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Extraction of biological interaction networks from scientific literature

A. Skusa, A. Ruegg, J. Kohler
2005 Briefings in Bioinformatics  
This paper summarises the most important steps in network extraction and reviews common approaches and solutions for the extraction of biological networks from scientific literature.  ...  The extraction of networks from text is an important technique that requires the integration of several different computational disciplines.  ...  JK gratefully acknowledges support from the Biotechnology and Biological Sciences Research Council of the United Kingdom including that from Grant BBS/B/13640.  ... 
doi:10.1093/bib/6.3.263 pmid:16212774 fatcat:mxobulwsqzegndkf7j5up4nqw4

Reconstructing transcriptional Regulatory Networks using data integration and Text Mining

Rafael T. Pereira, Hugo Costa, Sonia Carneiro, Miguel Rocha, Rui Mendes
2015 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors).  ...  And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.  ...  ACKNOWLEDGMENT This work was supported by grant from the CNPq -"National Council of Technological and Scientific Development, Brasil".  ... 
doi:10.1109/bibm.2015.7359907 dblp:conf/bibm/PereiraCCRM15 fatcat:ywerjm5k2rhwtjcxovbpnoav4q

Automatic Extraction of Information on Protein-Protein Interaction from Scientific Literature

Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi
1999 Genome Informatics Series  
Acknowledgement This work was supported in part by a Grant-in-Aid for Scientific Research on Priority Areas , "Genome Science", from the Ministry of Education, Science, Sports and Culture in Japan.  ...  Here, we propose a system for the information extraction of protein-protein interactions from scientific text.  ...  Most of the data resources on biological functions such as expressed patterns and interactions are still only in the biological literature.  ... 
doi:10.11234/gi1990.10.296 fatcat:rp6iayqrs5gshdlkrymgyxboim

PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool

Sapan Mandloi, Saikat Chakrabarti
2015 Scientific Reports  
It also analyzes scientific collaboration by extraction and creation of "co-authorship network," for a given search context.  ...  various interactions of biological entities for better understanding  ...  Biological pathways (signaling and/or metabolic) of the observed proteins and their PPI network are overlaid to provide a meta-interaction network of cellular systems.  ... 
doi:10.1038/srep10021 pmid:25989388 pmcid:PMC4437304 fatcat:rxqm5ds54nfklfjtcf5ekwzc24

Novel biological networks modulated by complement

2005 Clinical Immunology  
Using a novel approach called systems literature analysis that allows the rapid extraction of text-based associations between genes and pathways from the ever expanding scientific article database, we  ...  have selected a broad range of biologic processes modulated by complement proteins and have constructed an integrated map of complement-mediated networks that incorporates well over 85 diverse biologic  ...  This research was supported by National Institutes of Health Grants AI 30040, GM-56698, GM-62134, DK-059422 to JDL.  ... 
doi:10.1016/j.clim.2005.03.012 pmid:15893689 fatcat:eoeyjfzqlvdvjdmfwa34cdzsia

Towards extracting supporting information about predicted protein-protein interactions [article]

Adam Roth, Sandeep Subramanian, Madhavi Ganapathiraju
2015 bioRxiv   pre-print
One of the goals of relation extraction is to identify protein-protein interactions (PPIs) in biomedical literature.  ...  We describe UPSITE, a text mining tool for extracting evidence in support of a hypothesized interaction.  ...  DISCUSSION We have created UPSITE, a text mining algorithm for extracting supporting information about predicted proteinprotein interactions from scientific literature.  ... 
doi:10.1101/031591 fatcat:azxblwzvijcwjph2yhcgav26ee

Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts

See-Kiong Ng, Marie Wong
1999 Genome Informatics Series  
picture (such as protein-protein interaction pathways) as it takes shape amongst the rapidly expanding pool of globally accessible biological data (e.g.  ...  GENBANK) and scientific literature (e.g. MEDLINE).  ...  Further work Our ultimate goal is to be able to automatically organize the scientific knowledge extracted from online sources into networks of interactions which can be tracked, visualized, edited, analyzed  ... 
doi:10.11234/gi1990.10.104 fatcat:ak3su273lfdw5pvcqxkjpldl2i

BioPubMiner: Machine Learning Component-Based Biomedical Information Analysis Platform [chapter]

Jae-Hong Eom, Byoung-Tak Zhang
2004 Lecture Notes in Computer Science  
The extracted interactions are further analyzed with a set of features of each entity that were collected from the related public database to infer more interactions from the original interactions.  ...  The performance of entity and interaction extraction was tested with selected MEDLINE abstracts.  ...  Acknowledgements This research was supported by the Korean Ministry of Science and Technology under the NRL Program and the Systems Biology Program.  ... 
doi:10.1007/978-3-540-30561-3_2 fatcat:bfcztxddrjb6xlisdb5zqhrk7q

