A multilingual gold-standard corpus for biomedical concept recognition: The Mantra GSC

Journal of the American Medical Informatics Association

Volumn 22, Issue 5, 2015, Pages 948-956

  Kors, Jan A ^a   Clematide, Simon ^b   Akhondi, Saber A ^a   Van Mulligen, Erik M ^a   Rebholz Schuhmann, Dietrich ^b  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Concept identification; Gold standard corpus; Inter annotator agreement; Multilinguality; Semantic enrichment

Indexed keywords

ARTICLE; BIOMEDICINE; GOLD STANDARD; GOLD STANDARD CORPORA; HUMAN; LANGUAGE; MEDICAL TERMINOLOGY; UNIFIED MEDICAL LANGUAGE SYSTEM; INFORMATION RETRIEVAL; MULTILINGUALISM; NATURAL LANGUAGE PROCESSING; NOMENCLATURE; PROCEDURES; SEMANTICS;

INFORMATION STORAGE AND RETRIEVAL; MULTILINGUALISM; NATURAL LANGUAGE PROCESSING; SEMANTICS; TERMINOLOGY AS TOPIC; UNIFIED MEDICAL LANGUAGE SYSTEM;

EID: 84953344270     PISSN: 10675027     EISSN: 1527974X     Source Type: Journal    
DOI: 10.1093/jamia/ocv037     Document Type: Article

References (28)

1. Ohno-Machado L. NIH's Big Data to Knowledge initiative and the advancement of biomedical informatics. J Am Med Inform Assoc. 2014;21: 193.
2. Krauthammer M, Nenadic G. Term identification in the biomedical literature. J Biomed Inform. 2004;37:512-526.
3. Rebholz-Schuhmann D, Jimeno Yepes AJ, Van Mulligen EM, et al. CALBC silver standard corpus. J Bioinform Comput Biol. 2010;8:163-179.
4. Rebholz-Schuhmann D, Jimeno Yepes A, Li C, et al. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. J Biomed Semantics. 2011;2 (Suppl 5):S11.
5. Bodenreider O. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004;32:D267-D270.
6. Rebholz-Schuhmann D, Clematide S, Rinaldi F, et al. Entity recognition in parallel multi-lingual biomedical corpora: the CLEF-ER laboratory overview. In: Forner P, Müller H, Paredes R, et al., eds. Information Access Evaluation. Multilinguality, Multimodality, and Visualization. Berlin Heidelberg: Springer; 2013:353-367.
7. Mantra project website. http://www.mantra-project.eu Accessed April 17, 2015.
8. Leaman R, Miller C, Gonzalez G. Enabling recognition of diseases in biomedical text with machine learning: corpus and benchmark. Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM); Jeju Island, South Korea, 2009: 82-89.
9. Gurulingappa H, Rajput AM, Roberts A, et al. Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. J Biomed Inform. 2012;45: 885-892.
10. Bada M, Eckert M, Evans D, et al. Concept annotation in the CRAFT corpus. BMC Bioinformatics. 2012;13:161.
11. Pradhan S, Elhadad N, South BR, et al. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. J Am Med Inform Assoc. 2015;22:143-154.
12. Hirschman L, Colosimo M, Morgan A, et al. Overview of BioCreAtIvE task 1B: normalized gene lists. BMC Bioinformatics. 2005;6 (Suppl 1):S11.
13. Morgan AA, Lu Z, Wang X, et al. Overview of BioCreative II gene normalization. Genome Biol. 2008;9 (Suppl 2):S3.
14. Lu Z, Kao HY, Wei CH, et al. The gene normalization task in BioCreative III. BMC Bioinformatics. 2011;12 (Suppl 8):S2.
15. Volk M, Ripplinger B, Vintar S, et al. Semantic annotation for concept-based cross-language medical information retrieval. Int J Med Inform. 2002;67: 97-112.
16. Open Source Parallel Corpus (OPUS), European Medicines Agency documents. http://opus.lingfil.uu.se/EMEA.php Accessed April 17, 2015.
17. IFI CLAIMS patent database. http://www.ificlaims.com/index.php?page=-products_claims_databases2 Accessed April 17, 2015.
18. Bodenreider O, McCray AT. Exploring semantic groups through visual approaches. J Biomed Inform. 2003;36:414-432.
19. Stenetorp P, Pyysalo S, TopićG, et al. brat: a web-based tool for NLP-assisted text annotation. Proceedings of the Demonstrations Session at EACL 2012; Association for Computational Linguistics; 2012: 103-107.
20. Schuemie MJ, Jelier R, Kors JA. Peregrine: lightweight gene name normalization by dictionary lookup. Proceedings of the BioCreAtIvE II Workshop; Madrid, Spain; 2007: 131-133.
21. Hahn U, Buyko E, Landefeld R, et al. An overview of JCoRe, the JULIE lab UIMA component repository. Proceedings of the Language Resources and Evaluation Conference (LREC); Marrakech, Morocco; 2008: 1-7.
22. Rebholz-Schuhmann D, Arregui M, Gaudan S, et al. Text processing through Web services: calling Whatizit. Bioinformatics. 2008;24:296-298.
23. Averbis Extraction Platform. http://www.averbis.de/en/technologies/text_analytics Accessed April 17, 2015.
24. Linguamatics I2E text mining software. http://www.linguamatics.com/welcome/software/I2E.html Accessed April 17, 2015.
25. Rebholz-Schuhmann D, Clematide S, Rinaldi F, et al. Multilingual semantic resources and parallel corpora in the biomedical domain: the CLEF-ER challenge. Conference and Labs of the Evaluation Forum (CLEF) 2013. CLEF-ER working notes. http://www.clef-initiative.eu/edition/clef2013/working-notes Accessed April 17, 2015.
26. Lewin I, Kafkas S, Rebholz-Schuhmann D. Centroids: gold standards with distributional variation. Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC-2012); European Language Resources Association; 2012: 3894-3900.
27. Lewin I, Clematide S. Deriving an English biomedical silver standard corpus for CLEF-ER. Conference and Labs of the Evaluation Forum (CLEF) 2013. CLEF-ER working notes. http://www.clef-initiative.eu/edition/clef2013/working-notes Accessed April 17, 2015.
28. https://uts.nlm.nih.gov/home.html Accessed April 17, 2015.