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Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers
2011 BMC Bioinformatics  
One of the tasks of the Biocreative 2010 Challenge III was devoted to the evaluation of NLP systems developed to identify articles for curation and extraction of protein-protein interaction (PPI) data.  ...  The BioGRID and MINT protein interaction databases both participated in the generation of the test publication set for gene normalization, annotated the development and test sets for article classification  ...  The BioCreative Challenge III competition of 2010 demonstrates that alliances between text mining groups and protein interaction databases, such as BioGRID and MINT, facilitate the research interests of  ... 
doi:10.1186/1471-2105-12-s8-s8 pmid:22151178 pmcid:PMC3269943 fatcat:qkhfjgydozhh5gwgz334hnlul4

An Overview of BioCreative II.5

F Leitner, S A Mardis, M Krallinger, G Cesareni, L A Hirschman, A Valencia
2010 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
The BioCreative II.5 challenge evaluated automatic annotations from 15 text mining teams based on a gold standard created by reconciling annotations from curators, authors, and automated systems.  ...  We present the results of the BioCreative II.5 evaluation in association with the FEBS Letters experiment, where authors created Structured Digital Abstracts to capture information about protein-protein  ...  The upcoming BioCreative III evaluation (September 2010) will include a task focused on interactive use of automated systems for the protein normalization task and the selection of appropriate user-centric  ... 
doi:10.1109/tcbb.2010.61 pmid:20704011 fatcat:em2jhe322fb2hb65qwewzhfiee

Proceedings of the second biocreative challenge evaluation workshop

Lynette Hirschman, Martin Krallinger, Alfonso Valencia
2007 Zenodo  
Proceedings of the Second BioCreative Challenge Evaluation Workshop  ...  of the AIIA-GMT system to the BioCreative III Gene Normalization data.  ...  Acknowledgements We especially thank the BioGRID (Andrew Chatr-aryamontri) and MINT (Gianni Cesareni) databases and their curators for generating the data collections; without their enormous effort the  ... 
doi:10.5281/zenodo.6519852 fatcat:k6q4vrkd65hbthlvwnhy2ufiey

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
Acknowledgements The authors are partially supported by the FLAGSHIP "InterOmics" project (PB.P05) funded by the Italian MIUR and CNR institutions, and by the cooperative programme 2010-2012 between the  ...  National Research Council of Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica  ...  Today we can use database integration tools and text mining for the prediction of biological networks.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
Association Biomedical concepts Database Dictionaries Hepatitis C Virus Hepatocellular carcinoma Hypothesis generation Protein-protein interactions Text mining iii Abstract To ameliorate Hepatitis C Virus  ...  IDs of journal articles reporting the interactions, annotated protein interaction IDs from external databases, and via "string searches".  ...  Notable projects such as BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) and Knowledge Discovery and Data Mining (KDD) Challenge Cup (Yeh et al., 2003) developed systems  ... 
fatcat:dxh5kptlxfdojbqc7dngtunu4a

DEVELOPMENT OF A HEPATITIS C VIRUS KNOWLEDGEBASE WITH COMPUTATIONAL PREDICTION OF FUNCTIONAL HYPOTHESIS OF THERAPEUTIC RELEVANCE KOJO KWOFIE SAMUEL

Vladimir Bajic, Alan Christoffels
2011 unpublished
Association Biomedical concepts Database Dictionaries Hepatitis C Virus Hepatocellular carcinoma Hypothesis generation Protein-protein interactions Text mining iii Abstract To ameliorate Hepatitis C Virus  ...  IDs of journal articles reporting the interactions, annotated protein interaction IDs from external databases, and via "string searches".  ...  Notable projects such as BioCreAtIvE challenge (Critical Assessment of Information Extraction in Biology) and Knowledge Discovery and Data Mining (KDD) Challenge Cup (Yeh et al., 2003) developed systems  ... 
fatcat:khbuvbkjujbk3dvhoinrnwxqq4