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Data-driven materials research enabled by natural language processing and information extraction

Elsa A. Olivetti, Jacqueline M. Cole, Edward Kim, Olga Kononova, Gerbrand Ceder, Thomas Yong-Jin Han, Anna M. Hiszpanski
2020 Applied Physics Reviews  
DATA AVAILABILITY Data sharing is not applicable to this article as no new data were created or analyzed in this study.  ...  A means to automatically extract materials-physics data from scientific documents is, therefore, required.  ...  These were sourced from just over 400 000 academic papers using ChemDataExtractor. 33 The information density of data extraction (number of data records obtained: number of papers sampled) is quite low  ... 
doi:10.1063/5.0021106 fatcat:75aap3lkjvhprleptl3bbp6w64

Bridging semantics and syntax with graph algorithms—state-of-the-art of extracting biomedical relations

Yuan Luo, Özlem Uzuner, Peter Szolovits
2016 Briefings in Bioinformatics  
The ability to accurately capture both semantic and syntactic structures in text expressing these relations becomes increasingly critical to enable deep understanding of scientific papers and clinical  ...  However, a number of problems at the frontiers of biomedical relation extraction continue to pose interesting challenges and present opportunities for great improvement and fruitful research.  ...  Acknowledgement The work was supported in part by Grant Number U54LM008748 from the National Library of Medicine, NIH 154HG007963 from the National Human Genome Research Institute and by the Scullen Center  ... 
doi:10.1093/bib/bbw001 pmid:26851224 pmcid:PMC5221425 fatcat:z6sptxngubempdx6kthsyab7be

Concept recognition for extracting protein interaction relations from biomedical text

William A Baumgartner, Zhiyong Lu, Helen L Johnson, J Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K White, Olga Medvedeva, K Bretonnel Cohen, Lawrence Hunter
2008 Genome Biology  
Results: Through the modular construction of a protein interaction relation extraction system, we present several use cases of concept recognition in biomedical text, and relate these use cases to potential  ...  As a demonstration of the potential effectiveness of integrating concept recognition, we have constructed a protein interaction relation extraction system, the components of which were generated through  ...  Acknowledgements We thank the two anonymous reviewers of our BioCreative Workshop Proceedings paper for their insightful feedback which also influenced the writing of this paper.  ... 
doi:10.1186/gb-2008-9-s2-s9 pmid:18834500 pmcid:PMC2559993 fatcat:dlkdq6hbdff5lhjc4ffdkwlqni

BioCreative II Workshop Proceedings

Lynette, Martin, Alfonso
2007 Zenodo  
(IAS) 41 Assessment of the Second BioCreative PPI task: Automatic Extraction of Protein-Protein Interactions 55 Annotating molecular interactions in the MINT database 61 IntAct - Serving the text-mining  ...  community with high quality molecular interaction data 69 IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task 77 Identifying Gene Mentions by Case-Based Classifi cation  ...  Acknowledgements The txm pipeline on which this system was based was carried out as part of a joint project with Cognia (http://www.cognia.com), supported by the Text Mining Programme of ITI Life Sciences  ... 
doi:10.5281/zenodo.4274543 fatcat:3sa3fvgngffjrblxzgswof42tq

Biomedical Literature Mining for Biological Databases Annotation [chapter]

Margherita Berardi, Donato Malerba, Roberta Piredda, Marcella Attimonelli, Gaetano Scioscia, Pietro Leo
2008 Data Mining in Medical and Biological Research  
As of now, PubMed remains the richest and most updated source of information about biological data despite its unstructured nature.  ...  In this chapter, we present a framework for biomedical information extraction from text that integrates a data mining module for extraction rule discovery.  ...  in the promising areas of medicine and biology from around the world.  ... 
doi:10.5772/6419 fatcat:mvn4karkbnad5dcfa4ohjiw6cq

A Survey on Event Extraction for Natural Language Understanding: Riding the Biomedical Literature Wave

Giacomo Frisoni, Gianluca Moro, Antonella Carbonaro
2021 IEEE Access  
To cope with the everincreasing number of publications, researchers are experiencing a surge of interest in extracting valuable, structured, concise, and unambiguous information from plain texts.  ...  After being studied for years, automatic event extraction is on the road to significantly impact biology in a wide range of applications, from knowledge base enrichment to the formulation of new research  ...  G.F. conducted the review and wrote the manuscript. G.M. and A.C. supervised all steps of the work and revised each section.  ... 
doi:10.1109/access.2021.3130956 fatcat:wlr7zeikdva77ojuppqx3vmocy

Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches

Pantelis Natsiavas, Andigoni Malousi, Cédric Bousquet, Marie-Christine Jaulent, Vassilis Koutkias
2019 Frontiers in Pharmacology  
The 80 finally selected articles were reviewed on full-text, while the mapping process relied on a set of concrete criteria (concerning specific KE and DS core activities, special DS topics, employed data  ...  Journal articles published between 2006 and 2017 were retrieved from PubMed/MEDLINE and Web of Science® (873 in total) and filtered based on a comprehensive set of inclusion/exclusion criteria.  ...  Knowledge extraction The most widely used knowledge extraction approach refers to the use of NLP techniques applied on unstructured data, i.e., free-text, originated from biomedical literature, social  ... 
doi:10.3389/fphar.2019.00415 pmid:31156424 pmcid:PMC6533857 fatcat:pljcyqcp6red7pdwa5burxgbx4

