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The CALBC RDF Triple Store: retrieval over large literature content
[article]
2010
arXiv
pre-print
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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
2013
Journal of Biomedical Semantics
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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
2012
BMC Bioinformatics
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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
2014
F1000Research
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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
2014
F1000Research
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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]
2011
Biomedical Engineering, Trends, Research and Technologies
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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
2013
Journal of Biomedical Semantics
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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
2016
Bioinformatics
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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
2015
Journal of Cheminformatics
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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
2012
Briefings in Bioinformatics
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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
2015
Journal of Cheminformatics
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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
2015
Briefings in Bioinformatics
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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
2017
Journal of Biomedical Semantics
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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]
2015
bioRxiv
pre-print
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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
2013
PLoS ONE
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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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