Better Rules, Few Features: A Semantic Approach to Selecting Features from Text
ICDM '01 Proceedings of the 2001 IEEE International Conference on Data Mining
Constructing Biological Knowledge Bases by Extracting Information from Text Sources
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Rutabaga by any other name: extracting biological names
Journal of Biomedical Informatics - Special issue: Sublanguage
Information extraction from biomedical text
Journal of Biomedical Informatics - Special issue: Sublanguage
Probabilistic term variant generator for biomedical terms
Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval
Automatically identifying gene/protein terms in MEDLINE abstracts
Journal of Biomedical Informatics
A simple rule-based part of speech tagger
ANLC '92 Proceedings of the third conference on Applied natural language processing
Extracting the names of genes and gene products with a hidden Markov model
COLING '00 Proceedings of the 18th conference on Computational linguistics - Volume 1
A methodology for automatic term recognition
COLING '94 Proceedings of the 15th conference on Computational linguistics - Volume 2
ACL '02 Proceedings of the 40th Annual Meeting on Association for Computational Linguistics
Tuning support vector machines for biomedical named entity recognition
BioMed '02 Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain - Volume 3
Contrast and variability in gene names
BioMed '02 Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain - Volume 3
Gene name extraction using FlyBase resources
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Using domain-specific verbs for term classification
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Enhancing performance of protein name recognizers using collocation
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Two-phase biomedical NE recognition based on SVMs
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Boosting precision and recall of dictionary-based protein name recognition
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Effective adaptation of a Hidden Markov Model-based named entity recognizer for biomedical domain
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Bio-medical entity extraction using Support Vector Machines
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Protein name tagging for biomedical annotation in text
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
An investigation of various information sources for classifying biological names
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
Selecting text features for gene name classification: from documents to terms
BioMed '03 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine - Volume 13
The GENIA corpus: an annotated research abstract corpus in molecular biology domain
HLT '02 Proceedings of the second international conference on Human Language Technology Research
Mining biomedical abstracts: what’s in a term?
IJCNLP'04 Proceedings of the First international joint conference on Natural Language Processing
Introduction: named entity recognition in biomedicine
Journal of Biomedical Informatics - Special issue: Named entity recognition in biomedicine
Finding new terminology in very large corpora
Proceedings of the 3rd international conference on Knowledge capture
Mining semantically related terms from biomedical literature
ACM Transactions on Asian Language Information Processing (TALIP)
Terminology-based knowledge mining for new knowledge discovery
ACM Transactions on Asian Language Information Processing (TALIP)
Identifying important concepts from medical documents
Journal of Biomedical Informatics
Improving the scalability of semi-Markov conditional random fields for named entity recognition
ACL-44 Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics
Journal of Biomedical Informatics
The influence of basic tokenization on biomedical document retrieval
SIGIR '07 Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval
Methodological Review: Extracting interactions between proteins from the literature
Journal of Biomedical Informatics
Experimental Study on a Two Phase Method for Biomedical Named Entity Recognition
IEICE - Transactions on Information and Systems
Rule-Based Protein Term Identification with Help from Automatic Species Tagging
CICLing '07 Proceedings of the 8th International Conference on Computational Linguistics and Intelligent Text Processing
Species disambiguation for biomedical term identification
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
The role of roles in classifying annotated biomedical text
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Reranking for biomedical named-entity recognition
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
NLPXML '06 Proceedings of the 5th Workshop on NLP and XML: Multi-Dimensional Markup in Natural Language Processing
Methodological Review: What can natural language processing do for clinical decision support?
Journal of Biomedical Informatics
Towards role-based filtering of disease outbreak reports
Journal of Biomedical Informatics
Two learning approaches for protein name extraction
Journal of Biomedical Informatics
Discovering genes-diseases associations from specialized literature using the grid
IEEE Transactions on Information Technology in Biomedicine - Special section on biomedical informatics
A system for semantic analysis of chemical compound names
ACLstudent '09 Proceedings of the ACL-IJCNLP 2009 Student Research Workshop
Issues on quality assessment of SNOMED CT® subsets: term validation and term extraction
WBIE '09 Proceedings of the Workshop on Biomedical Information Extraction
A cross-lingual framework for monolingual biomedical information retrieval
CIKM '10 Proceedings of the 19th ACM international conference on Information and knowledge management
Biomedical information retrieval: the BioTracer approach
ITBAM'10 Proceedings of the First international conference on Information technology in bio- and medical informatics
Recognizing medication related entities in hospital discharge summaries using support vector machine
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics: Posters
IEA/AIE'10 Proceedings of the 23rd international conference on Industrial engineering and other applications of applied intelligent systems - Volume Part I
Ontology population and enrichment: state of the art
Knowledge-driven multimedia information extraction and ontology evolution
Voting techniques for a multi-terminology based biomedical information retrieval
AIME'11 Proceedings of the 13th conference on Artificial intelligence in medicine
Supporting biomedical information retrieval: the bioTracer approach
Transactions on large-scale data- and knowledge-centered systems IV
Headwords and suffixes in biomedical names
KDLL'06 Proceedings of the 2006 international conference on Knowledge Discovery in Life Science Literature
Detecting invalid dictionary entries for biomedical text mining
KDLL'06 Proceedings of the 2006 international conference on Knowledge Discovery in Life Science Literature
Mining biomedical abstracts: what’s in a term?
IJCNLP'04 Proceedings of the First international joint conference on Natural Language Processing
Two-phase biomedical named entity recognition using a hybrid method
IJCNLP'05 Proceedings of the Second international joint conference on Natural Language Processing
Massive biomedical term discovery
DS'05 Proceedings of the 8th international conference on Discovery Science
Using an ensemble system to improve concept extraction from clinical records
Journal of Biomedical Informatics
A multi-strategy approach to biological named entity recognition
Expert Systems with Applications: An International Journal
Artificial Intelligence in Medicine
Inferring conceptual relationships to improve medical records search
Proceedings of the 10th Conference on Open Research Areas in Information Retrieval
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Sophisticated information technologies are needed for effective data acquisition and integration from a growing body of the biomedical literature. Successful term identification is key to getting access to the stored literature information, as it is the terms (and their relationships) that convey knowledge across scientific articles. Due to the complexities of a dynamically changing biomedical terminology, term identification has been recognized as the current bottleneck in text mining, and--as a consequence--has become an important research topic both in natural language processing and biomedical communities. This article overviews state-of-the-art approaches in term identification. The process of identifying terms is analysed through three steps: term recognition, term classification, and term mapping. For each step, main approaches and general trends, along with the major problems, are discussed. By assessing previous work in context of the overall term identification process, the review also tries to delineate needs for future work in the field.