Program Committee

2006 2006 Sixth IEEE International Workshop on Source Code Analysis and Manipulation  
Including the papers on embeddings, there were 15 rejections: the acceptance rate for full papers was 58% a sign of the consistently high quality of papers submitted to the conference.  ...  There were 4 invited talks, 41 full papers, 15 posters and 4 invited talks on TEL.  ...  to the paper.  ... 
doi:10.1109/scam.2006.23 dblp:conf/scam/X06c fatcat:2dhsf7loj5hlffu2jxpmlo2qcq

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz (+65 others)
2020 F1000Research  
We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences  ...  the reusability of biological data.  ...  Acknowledgements BH15 is supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience Database Center (NBDC  ... 
doi:10.12688/f1000research.18236.1 pmid:32308977 pmcid:PMC7141167 fatcat:oaglnztjrrhpvgluujl3reudoe

Towards "On the Go" Matching of Linked Open Data Ontologies

Isabel F. Cruz, Matteo Palmonari, Federico Caimi, Cosmin Stroe
2011 International Joint Conference on Artificial Intelligence  
In this paper we summarize our experience in providing a semantic extension to the geo-catalogue of the Autonomous Province of Trento (PAT) in Italy.  ...  The semantic extension is based on the adoption of the S-Match semantic matching tool and on the use of a specifically designed faceted ontology codifying domain specific knowledge.  ...  Abstract This paper adopts an unsupervised subclass discovery approach to automatically improve the taxonomy of Wikipedia vandalism.  ... 
dblp:conf/ijcai/CruzPCS11 fatcat:62apmemu2zgirduzh6zomuw7wi

Proceedings of the BioCreative V.5 Challenge Evaluation Workshop

Martin Krallinger, Alfonso Valencia
2022 Zenodo  
Proceedings of the BioCreative V.5 Challenge Evaluation Workshop  ...  The Spanish National Bioinformatics Institute (INB) unit at the Spanish National Cancer Research Centre (CNIO) is a member of the INB, PRB2-ISCIII and is supported by grant PT13/0001/0030, of the PE I+  ...  Acknowledgment We acknowledge the OpenMinted (654021) and the ELIXIR-EXCELERATE (676559) H2020 projects, and the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Lan-guage Technology  ... 
doi:10.5281/zenodo.6519885 fatcat:gzzr6ogkwvfe3eglv6anrzt5s4

Absolute Quantification of the Glycolytic Pathway in Yeast:

Kathleen M. Carroll, Deborah M. Simpson, Claire E. Eyers, Christopher G. Knight, Philip Brownridge, Warwick B. Dunn, Catherine L. Winder, Karin Lanthaler, Pınar Pir, Naglis Malys, Douglas B. Kell, Stephen G. Oliver (+2 others)
2011 Molecular & Cellular Proteomics  
In addition, the quantification data from the label-free approach used in this paper and the QconCAT quantification data are included for comparison.  ...  Assuming 4 -5 pg of protein from a typical haploid yeast cell and an average protein molecular weight of 50 kDa, this gives a total constituency of ϳ50 million protein molecules.  ...  .), and BB/ C505140/1 (to S. G. O.); and a contract from the European Commission under the FP7 Collaborative Programme, UNICELLSYS (to S. G.  ... 
doi:10.1074/mcp.m111.007633 pmid:21931151 pmcid:PMC3237070 fatcat:exxjfdrqpvbc7hdgrevf5ybkcm

An Effective Approach to Biomedical Information Extraction with Limited Training Data [article]

Siddhartha Jonnalagadda
2011 arXiv   pre-print
Overall, the two main contributions of this work include the application of sentence simplification to association extraction as described above, and the use of distributional semantics for concept extraction  ...  This approach renders all the advantages offered in other semi-supervised machine learning systems, and, unlike other proposed semi-supervised approaches, it can be used on top of different basic frameworks  ...  Efficient extraction of protein-protein interactions from full-text articles. IEEE/ACM TCBB. 2010 3. Siddhartha Jonnalagadda, Robert Leaman, Trevor Cohen and Graciela Gonzalez.  ... 
arXiv:1107.5752v2 fatcat:n7rtfgpvarh7do2xar6opjec5q

Organizing institutions

2015 2015 21st International Conference on Automation and Computing (ICAC)  
Acknowledgments The authors thank the Fundação Araucária of Paraná, Brazil and the Portuguese Fundação para a Ciência e Tecnologia through the financial support of INESC-ID funding under project PEst-OE  ...  We thank the organizing committee for their commitment to the success of the event, the authors for their submissions and the program committee for their hard work. Acknowledgements.  ...  NLP aims at extracting information directly from unstructured texts, and depends on the natural language pre-processing such as in Ondux [Cortez et al. 2010] and JUDIE [Cortez et al. 2011] .  ... 
doi:10.1109/iconac.2015.7313649 fatcat:prpaqk2d4bhnlom25xxztiimaq

Organizing institutions

2016 2016 10th International Conference on Software, Knowledge, Information Management & Applications (SKIMA)  
Acknowledgments The authors thank the Fundação Araucária of Paraná, Brazil and the Portuguese Fundação para a Ciência e Tecnologia through the financial support of INESC-ID funding under project PEst-OE  ...  We thank the organizing committee for their commitment to the success of the event, the authors for their submissions and the program committee for their hard work. Acknowledgements.  ...  NLP aims at extracting information directly from unstructured texts, and depends on the natural language pre-processing such as in Ondux [Cortez et al. 2010] and JUDIE [Cortez et al. 2011] .  ... 
doi:10.1109/skima.2016.7916183 fatcat:ctichxcphnhj7ci3h4lu662gbi
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