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A Text Mining Framework for Accelerating the Semantic Curation of Literature [chapter]

Riza Batista-Navarro, Jennifer Hammock, William Ulate, Sophia Ananiadou
2016 Lecture Notes in Computer Science  
Aiming to accelerate the development of a corpus of biodiversity documents, we propose a text mining framework that hastens curation through an iterative feedback-loop process of (1) manual annotation,  ...  However, gold standard, semantically annotated textual corpora are critical for the development of these advanced tools.  ...  The framework is implemented as processing workflows in Argo 2 , a Web-based text mining workbench [2] .  ... 
doi:10.1007/978-3-319-43997-6_44 fatcat:ukx2okm6gvhbtidetkaw2exmd4

A Curation Pipeline and Web-Services for PDF Documents

André Santos, Sérgio Matos, David Campos, José Luís Oliveira
2016 International Symposium for Semantic Mining in Biomedicine  
The continuous growth of the biomedical literature and the need to efficiently find and extract information from its content led to the development of various text mining tools.  ...  To address this limitation, we extended the web-based literature curation tool Egas, adding support for direct document curation and annotation over PDF files, with side-by-side visualization of the original  ...  Egas Egas is a web-based platform for biomedical text mining and collaborative curation that supports inline annotation of concept occurrences and of relations between these concepts.  ... 
dblp:conf/smbm/SantosMCO16 fatcat:yszrg3n5rjd7zgg7rmssivhgvm

An Approach towards Semi-automated Biomedical Literature Curation and Enrichment for a Major Biological Database

Fabio Rinaldi, Oscar Lithgow-Serrano, Alejandra López-Fuentes, Socorro Gama-Castro, Yalbi I. Balderas-Martínez, Hilda Solano-Lira, Julio Collado-Vides
2015 POLIBITS Research Journal on Computer Science and Computer Engineering With Applications  
The aim of our activity is to improve the efficiency of this process by leveraging upon natural language processing technologies in a text mining system.  ...  Biological experts routinely extract core information from the scientific literature using a manual process known as scientific curation.  ...  Biomedical text mining can be used to partially automate the process of biomedical literature curation by using sophisticated algorithms for discovering biomedical entities together with interaction and  ... 
doi:10.17562/pb-52-3 fatcat:akvxswq7u5havf45rrx56sfjna

The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia

Satoshi Mizuno, Soichi Ogishima, Hidekazu Nishigori, Daniel G. Jamieson, Karin Verspoor, Hiroshi Tanaka, Nobuo Yaegashi, Jun Nakaya, Anne Croy
2016 PLoS ONE  
In such a situation, it is necessary to develop an interoperable and standardized semantic framework to research the pathology of PE more comprehensively and to achieve interoperability of heterogenic  ...  However, most of these data are not semantically structured.  ...  This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.  ... 
doi:10.1371/journal.pone.0162828 pmid:27788142 pmcid:PMC5082890 fatcat:fktpk77t2fdmxni5w2absceacu

Introduction: selected extended articles from the 2nd International Workshop on Semantics-Powered Data Analytics (SEPDA 2017)

Zhe He, Cui Tao, Jiang Bian, Rui Zhang, Jingshan Huang
2018 BMC Medical Informatics and Decision Making  
Acknowledgments The Guest Editors of this supplement would like to thank the authors and the reviewers for their scientific contribution and congratulate them on their high quality work.  ...  s work, "An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival," they created a semantic data integration framework to address the syntactic, schematic  ...  How to automatically curate these KBs from free-text data is also an active research area.  ... 
doi:10.1186/s12911-018-0624-8 pmid:30066636 pmcid:PMC6069756 fatcat:qjkptie33fephlhestivneevg4

The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track

Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel Peitsch, Juliane Fluck
2016 Database: The Journal of Biological Databases and Curation  
BELIEF provides a webbased curation interface, the BELIEF Dashboard, that incorporates text mining techniques to support the biocurator in the generation of BEL networks.  ...  Considering the complexity of the task for new users-learning BEL, working with a completely new interface, and performing complex curation-a score so close to the overall SUS average highlights the usability  ...  Various discussions and feedback rounds helped us to create a usable curation environment for the biocurators.  ... 
doi:10.1093/database/baw136 pmid:27694210 pmcid:PMC5045868 fatcat:fkuoxt7j6ffnxoknhsqmqjvdrq

Biomedical knowledge engineering approaches driven by processing the primary experimental literature

Ingulfsen Tommy
2008 Frontiers in Neuroinformatics  
We are grateful to Alan Watts and Arshad Khan for their support in developing the basic ideas of the KE-f-ED model, as well as many of our colleagues at ISI and USC for their ongoing contributions and  ...  Acknowledgements: This work was funded by grant R01 GM-083871 from NIGMS and support from the Center for Health Informatics (CHI) at ISI.  ...  We also describe how this approach provides a framework suitable for text mining that leverages information extraction (IE) technology.  ... 
doi:10.3389/conf.neuro.11.2008.01.011 fatcat:mqtyr7mbonhgpljwcy34zwggfu

