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Gupta, Rajinder and Mantri, Shrikant S. (2016) Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over. Frontiers in Genetics, 7 (46). ISSN 16648021

Biomolecular Relationships Discovered from Biological Labyrinth.pdf

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Many brilliant minds are at work to decipher the biological labyrinth and as a result immense amount of information about biological entities and their relationships is getting accumulated in the form of published literature (Hunter and Cohen, 2006). To cater the needs of a researcher, many tools are designed to perform tasks of Named Entity Recognition (NER), Information Retrieval (IR), and Information Extraction (IE) viz. A Combined Clinical Concept Annotator (Kang et al., 2012), BANNER (Leaman and Gonzalez, 2008), Biblio-MetReS (Usie et al., 2014), BioTextQuest+ (Papanikolaou et al., 2014), BIOSMILE Web Search (Dai et al., 2008), E3Miner (Lee et al., 2008), EBIMed (Rebholz-Schuhmann et al., 2007), eFIP (Arighi et al., 2011), FACTA+ (Tsuruoka et al., 2008), GNSuite1, iHOP (Hoffmann and Valencia, 2004), MyMiner (Salgado et al., 2012), RLIMS-P(Hu et al., 2005), Anni (Jelier et al., 2008), CoPub (Frijters et al., 2008), MedScan (Novichkova et al., 2003), PPInterFinder (Raja et al., 2012), pGenN (Ding et al., 2015), SciMiner (Hur et al., 2009), BIGNER (Li et al., 2009), hybrid named entity tagger (Raja et al., 2014), and more such tools can be obtained from BIONLP resource2 and in detail analysis of many NLP tools is given by Krallinger et al. (2008) and Fleuren and Alkema (2015). Table 1 gives an informational and statistical insight into some of these literature mining tools, shedding light on their efficiency translated by statistical parameters viz. F-score, recall, and precision. Many tools are domain specific like kinase family specific but still calls for human intervention for exactitude and thus limit their usage. Moreover, the data output formats are sometimes too vague as name highlighting; to be put to use for bigger literature searches.

Item Type: Article
Uncontrolled Keywords: literaturemining,namedentityrecognition,informationretrieval,informationextraction,community efforts,relationshipdatabase,interactions,relationships
Subjects: Agri-Biotechnology
Depositing User: Dr. Author @NABI
Date Deposited: 12 Mar 2021 04:48
Last Modified: 12 Mar 2021 04:48
URI: http://nabi.sciencecentral.in/id/eprint/47

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