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A Language Modeling Text Mining Approach to the Annotation of Protein Community
2006
Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06)
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This paper discusses an ontology based language modeling text mining approach to the annotation of protein community. ...
Thus, we present an ontology based mixture language model approach to annotate protein community. Compared to traditional method, we have the following three advantages. ...
CONCLUSIONS In this paper, we present an ontology based language modeling text mining approach to the annotation of protein community, which provides a different perspective in evaluating and annotating ...
doi:10.1109/bibe.2006.253310
dblp:conf/bibe/ZhangWZH06
fatcat:mhyyavrqyrh6vocbmt3c4rl7sa
ISMB 2003 Text Mining SIG Meeting Report
2003
Comparative and Functional Genomics
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Acknowledgements The organizers of the workshop would like to thank especially all the speakers for their presentations, Marc Light for co-organizing the event, Steven Leard and the ISCB (The International ...
Society for Computational Biology) for organizing the logistics and the infrastructure, and the EU projects ORIEL (Contract number: IST-2001-32688) and TEMBLOR (Contract number: VEQLRT 2001 00015) for ...
A corpus of texts relevant to the study of protein structures was assembled. ...
doi:10.1002/cfg.338
pmid:18629019
pmcid:PMC2447301
fatcat:vmqqau3myrgsfdfhwotqljapje
The State of the Art on Knowledge Graph Construction from Text: Named Entity Recognition and Relation Extraction Perspectives
2022
Zenodo
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This presentation covers the state-of-the-art benchmark dataset resources as well as the best neural models for the respective task perspectives. ...
This led to annotation and development of social media or twitter-specific NER corpora and tools. ■ A semantically annotated corpus for biomedical text mining. • Includes annotations for genes, proteins ...
annotated corpus for biomedical text mining. • Includes annotations for genes, proteins, and other concepts in the Genia ontology. • Includes various levels of annotations other than named entities such ...
doi:10.5281/zenodo.6521883
fatcat:swra4e7rf5dljhjojl7nc2cq4i
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience
2012
Database: The Journal of Biological Databases and Curation
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A range of text mining strategies has been devised to assist in the automated extraction of biological data. ...
Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information ...
Acknowledgements We would like to thank Lynette Hirschman and Christian Blaschke for their active feedback in the BioCreative tasks described in this article. ...
doi:10.1093/database/bas017
pmid:22438567
pmcid:PMC3309177
fatcat:3q2zwcobxfaebl4rw4hsnddid4
Application of Biomedical Text Mining
[chapter]
2018
Artificial Intelligence - Emerging Trends and Applications
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The aim is to provide a way to quickly understand biomedical text mining for some researchers. ...
With the enormous volume of biological literature, increasing growth phenomenon due to the high rate of new publications is one of the most common motivations for the biomedical text mining. ...
Based on the rapid development of omics era, the BioCreative called Critical Assessment of Information Extraction system in Biology is a community-wide effort for the evaluation of text mining and information ...
doi:10.5772/intechopen.75924
fatcat:5o27ptssi5fwzbelnpktkwplby
Text-mining approaches in molecular biology and biomedicine
2005
Drug Discovery Today
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Also , the use of text mining to aid the interpretation of microarray data and the analysis of pathology reports will be discussed. ...
To extract relevant information using automatic techniques, text-mining and information-extraction approaches have been developed. ...
Applications of text mining Functional annotation Annotation of the function of genes and proteins is the principal goal of genome analysis. ...
doi:10.1016/s1359-6446(05)03376-3
pmid:15808823
fatcat:w5i3ciuq4zhk7oq4kbbv5wqfma
The Treasury Chest of Text Mining: Piling Available Resources for Powerful Biomedical Text Mining
2021
BioChem
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When applied to biomedical literature, text mining is named biomedical text mining and its specificity lies in both the type of analyzed documents and the language and concepts retrieved. ...
Text mining (TM) is a semi-automatized, multi-step process, able to turn unstructured into structured data. ...
The funding agencies had no role in the design of the study, in the collection, analyzes, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. ...
doi:10.3390/biochem1020007
fatcat:qve6xgoxuvbwzpqz6q45s7wlly
Proceedings of the Second International Symposium for Semantic Mining in Biomedicine
2006
BMC Bioinformatics
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The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/7?issue=S3. ...
Acknowledgements This article has been published as part of BMC Bioinformatics Volume 7, Supplement 3, 2006: Second International Symposium on Semantic Mining in Biomedicine. ...