Text mining for biology - the way forward: opinions from leading scientists

Russ B Altman, Casey M Bergman, Judith Blake, Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Jensen, Martin Krallinger (+6 others)
2008 Genome Biology  
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  ...  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  ...  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-s7 pmid:18834498 pmcid:PMC2559991 fatcat:6cerr44envaqrfatnatmiy5nbq

Computational Approaches to Phenotyping: High-Throughput Phenomics

Y. A. Lussier, Y. Liu
2007 Proceedings of the American Thoracic Society online  
The recent completion of the Human Genome Project has made possible a high-throughput "systems approach" for accelerating the elucidation of molecular underpinnings of human diseases, and subsequent derivation  ...  Key state-of-the-art technological advancements critical for HTP phenomics research are covered in this review.  ...  Acknowledgment : The authors thank Lee Sam for his advice on improving the manuscript.  ... 
doi:10.1513/pats.200607-142jg pmid:17202287 pmcid:PMC2647609 fatcat:gb4dc7uvkjg6tbg5epfudwlh3u

Cardiovascular Health and Physical Activity: A Model for Health Promotion and Decision Support Ontologies

Vimala Ponna, Aaron Baer, Matthew Lange
2016 International Conference on Biomedical Ontology  
These conceptual maps lay the foundation for accelerated creation of health-focused ontologies, which ultimately equip DSS with CVHF knowledge related PA and DI.  ...  This dearth of CVHF-PA/DI structured knowledge repositories has resulted in a scarcity of user-friendly tools for scientifically validated information retrieval about CVHF improvement.  ...  workflow for easy data mining and concept lattice extraction from literature.  ... 
dblp:conf/icbo/PonnaBL16 fatcat:y6dlzwdom5cfbg6jk56inkz43i

Literature mining for context-specific molecular relations using multimodal representations (COMMODAR)

Jaehyun Lee, Doheon Lee, Kwang Hyung Lee
2020 BMC Bioinformatics  
In this paper, we propose COMMODAR, a machine learning-based literature mining framework for context-specific molecular relations using multimodal representations.  ...  The main idea of COMMODAR is the feature augmentation by the cooperation of multimodal representations for relation extraction.  ...  About this supplement This article has been published as part of BMC Bioinformatics, Volume 21 Supplement 5, 2020: Proceedings of the 13th International Workshop on Data and Text Mining in Biomedical Informatics  ... 
doi:10.1186/s12859-020-3396-y pmid:33106154 fatcat:s3oha7endfcqhnxifzdckxxi5a

An Approach for Discovering and Exploring Semantic Relationships between Genes

Nicoletta Dessì, Matteo Pani, Barbara Pes, Diego Reforgiato Recupero
2017 Extended Semantic Web Conference  
This paper presents an approach for extracting, integrating and mining the annotations from a large corpus of gene summaries.  ...  It includes: i) a method for extracting annotations from several ontologies, mapping them into concepts and evaluating the semantic relatedness of genes, ii) the definition of a NoSQL graph database that  ...  The integration of concepts resulting from the annotation of a corpus of documents is considered the next step of text-mining research community [4] and presents tremendous opportunities for accelerating  ... 
dblp:conf/esws/DessiPPR17 fatcat:dz2xu3dleja3ppn4cmtunw4af4

Infrastructure for Annotation-Driven Information Extraction from the Primary Scientific Literature: Principles and Practice

Gully Burns, Donghui Feng, Tommy Ingulfsen, Eduard Hovy
2007 2007 IEEE Congress on Services (Services 2007)  
We also discuss how the process of annotating text for IE directly supports designing schema for databases.  ...  We provide a preliminary, detailed example of the use of the infrastructure to support the construction of a database pertaining to neuroanatomical tract-tracing experiments.  ...  Conclusion In this paper, we present a computational infrastructure for a reconfigurable text-mining system to construct a database of experimental data from the published literature.  ... 
doi:10.1109/services.2007.34 dblp:conf/IEEEscc/BurnsFIH07 fatcat:mni6j6ntonabpgc3c2v44st6c4

Integration of Protein Data Sources Through PO [chapter]

Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang
2006 Lecture Notes in Computer Science  
The establishment of semantic interoperation over conceptual framework of PO enables us to get a better insight on how information can be integrated systematically and how queries can be composed.  ...  The semantic interoperation between protein data sources is based on semantic relationships between concepts of PO.  ...  Mining of Scientific Text and Literature is done to generate list of keywords that is used as GO terms.  ... 
doi:10.1007/11827405_51 fatcat:roorateiqvdsjodtlfx4gi22ce

Event extraction for systems biology by text mining the literature

Sophia Ananiadou, Sampo Pyysalo, Jun'ichi Tsujii, Douglas B. Kell
2010 Trends in Biotechnology  
To computationally mine the literature for such events, text mining methods that can detect, extract and annotate them are required.  ...  Systems biology recognizes in particular the importance of interactions between biological components and the consequences of these interactions.  ...  We would like to thank Paul Thompson and John McNaught (National Centre for Text Mining, University of Manchester) for their helpful comments and support in producing this manuscript.  ... 
doi:10.1016/j.tibtech.2010.04.005 pmid:20570001 fatcat:thw62syppnhd3jzd52ajqs5wum
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