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The CALBC RDF Triple Store: retrieval over large literature content [article]

Samuel Croset, Christoph Grabmüller, Chen Li, Silvestras Kavaliauskas, Dietrich Rebholz-Schuhmann
2010 arXiv   pre-print
The CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions  ...  Integration of the scientific literature into a biomedical research infrastructure requires the processing of the literature, identification of the contained named entities (NEs) and concepts, and to represent  ...  This work was funded from the EU Support Action grant 231727  ... 
arXiv:1012.1650v1 fatcat:gmd6wycjyrblhbix7vnzuvvciq

Monitoring named entity recognition: the League Table

Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Antonio Yepes, Ian Lewin
2013 Journal of Biomedical Semantics  
A number of solutions have been presented and evaluated against gold standard corpora (GSC). The benchmarking against GSCs is crucial, but left to the individual researcher.  ...  For access please go to http://wwwdev.ebi.ac.uk/Rebholz-srv/calbc/assessmentGSC/. Contact: rebholz@ifi.uzh.ch.  ...  Acknowledgements This work was funded by the EU Support Action grant 231727 ("CALBC", www. calbc.eu) under the 7th EU Framework Programme (ICT 2007.4.2).  ... 
doi:10.1186/2041-1480-4-19 pmid:24034148 pmcid:PMC4015903 fatcat:blv6w5lrfba7ti5vzcuw67g55a

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter
2012 BMC Bioinformatics  
The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released).  ...  Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.  ...  Acknowledgements The authors gratefully acknowledge their support from NIH, 5R01 LM008111, 2R01 LM009254, 5 T15 LM009451, and 3 T15 LM009451.  ... 
doi:10.1186/1471-2105-13-161 pmid:22776079 pmcid:PMC3476437 fatcat:kuulhujx4ratnkoywafxggkhmi

An analysis on the entity annotations in biological corpora

Mariana Neves
2014 F1000Research  
Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain.  ...  few, in spite of their importance in the biological domain.  ...  Silver-standard corpora, such as CALBC 15 , were also not included here.  ... 
doi:10.12688/f1000research.3216.1 pmid:25254099 pmcid:PMC4168744 fatcat:eypyq7g3wjhwdjuao6zu4iq5nq

An analysis on the entity annotations in biological corpora

Mariana Neves
2014 F1000Research  
Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain.  ...  few, in spite of their importance in the biological domain.  ...  Silver-standard corpora, such as CALBC 15 , were also not included here.  ... 
doi:10.12688/f1000research.3456 fatcat:6ojbd65bnjd2hijdqx7a74spye

Social and Semantic Web Technologies for the Text-to-Knowledge Translation Process in Biomedicine [chapter]

Carlos Cano, Alberto Labarga, Armando Blanco, Leonid Peshki
2011 Biomedical Engineering, Trends, Research and Technologies  
Blanco are supported by the projects P08-TIC-4299 of J.  ...  initial stage of experiment planning to the final interpretation and communication of the results.  ...  The CALBC challenge involves both Name Entity Recognition and Concept recognition tasks.  ... 
doi:10.5772/13560 fatcat:cmrfewlbhze3zmj55o3fbfozfi

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources

Dietrich Rebholz-Schuhmann, Senay Kafkas, Jee-Hyub Kim, Chen Li, Antonio Yepes, Robert Hoehndorf, Rolf Backofen, Ian Lewin
2013 Journal of Biomedical Semantics  
As expected, the false negative errors characterize the test corpora and -on the other hand -the profiles of the false positive mistakes characterize the tagging solutions.  ...  Conclusion: The standard ML-Tag solutions achieve high performance, but not across all corpora, and thus should be trained using several different corpora to reduce possible biases.  ...  Acknowledgements This work was funded by the EU Support Action grant 231727 ("CALBC", www.  ... 
doi:10.1186/2041-1480-4-28 pmid:24112383 pmcid:PMC4021975 fatcat:r3pwqrgypzcphnbgscrxyeyeam

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

Robert Leaman, Zhiyong Lu
2016 Bioinformatics  
Results: We validated TaggerOne with multiple gold-standard corpora containing both mentionand concept-level annotations.  ...  These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model.  ...  Acknowledgements We thank the anonymous reviewers for their comments and suggestions.  ... 
doi:10.1093/bioinformatics/btw343 pmid:27283952 pmcid:PMC5018376 fatcat:dbt2imjex5h2xcwxgrwyftp46a

