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BioCreAtIvE Task 1A: gene mention finding evaluation

Alexander Yeh, Alexander Morgan, Marc Colosimo, Lynette Hirschman
2005 BMC Bioinformatics  
We report here on task 1A, which deals with finding mentions of genes and related entities in text.  ...  "Finding mentions" is a basic task, which can be used as a building block for other text mining tasks, but the teams that tried to use their task 1A systems to help on other BioCreAtIvE tasks report mixed  ...  John Wilbur and Lorraine Tanabe of the National Center for Biotechnology Information provided the data and evaluation software used in the evaluation. Copyright © 2004 the MITRE Corporation.  ... 
doi:10.1186/1471-2105-6-s1-s2 pmid:15960832 pmcid:PMC1869012 fatcat:qif7ykrwcrhfldn5fzyvmp6b6u

BioCreative III interactive task: an overview

Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Giglio, Ian Harrow, Eva Huala, Martin Krallinger (+15 others)
2011 BMC Bioinformatics  
The task focused on gene normalization (identifying gene mentions in the article and linking these genes to standard database identifiers), gene ranking based on the overall importance of each gene mentioned  ...  The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain.  ...  The BioCreative III workshop was supported under NSF grant DBI-0850319.  ... 
doi:10.1186/1471-2105-12-s8-s4 pmid:22151968 pmcid:PMC3269939 fatcat:p4k5g76ccbaczmatbogvotww4q

Overview of BioCreAtIvE task 1B: normalized gene lists

Lynette Hirschman, Marc Colosimo, Alexander Morgan, Alexander Yeh
2005 BMC Bioinformatics  
This paper summarizes the BioCreAtIvE task 1B, the "Normalized Gene List" task, which was inspired by the gene list supplied for each curated paper in a model organism database.  ...  The task was to produce the correct list of unique gene identifiers for the genes and gene products mentioned in sets of abstracts from three model organisms (Yeast, Fly, and Mouse).  ...  Overall, we judged that the BioCreAtIvE task 1B evaluation was a success.  ... 
doi:10.1186/1471-2105-6-s1-s11 pmid:15960823 pmcid:PMC1869004 fatcat:5bdlzcyidzdyrpudo2p6dn6f3m

Overview of the interactive task in BioCreative V

Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai (+44 others)
2016 Database: The Journal of Biological Databases and Curation  
The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated.  ...  The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration  ...  Acknowledgements We would like to acknowledge all the users and team members who have participated in this activity throughout BioCreative. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw119 pmid:27589961 pmcid:PMC5009325 fatcat:ldpn6gjxircjlibqtysi57cztq

Evaluation of BioCreAtIvE assessment of task 2

Christian Blaschke, Eduardo Leon, Martin Krallinger, Alfonso Valencia
2005 BMC Bioinformatics  
Results: The Critical Assessment for Information Extraction in Biology (BioCreAtIvE) contest consists of a community wide competition aiming to evaluate different strategies for text mining tools, as applied  ...  We report on task two which addressed the automatic extraction and assignment of Gene Ontology (GO) annotations of human proteins, using full text articles.  ...  The identification of the protein names is actually a variant of the named entity task, which is known to perform well, around 80 percent for the protein and genes in case of task 1A.  ... 
doi:10.1186/1471-2105-6-s1-s16 pmid:15960828 pmcid:PMC1869008 fatcat:2pbvytvsqjcdbivxu7yia6oyue

Overview of the Interactive Task in BioCreative V

Qinghua Wang, Fabio Rinaldi, Et Al
The tasks proposed are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated.  ...  The tasks proposed are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated.  ...  BioCreative is partially funded by NIH/NIGMS R13-GM109648-01A1; DOE: DE-SC0010838; NIH Intramural Research Program, National Library of Medicine.  ... 
doi:10.5167/uzh-116471 fatcat:elfvz7vs3zcx3obt33nak26rii

Overview of BioCreAtIvE: critical assessment of information extraction for biology

Lynette Hirschman, Alexander Yeh, Christian Blaschke, Alfonso Valencia
2005 BMC Bioinformatics  
Results: BioCreAtIvE focused on two tasks.  ...  The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization), where the best systems achieved a balanced 80% precision / recall or better, which potentially  ...  MITRE US BioCreAtIvE task 1A: gene mention finding evaluation 2 1A Tanabe, L., Xie, T.N. Thom, L.H., Matten, W. Wilbur, W.J.  ... 
doi:10.1186/1471-2105-6-s1-s1 pmid:15960821 pmcid:PMC1869002 fatcat:kktugbhkrzgwvnnwuo7jxszkaq

Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

Martin Krallinger, Alexander Morgan, Larry Smith, Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman, Alfonso Valencia
2008 Genome Biology  
These tasks included the recognition of gene mentions in abstracts (gene mention task); the extraction of a list of unique identifiers for human genes mentioned in abstracts (gene normalization task);  ...  An overall improvement in terms of balanced precision and recall was observed for the best submissions for the gene mention (F score 0.87); for the gene normalization task, the best results were comparable  ...  The PPI task and the second BioCreative assessment workshop was sponsored by the European Science Foundation (ESF) and the NOE ENFIN.  ... 
doi:10.1186/gb-2008-9-s2-s1 pmid:18834487 pmcid:PMC2559980 fatcat:oebtobhdtbfexgyrmymmy7o6vi

Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization

Cheng-Ju Kuo, Maurice HT Ling, Chun-Nan Hsu
2011 BMC Bioinformatics  
However, unlike similar tasks in the past BioCreative challenges, the BioCreative III GN task is particularly challenging because it is not species-specific.  ...  Results: We present our GN system participated in the BioCreative III GN task.  ...  normalization task.  ... 
doi:10.1186/1471-2105-12-s8-s6 pmid:22152021 pmcid:PMC3269941 fatcat:5ubvyowfgveudhu74sxadmmft4

Various criteria in the evaluation of biomedical named entity recognition

Richard Tzong-Han Tsai, Shih-Hung Wu, Wen-Chi Chou, Yu-Chun Lin, Ding He, Jieh Hsiang, Ting-Yi Sung, Wen-Lian Hsu
2006 BMC Bioinformatics  
JNLPBA and BioCreAtIvE are two major Bio-NER tasks using these corpora. Both tasks take different approaches to corpus annotation and use different matching criteria to evaluate system performance.  ...  In Experiment 2, we apply hypothesis testing and correlation coefficient to find alternatives to BioCreAtIvE's evaluation scheme.  ...  -2004 Task 1A [6] .  ... 
doi:10.1186/1471-2105-7-92 pmid:16504116 pmcid:PMC1402329 fatcat:6gsxtu2afzcozisohq5bqbbv64

Text Detective: a rule-based system for gene annotation in biomedical texts

Javier Tamames
2005 BMC Bioinformatics  
Results: In BioCreAtIvE evaluation, Text Detective achieved results of 84% precision, 71% recall for task 1A, and 79% precision, 71% recall for mouse genes in task 1B.  ...  The identification of mentions of gene or gene products in biomedical texts is a critical step in the development of text mining applications in biosciences.  ...  We find that this is the case for 20-25% of our false negatives in our participation in BioCreAtIvE task 1A.  ... 
doi:10.1186/1471-2105-6-s1-s10 pmid:15960822 pmcid:PMC1869003 fatcat:2at5jiclbfaddnpzzg3p6u7o5y

Gene name identification and normalization using a model organism database

Alexander A. Morgan, Lynette Hirschman, Marc Colosimo, Alexander S. Yeh, Jeff B. Colombe
2004 Journal of Biomedical Informatics  
For gene mention tagging, we adopted a statistical approach.  ...  We focused on listing the normalized form of genes and gene products discussed in an article. We broke this into two steps: gene mention tagging in text, followed by normalization of gene names.  ...  Participants were evaluated on the list of unique identifiers, and not on tagging gene names in running text, although another BioCreAtIvE task, Task 1A, using annotated data provided by Lorraine Tanabe  ... 
doi:10.1016/j.jbi.2004.08.010 pmid:15542014 fatcat:f2r63l3ecfhrtjxm2eo2omfxvq

Overview of BioCreative II gene mention recognition

Larry Smith, Lorraine K Tanabe, Rie Ando, Cheng-Ju Kuo, I-Fang Chung, Chun-Nan Hsu, Yu-Shi Lin, Roman Klinger, Christoph M Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu (+22 others)
2008 Genome Biology  
Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop.  ...  In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions.  ...  This article has been published as part of Genome Biology Volume 9 Supplement 2, 2008: The BioCreative II -Critical Assessment for Information Extraction in Biology Challenge.  ... 
doi:10.1186/gb-2008-9-s2-s2 pmid:18834493 pmcid:PMC2559986 fatcat:eguamlzmd5ec7btwyq3mr6v4fi

Overview of BioCreative II gene normalization

Alexander A Morgan, Zhiyong Lu, Xinglong Wang, Aaron M Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jörg Hakenberg, Chengjie Sun, Heng-hui Liu (+8 others)
2008 Genome Biology  
For BioCreative II, the task was to list the Entrez Gene identifiers for human genes or gene products mentioned in PubMed/MEDLINE abstracts.  ...  The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature.  ...  This article has been published as part of Genome Biology Volume 9 Supplement 2, 2008: The BioCreative II -Critical Assessment for Information Extraction in Biology Challenge.  ... 
doi:10.1186/gb-2008-9-s2-s3 pmid:18834494 pmcid:PMC2559987 fatcat:qxd4defmunckvn7pheotofs4aq

Moara: a Java library for extracting and normalizing gene and protein mentions

Mariana L Neves, José-María Carazo, Alberto Pascual-Montano
2010 BMC Bioinformatics  
Gene/protein recognition and normalization are important preliminary steps for many biological text mining tasks, such as information retrieval, protein-protein interactions, and extraction of semantic  ...  Despite dedication to these problems and effective solutions being reported, easily integrated tools to perform these tasks are not readily available.  ...  Table 1 1 Results for the CBR-Tagger evaluated with the BioCreative 2 GM test setThe BioCreative 2 Gene Mention test set consists of 5,000 sentences.  ... 
doi:10.1186/1471-2105-11-157 pmid:20346105 pmcid:PMC2851609 fatcat:hygmaaiburdnvpqg24npgux4sy
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