NDLI: An Overview of BioCreative II.5

Content Provider	ACM Digital Library
Author	Leitner, Florian Hirschman, Lynette A. Valencia, Alfonso Mardis, Scott A. Krallinger, Martin Cesareni, Gianni
Abstract	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 interactions. 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. The tasks were to rank articles for curation based on curatable protein-protein interactions; to identify the interacting proteins (using UniProt identifiers) in the positive articles (61); and to identify interacting protein pairs. There were 595 full-text articles in the evaluation test set, including those both with and without curatable protein interactions. The principal evaluation metrics were the interpolated area under the precision/recall curve (AUC iP/R), and (balanced) F-measure. For article classification, the best AUC iP/R was 0.70; for interacting proteins, the best system achieved good macroaveraged recall (0.73) and interpolated area under the precision/recall curve (0.58), after filtering incorrect species and mapping homonymous orthologs; for interacting protein pairs, the top (filtered, mapped) recall was 0.42 and AUC iP/R was 0.29. Ensemble systems improved performance for the interacting protein task.
Starting Page	385
Ending Page	399
Page Count	15
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2010.61
Volume Number	7
Issue Number	3
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2010-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Text mining, text analysis, natural language processing, molecular biology, biological curation.
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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