The CHEMDNER corpus of chemicals and drugs and its annotation principles

Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Batista-Navarro (+41 others)
2015 Journal of Cheminformatics  
In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts.  ...  Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents.  ...  The full contents of the supplement are available online at http://www. jcheminf.com/supplements/7/S1.  ... 
doi:10.1186/1758-2946-7-s1-s2 pmid:25810773 pmcid:PMC4331692 fatcat:7lpufmelsjfa7jbx6rxkam7tka

Mining the pharmacogenomics literature--a survey of the state of the art

U. Hahn, K. B. Cohen, Y. Garten, N. H. Shah
2012 Briefings in Bioinformatics  
Finally, we consider some of the novel applications that have already been developed in the field of pharmacogenomic text mining and point out perspectives for future research.  ...  such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives.We also discuss infrastructure and resources needed for advanced text analytics, e.g. document corpora  ...  The CALBC silver standard initiative [130, 131] can be considered as a step in the direction of addressing this problem; see the discussion of CALBC in the final paragraph of Section 'Annotated corpora  ... 
doi:10.1093/bib/bbs018 pmid:22833496 pmcid:PMC3404399 fatcat:por4dnthkrcxjdsir6uc64kdaq

Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics

Riza Batista-Navarro, Rafal Rak, Sophia Ananiadou
2015 Journal of Cheminformatics  
corpora.  ...  The recent public release of a large chemical entity-annotated corpus as a resource for the CHEMDNER track of the Fourth BioCreative Challenge Evaluation (BioCreative IV) workshop greatly alleviated this  ...  The full contents of the supplement are available online at http://www. jcheminf.com/supplements/7/S1.  ... 
doi:10.1186/1758-2946-7-s1-s6 pmid:25810777 pmcid:PMC4331696 fatcat:i6ctd3vokvawzoh2wjviiq73pu

Community challenges in biomedical text mining over 10 years: success, failure and the future

Chung-Chi Huang, Zhiyong Lu
2015 Briefings in Bioinformatics  
Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties.  ...  One effective way to improve the state of the art is through competitions.  ...  We also thank all the task organizers and participants for their efforts in the community challenges.  ... 
doi:10.1093/bib/bbv024 pmid:25935162 pmcid:PMC4719069 fatcat:z7wlyvovnnbrrkufmqaxycqdyi

Semantic annotation in biomedicine: the current landscape

Jelena Jovanović, Ebrahim Bagheri
2017 Journal of Biomedical Semantics  
Over the last dozen years, the biomedical research community has invested significant efforts in the development of biomedical semantic annotation technology.  ...  The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such  ...  Funding The second author graciously acknowledges funding from The Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
doi:10.1186/s13326-017-0153-x pmid:28938912 pmcid:PMC5610427 fatcat:jby2gq576vfdfmf4lsusahjrrm

Event Extraction from Biomedical Literature [article]

Abdur Rahman M.A. Basher, Alexander S. Purdy, Inanc Birol
2015 bioRxiv   pre-print
The breadth and scope of the biomedical literature hinders a timely and thorough comprehension of its content.  ...  mention 'cancer' in the title or abstract.  ...  Acknowledgment We thank the Sequencing Lab and the Bioinformatics Technology Lab (BTL) at Genome Sciences Centre, British Columbia Cancer Agency for their assistance with this article.  ... 
doi:10.1101/034397 fatcat:uq5y7yop2nhyfg4ijjy34mwd6e

Learning to Recognize Phenotype Candidates in the Auto-Immune Literature Using SVM Re-Ranking

Nigel Collier, Mai-vu Tran, Hoang-quynh Le, Quang-Thuy Ha, Anika Oellrich, Dietrich Rebholz-Schuhmann, Luis M. Rocha
2013 PLoS ONE  
Altogether we conclude that our approach coped well with the compositional structure of phenotypes in the auto-immune domain.  ...  The identification of phenotype descriptions in the scientific literature, case reports and patient records is a rewarding task for bio-medical text mining.  ...  [39] and GeneTag [40] and testing on a newly released full text corpus called CRAFT.  ... 
doi:10.1371/journal.pone.0072965 pmid:24155869 pmcid:PMC3796529 fatcat:jcy2fr7yrjgwngtfqvr4vhczdq
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