Edition (BARR2)

Additional resources

A list of additional resources for this track is provided below.

• Abbreviation/acronym taggers:
• Ab3P: another great abbreviation detection tool.
• BADREX: a GATE plugin that identifies term-abbreviation pairs using dynamic regular expressions.
• ExtractAbbrev (Java / Python 3): a very popular tool to detect abbreviations, developed by Schwartz and Hearst.
• MetaMap: a tool for recognizing medical concepts in text. It also detects abbreviations and disambiguates them (UMLS license is required for its use).


• Datasets and lexical resources:
• Allie: a search service for abbreviations and long forms utilized in Lifesciences.
• IATE: InterActive Terminology for Europe.
• ITRT: The International Thesaurus of Refugee Terminology.
• MediLexicon: world's largest online database of pharmaceutical and medical abbreviations.
• UNESCOTERM: the UNESCO terminology database.


• Resources of spanish biomedical acronyms and abbreviations:
• Diccionario Babylon - Siglas
• Diccionario de siglas medicas - Sociedad Española de Documentación Médica (SEDOM)
• Glosario siglas médicas
• Siglas médicas (laenfermeria WIKI)
• Wikilengua - Abreviaturas
• Diccionario de las Unidades de Medida


• NLP software:
• Apache OpenNLP: a machine learning based toolkit for the processing of natural language text.
• Freeling: a C++ library providing language analysis functionalities.
• IXA Pipes: a modular set of NLP tools which provides easy access to NLP technology.
• Stanford CoreNLP: a very popular set of natural language analysis tools.


• Biomedical NLP software:
• Apache cTakes: an open-source tool to extract information from medical records.
• GENIAtagger: part-of-speech tagging, shallow parsing, and named entity recognition for biomedical text.
• MedTagger: a biomedical named entity recognizer and relation extractor.
• MetaMap: a tool for recognizing medical concepts in text.


• Sentence splitters (most NLP softwares, like the mentioned ones above, have sentence splitters integrated):
• CCG Sentence Segmentation Tool: this tool reads plain text and rewrites it with one sentence per line.
• GENIA sentence splitter: a sentence splitter optimized for biomedical texts.
• splitta: very high accuracy sentence boundary detection (English only).


• Machine translation software:
• Apertium: An open-source rule-based machine translation platform
• OpenNMT: open-source (MIT) neural machine translation system.
• More machine translation tools.


• Machine Learning:
• Apache Spark MLlib: Apache Spark's scalable machine learning library.
• Google Tensorflow: a software library for numerical computation using data flow graphs.
• Scikit-learn: a simple and efficient tools for data mining and data analysis
• Weka: a collection of machine learning algorithms for data mining tasks.