Named entity recognition

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Named entity recognition
Abbreviations: NER

Named entity extraction

Category: Named entity recognition

Text mining
Sequence tagging


Biomedical named entity recognition

Databases: Microsoft Academic Search Wikipedia with DBpedia
Papers: DOAJ Google Scholar PubMed
Ontologies: MeSH NeuroLex Wikidata Wikipedia
Other: Google Twitter WolframAlpha

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Named entity recognition (NER)

A related field is index recommendation.


[edit] Methods

  1. Conditional random fields[1]

[edit] Tools

  1. ABNER[2]
  2. BANNER [1][3]
  3. BioCreAtIvE Meta-server [2]
  4. C&C NER tagger Curran and Clark, 2003.[4]
  5. LingPipe [3]
  6. Mallet
  7. NERD: Named Entity Recognition and Disambiguation,
  8. (NLTK taggers)
  9. OpenCalais
  10.[5][6], a web-service and browser plugin that recognize "gene, protein, or small molecule" (and apparently other concepts)
  11. Stanford NER [4]
  12. Textpresso
  13. Wikifier[7]
  14. Zemanta [5]

[edit] Corpora/data sets

  1. BioCreative 2 [6] 15'000 biomedical sentences with assocated gene (protein!?) extracted
  2. BBN Pronoun Coreference and Entity Type Corpus (Weischedel and Brunstein, 2005)
  3. CoNLL-03, Tjong Kim Sang and De Meulder, 2003.[8]
  4. GENETAG[9]
  5. GENIA term annotation [7] 1999 annotated MEDLINE abstracts.[10][11]
  6. MUC-6, MUC-7, Nancy Chinchor, 1998.[12]
  7. Pascal Challenge [8] 1100 conference and workshop call for papers [13]
  8. "Jimeno-2008": Annotated corpora for diseases. 597 (old)/ 856 (new) sentences [9].[14]

[edit] Papers

[edit] Reviews

  1. A survey of current work in biomedical text mining (2005)
  2. A survey of named entity recognition and classification (2007)
  3. BANNER: an executable survey of advances in biomedical named entity recognition (2008)
  4. Introduction: named entity recognition in biomedicine (2004)

[edit] Original articles

  1. A tweet consumers' look at Twitter trends
  2. An algorithm that learns what's in a name
  3. An approach for named entity recognition in poorly structured data
  4. Automated recognition of brain region mentions in neuroscience literature
  5. Biomedical named entity recognition using conditional random fields and rich feature sets
  6. ChemSpot: a hybrid system for chemical named entity recognition
  7. Exploiting Wikipedia as external knowledge for named entity recognition
  8. Introducing meta-services for biomedical information extraction
  9. Learning to link with Wikipedia
  10. Named entity recognition in Wikipedia
  11. Named entity recognition using an HMM-based chunk tagger
  12. Named entity recognition without gazetteers
  13. NERD: a framework for evaluating named entity recognition tools in the web of data
  14. Question analysis: how Watson reads a clue
  15. Recognizing names in biomedical texts: a machine learning approach
  16. Rutabaga by any other name: extracting biological names
  17. Tagging gene and protein names in biomedical text
  18. Using encyclopedic knowledge for named entity disambiguation
  19. What makes a gene name? Named entity recognition in the biomedical literature

[edit] Indexing recommendation and keyword extraction

  1. Automatic keyword extraction from individual documents
  2. A bottom-up approach to MEDLINE indexing recommendations
  3. MEDLINE MeSH indexing: lessons learned from machine learning and future directions

[edit] External links


[edit] References

  1. Conditional random fields: probabilistic models for segmenting and labeling sequence data
  2. Biomedical named entity recognition using conditional random fields and rich feature sets
  3. BANNER: an executable survey of advances in biomedical named entity recognition
  4. Investigating GIS and smoothing for maximum entropy taggers
  5. Reflect: augmented browsing for the life scientist
  6. Curating protein and chemical tags with reflect
  7. Learning to link with Wikipedia
  8. Introduction to the CoNLL-2003 shared task: language-independent named entity recognition
  9. GENETAG: a tagged corpus for gene/protein named entity recognition
  10. GENIA corpus - a semantically annotated corpus for bio-textmining
  11. GENIA Corpus: an annotated research abstract corpus in molecular biology domain
  12. Overview of MUC-7
  13. Evaluating machine learning for information extraction
  14. Assessment of disease named entity recognition on a corpus of annotated sentences
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