Integrated Bio-Entity Network: A System for Biological Knowledge Discovery

Lindsey Bell, Rajesh Chowdhary, Jun S. Liu, Xufeng Niu, Jinfeng Zhang, Ying Xu
2011 PLoS ONE  
of unstructured text in scientific literature.  ...  Most of such information is buried in scientific literature as unstructured text.  ...  Acknowledgments We would like to thank all the authors and curators of the databases we have used in this work for their contributions to a well maintained scientific knowledge base, which made this study  ... 
doi:10.1371/journal.pone.0021474 pmid:21738677 pmcid:PMC3124513 fatcat:5qfmq6samfb2nedy4tjijcwupy

Can the vector space model be used to identify biological entity activities?

Wesley D Maciel, Alessandra C Faria-Campos, Marcos A Gonçalves, Sérgio VA Campos
2011 BMC Genomics  
Our objective is to use the VSM to identify the known interactions from the literature and construct a network.  ...  Biological systems are commonly described as networks of entity interactions. Some interactions are already known and integrate the current knowledge in life sciences.  ...  Acknowledgements WDM acknowledges support from CAPES by the grant of the special program BIOMICRO. All authors acknowledge support from FAPEMIG by the grant of publication fees.  ... 
doi:10.1186/1471-2164-12-s4-s1 pmid:22369514 pmcid:PMC3287578 fatcat:as6r5uvujfeebdc5ljgbq26kzu

Incremental Construction of Biological Networks by Relation Extraction from Literature

Dragana Miljkovic, Vid Podpečan, Tjaša Stare, Igor Mozetič, Kristina Gruden, Nada Lavrač
2015 Current Bioinformatics  
The Bio3graph approach to information extraction from biological literature is extended with new features which allow for periodical updates of network structures using newly published scientific literature  ...  Keywords: biological literature, biological networks, information extraction, plant defence the approach proposed by Ono et al. [18] .  ...  [9] provide state-of-the-art reviews of available systems for biological network extraction from scientific literature and discuss aspects, phases and challenges of the topic.  ... 
doi:10.2174/157489361002150518125321 fatcat:mjppyyrj6rhavjpzzgb35os3li

Integrative data mining in systems biology: from text to network mining

Yonghong Peng, Xuegong Zhang
2007 Artificial Intelligence in Medicine  
of biological networks; (2) the analysis of networks constructed; (3) the use of networks to interpret dynamics and functions of interacting genes and proteins.  ...  Although the scientific observations are still preliminary, the paper presents an interesting approach to integrate TCM literature and modern biomedical literature data to discover novel gene networks  ... 
doi:10.1016/j.artmed.2007.08.001 pmid:17888638 fatcat:xgyxk5ae3vdmllgvh6gvsouk74

Text Mining for Building Biomedical Networks Using Cancer as a Case Study

Sofia I. R. Conceição, Francisco M. Couto
2021 Biomolecules  
Commonly, the data used to build a network comes from diverse high-throughput essays, however most of the interaction data is available through scientific literature.  ...  This can be surpassed by using text mining approaches which are capable of extracting knowledge from scientific documents.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biom11101430 pmid:34680062 pmcid:PMC8533101 fatcat:pfoi74nq5fewrgg3mchguwlbsa

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships

Adriano Barbosa-Silva, Theodoros G Soldatos, Ivan LF Magalhães, Georgios A Pavlopoulos, Jean-Fred Fontaine, Miguel A Andrade-Navarro, Reinhard Schneider, J Miguel Ortega
2010 BMC Bioinformatics  
Conclusions: Text mining tools combining the extraction of interacting bioentities and biological concepts with network displays can be helpful in developing reasonable hypotheses in different scientific  ...  Biological knowledge is represented in scientific literature that often describes the function of genes/ proteins (bioentities) in terms of their interactions (biointeractions).  ...  This work was supported by grants from Germany's National Genome Research Network (Bundesministerium für Bildung und Forschung) and from The Helmholtz Alliance on Systems Biology (Helmholtz-Gemeinschaft  ... 
doi:10.1186/1471-2105-11-70 pmid:20122157 pmcid:PMC3098111 fatcat:zi6re5enfbgmvhrjfybelsmo6e

Automatic pathway building in biological association networks

Anton Yuryev, Zufar Mulyukov, Ekaterina Kotelnikova, Sergei Maslov, Sergei Egorov, Alexander Nikitin, Nikolai Daraselia, Ilya Mazo
2006 BMC Bioinformatics  
Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks.  ...  Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined.  ...  Discussion We describe the computational approach to automatically build signaling pathways using the network database of Biological Associations extracted from scientific literature.  ... 
doi:10.1186/1471-2105-7-171 pmid:16563163 pmcid:PMC1435941 fatcat:dubkz6n7f5ffhcl5czwol2itde
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