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BioCreative specifications

Information


Unique identifier OMICS_13658
Name BioCreative
Alternative name Critical Assessment of Information Extraction systems in Biology
Interface Application programming interface
Restrictions to use None
Computer skills Advanced
Version 5.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Cecilia Arighi <>

Publications for Critical Assessment of Information Extraction systems in Biology

BioCreative in pipelines

 (3)
2012
PMCID: 3449393
PMID: 23055626
DOI: 10.6026/97320630008758

[…] of dictionaries []. mgi scans full text articles and performs entity recognition for mouse gene ‘mentions‘ based on a dictionary of mouse genes and human orthologs []. also, several teams at the biocreative task [] have also employed dictionary based approaches for term identification, rule based approaches are frequently used for text mining tasks. one of the most successful rules-based […]

2012
PMCID: 3756254
PMID: 23043124
DOI: 10.1136/amiajnl-2012-001173

[…] belong to a noun phrase, or at least overlap with it. the second rule removes a concept if it is part of a concept filter list, a common approach to increase precision as used by many systems in the biocreative competitions. our list contains 23 generic concepts (eg, ‘disease’, ‘abnormality’) that were wrongly annotated by peregrine in the training set., the rules in the nlp module […]

2010
PMCID: 2854679
PMID: 20418942
DOI: 10.1371/journal.pone.0009619

[…] re-thinking of how search should be done on bioscience journal articles. for instance, many researchers are using full text biology articles for information extraction (text mining), as seen in the biocreative competition , . the results of text extraction can then be exposed in search interfaces, as done in systems like ihop and chilibot (although both of these search only over abstracts)., […]


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BioCreative in publications

 (238)
PMCID: 5791373
PMID: 29382397
DOI: 10.1186/s13326-017-0168-3

[…] [], that observed that chemicals, diseases and their relations are the most popular search topics., a large corpus of annotated pubmed abstracts for cid relation extraction is now available from biocreative-v [] for furthering research and comparison of different methods. this is known as the chemical-disease relations (cdr) corpus. the main objective of the cid relation extraction task […]

PMCID: 5751782
PMID: 29297367
DOI: 10.1186/s12920-017-0316-8

[…] and 2 h for the cdr corpus., we validated the effectiveness of mcnn by applying it to two corpora containing both mention-level and concept-level annotations: the ncbi disease corpus [] and the biocreative v chemical disease relation task (cdr) corpus []. overall statistics for each dataset are provided in table . the ncbi disease corpus consists of 793 medline abstracts separated […]

PMCID: 5737204
PMID: 29220479
DOI: 10.1093/database/bax090

[…] combination networks [], the exploration of pseudomonas aeruginosa quorum sensing inhibitors [], and the visualization, prediction and benchmarking of chemical and gene entity annotations at biocreative v chemdner challenge []. overall, these experiences enabled the identification of desirable refinements and priority extensions., the logical next step in terms of software extension […]

PMCID: 5657032
PMID: 29123642
DOI: 10.5256/f1000research.11308.r21168

[…] understanding will facilitate objective evaluation of the evidence., to complement the classical peer-review system in the evaluation of the scientific evidence, several initiatives, such as casp , biocreative , dream , and sbv improver leverage the scientific community to verify methods of protein structure prediction, information extraction, gene network inference, and systems biology, […]

PMCID: 5558737
PMID: 28810903
DOI: 10.1186/s12859-017-1776-8

[…] boundary match in the single-class setting we apply in this study []. to the best of our knowledge this result remains the state of the art for this corpus., the top-performing system [] in the biocreative ii gene mention recognition task achieved an f-score of 87.21% by the official task evaluation criteria, which relax strict entity span matching by defining alternative boundaries […]


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BioCreative institution(s)
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA; Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA; International Centre of Health Information Technology, Taipei Medical University, Taipei, Taiwan; DETI/IEETA, University of Aveiro, Campus Universitario de Santiago, Aveiro, Portugal; National Centre for Text Mining, University of Manchester, Manchester, UK; Facultad de Ciencias, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico; BMD Software, Aveiro, Portugal; Northern Institute for Cancer Research, Newcastle University, New Castle, UK; Rutgers University-Camden, Camden, NJ, USA; Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico, Mexico; Department of Botany and Plant Pathology, Oregon State University Corvallis, OR, USA; Department of Computer Science and Information Engineering, National Taitung University, Taitung, Taiwan; College of Agriculture and Natural Resources, University of Delaware, Newark, DE, USA; Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, Sankt Augustin, Germany; SourceData, EMBO, Heidelberg, Germany; College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, UK; Institute of Translational Medicine, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Life Science Informatics, University of Bonn, Bonn, Germany; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Prince of Wales Clinical School, University of New South Wales NSW, Sydney, NSW, Australia; SRI International, Menlo Park, CA, USA; Oxford e-Research Centre, University of Oxford, Oxford, UK; Department of Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, ON, Canada; HGMD, Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff, UK; Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India; Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece; Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany; Innovation Center for Biomedical Informatics (ICBI), Georgetown University, WA, DC, USA; Institute of Computational Linguistics, University of Zurich, Zurich, Switzerland; GMGF, Aix-Marseille Université, Marseille, France; Inserm, Marseille, France; Department of Medical Sciences, iBiMED and IEETA, University of Aveiro, Aveiro, Portugal; Taipei Medical University Graduate Institute of Biomedical informatics, Taipei, Taiwan; Department of Genetics, University of Cambridge, Cambridge, UK; Institute of Information Science, Academia Sinica, Taipei, Taiwan; Freelance Scientific Curator, Cleveland, OH, USA; Institute of Sport and Physical Activity Research (ISPAR), University of Bedfordshire, Bedford, UK; Ontology Development Group, Oregon Health & Science University, Portland, OR, USA; WormBase Consortium, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada; Medical College of Wisconsin, Milwaukee, WI, USA; Reed Elsevier, Philadelphia, PA, USA; European Bioinformatics Institute, Hinxton, UK; Roche Innovation Center Basel, Basel, Switzerland; National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA; MaizeGDB USDA ARS and University of Missouri, Columbia, MO, USA; The MITRE Corporation, Bedford, MA, USA
BioCreative funding source(s)
National Institutes of Health [R13GM109648, P41HG003751 and U54GM114833]; Intramural Research Program at National Library of Medicine; National Institutes of Health Office of Director [R24OD011883]; the US Department of Energy [DE-SC0010838]; National Science Foundation [#1340112, DBI#1356374]; Ontario Research Fund; the European Molecular Biology Laboratory; Facultad de Ciencias, UNAM.

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