The approach is based on a parser using a hand-written grammar combined with a statistical language model that calculates lexicalized attachment probabilities. ...
doi:10.1186/1471-2105-7-s3-s1
fatcat:h26jwoukezbvtgt73qlrfhyapy
Text mining for systems biology
2014
Drug Discovery Today
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Scientific communication in biomedicine is, by and large, still text based, because we all feel the need to report scientific advancements in a way that enables us to make use of the high expressiveness ...
Modelling of complex biological processes, spanning pathways to entire diseases, can be done at various levels of granularity using a range of mathematical modelling approaches [2] . ...
[19] demonstrated the value of a combination of a pharmacokinetics ontology, a well-annotated reference corpus, and a text-mining system that recognizes most types of information relevant to pharmacokinetics ...
doi:10.1016/j.drudis.2013.09.012
pmid:24070668
fatcat:ajnerehdqndv5nk3l6jak42n5e
BioC: a minimalist approach to interoperability for biomedical text processing
2013
Database: The Journal of Biological Databases and Curation
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Acknowledgement The authors thank the anonymous reviewers for their useful suggestions in improving this manuscript. ................................................................................. ...
Introduction With the proliferation of natural language text, text mining has emerged as an important research area. ...
This web services-based approach to text mining, if successful, could serve as a proof-of-concept to decouple the potentially disparate technical infrastructures of text mining integrators and their service ...
doi:10.1093/database/bat064
pmid:24048470
pmcid:PMC3889917
fatcat:m5q3ltrfobg4fgkash3katpkia
Critical Assessment of Information Extraction Systems in Biology
2003
Comparative and Functional Genomics
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An increasing number of groups are now working in the area of text mining, focusing on a wide range of problems and applying both statistical and linguistic approaches. ...
Inspired by this example, the BioLINK group (Biological Literature, Information and Knowledge [1]) is organizing a CASP-like evaluation for the text data-mining community applied to biology. ...
The 'natural language processing' or MUC version of this task required that a system identify each mention of a gene or protein in the text. ...
doi:10.1002/cfg.337
pmid:18629031
pmcid:PMC2447314
fatcat:ui3y2qsegvbpdhg6qafs7esrxe
Report On Prototypes Constructed Using Big Data Approaches
2018
Zenodo
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While this serves as a useful prototype, further cleaning of the input data and better training of the model are still required. ...
Using it, annotations will be made to all past papers with known links to entries in the Protein Data Bank. These annotations are available in EuropePMC. ...
PDBe query system for all macromolecular structures in the PDB) as a corpus definition to a text processing service to take advantage of existing text mining facilities. ...
doi:10.5281/zenodo.1245644
fatcat:qi2f6wwmfraflackft5ble4qyi
The BioLink SIG Workshop at ISMB2004
2005
Comparative and Functional Genomics
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We would also like to thank the invited speakers, whose workshop abstracts appear in this overview. ...
Acknowledgements We would like to thank the Program Committee for their careful reviewing: Luc Dehaspe, Robert Gaizauskas, William Hersh, Karin Verspoor and Alexander Yeh. ...
BioMinT: a database curator's assistant for biomedical text processing -Anne-Lise Veuthey The goal of the BioMinT project is to develop a generic text mining tool that assists manual database annotation ...
doi:10.1002/cfg.455
pmid:18629301
pmcid:PMC2448605
fatcat:lfl62kerhbdvblziets4jxihqa
Adaptation of MelanomaMine and LiMTox to the analysis of paediatric cancers and application to biomedical publications on paediatric cancers
2021
Zenodo
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These tools will be used in the framework of the iPC project but also beyond, having a clear impact in the research community. ...
The workflow builds on the general framework of two text mining tools, LimTox and MelanomaMine. ...
endeavour, which requires the use of Natural Language Processing (NLP) and, in particular, text mining approaches. ...
doi:10.5281/zenodo.6546342
fatcat:ro3eopiyqbebrpfuk6cxuzujdq
Text mining for biology - the way forward: opinions from leading scientists
2008
Genome Biology
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and supporting community-based annotation; the importance of scaling text mining technology and inserting it into larger workflows; and suggestions for additional challenge evaluations, new applications ...
The responses identify several broad themes, including the possibility of fusing literature and biological databases through text mining; the need for user interfaces tailored to different classes of users ...
Acknowledgements The BioCreative II challenge and workshop were sponsored by the Frontiers of Functional Genomics Programme of the European Science Foundation (ESF) and by Genoma Espana http://gen-es.org ...
doi:10.1186/gb-2008-9-s2-s7
pmid:18834498
pmcid:PMC2559991
fatcat:6cerr44envaqrfatnatmiy5nbq
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