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Novel Protein-Protein Interactions Inferred from Literature Context

Herman H. H. B. M. van Haagen, Peter A. C. 't Hoen, Alessandro Botelho Bovo, Antoine de Morrée, Erik M. van Mulligen, Christine Chichester, Jan A. Kors, Johan T. den Dunnen, Gert-Jan B. van Ommen, Silvère M. van der Maarel, Vinícius Medina Kern, Barend Mons (+2 others)
2009 PLoS ONE  
The full set of predicted interactions is available in a downloadable matrix and through the webtool Nermal, which lists the most likely interaction partners for a given protein.  ...  We have developed a method that predicts Protein-Protein Interactions (PPIs) based on the similarity of the context in which proteins appear in literature.  ...  in MEDLINE as they are only mentioned in a full text article.  ... 
doi:10.1371/journal.pone.0007894 pmid:19924298 pmcid:PMC2774517 fatcat:m5jxzdvgf5b47enjmxndhonnwu

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins

Somnath Tagore, Alessandro Gorohovski, Lars Juhl Jensen, Milana Frenkel-Morgenstern, Roland L. Dunbrack
2019 PLoS Computational Biology  
Thus, the continual increase in scientific literature drives the need for efficient methods of data mining to improve the extraction of useful information from texts based on patients' genomic features  ...  An important application of text mining to tailored therapy in cancer encompasses the use of mutations and cancer fusion genes as moieties that change patients' cellular networks to develop cancer, and  ...  Moreover, when extracting protein-protein interactions (PPIs) of fusions, their actions can be described in varying ways (e.g., activate vs. interact vs. express vs. induce [4] ).  ... 
doi:10.1371/journal.pcbi.1007239 pmid:31437145 pmcid:PMC6705771 fatcat:khvc73jyljdvjpjkkdbkyedgxa

Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature

Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz, Sophia Ananiadou
2011 BMC Bioinformatics  
The contest's Protein-Protein Interaction (PPI) task consisted of two sub-tasks: Article Classification Task (ACT) and Interaction Method Task (IMT).  ...  ACT aimed to automatically select relevant documents for PPI curation, whereas the goal of IMT was to recognise the methods used in experiments for identifying the interactions in full-text articles.  ...  CR helped on text cleaning and the extraction of MeSH information. RB provided data and error analysis. RN constructed the mapping between MeSH and MI IDs. SA supervised all steps of the work.  ... 
doi:10.1186/1471-2105-12-s8-s11 pmid:22151769 pmcid:PMC3269934 fatcat:qmfgoxabnbd5nctdbokyn7jlfq

Assigning function to protein-protein interactions: a weakly supervised BioBERT based approach using PubMed abstracts [article]

Aparna Elangovan, Melissa Davis, Karin Verspoor
2022 arXiv   pre-print
This work demonstrates that analysis of biomedical abstracts for PPI function extraction is a feasible approach to substantially increasing the number of interactions annotated with function captured in  ...  Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of  ...  Acknowledgements We would like to thank the authors of Hsieh (2017)  ... 
arXiv:2008.08727v3 fatcat:bs6dc447bvhcbnfhu32wpfmqjy

HMNPPID—human malignant neoplasm protein–protein interaction database

Qingqing Li, Zhihao Yang, Zhehuan Zhao, Ling Luo, Zhiheng Li, Lei Wang, Yin Zhang, Hongfei Lin, Jian Wang, Yijia Zhang
2019 Human Genomics  
Protein-protein interaction (PPI) information extraction from biomedical literature helps unveil the molecular mechanisms of biological processes.  ...  The full contents of the supplement are available online at https://humgenomics.  ...  About this supplement This article has been published as part of Human Genomics Volume 13 Supplement 1, 2019: Selected articles from the IEEE BIBM International Conference on Bioinformatics & Biomedicine  ... 
doi:10.1186/s40246-019-0223-5 pmid:31639057 pmcid:PMC6805303 fatcat:c24aqznh35djbcats77w7g5hwu

A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature [article]

Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha
2011 arXiv   pre-print
We participated, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge.  ...  For the ACT, we show that the use of named entity recognition tools leads to a substantial improvement in the ranking and classification of articles relevant to protein-protein interaction.  ...  We also thank support from these grants for travel, hosting and providing facilities used to conduct part of this research.  ... 
arXiv:1103.4090v2 fatcat:oxqfmzxi6nhflpakkqxz4qnrsy

Getting to the (c)ore of knowledge: mining biomedical literature

Berry de Bruijn, Joel Martin
2002 International Journal of Medical Informatics  
Abstract Literature mining is the process of extracting and combining facts from scientific publications.  ...  In recent years, many computer programs have been designed to extract various molecular biology findings from Medline abstracts or full text articles.  ...  ) can be applied towards the correct analysis of abstracts or full text.  ... 
doi:10.1016/s1386-5056(02)00050-3 pmid:12460628 fatcat:ipgcakav7zhfnjy5leqp6tpnhe

BBP: Brucella genome annotation with literature mining and curation

Zuoshuang Xiang, Wenjie Zheng, Yongqun He
2006 BMC Bioinformatics  
It is partially due to the lack of a literature mining and curation system able to efficiently incorporate the large amount of literature data into genome annotation.  ...  To efficiently annotate Brucella genes using the large amount of literature publications, a literature mining and curation system coined Limix is developed to integrate computational literature mining  ...  Hans-Michael Muller from the California Institute of Technology for his technical help in our development of Textpresso-powered Brucella literature search engine.  ... 
doi:10.1186/1471-2105-7-347 pmid:16842628 pmcid:PMC1539029 fatcat:tjj2jljkwbhw7mcl3ojbzeubmq

Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson

Sonja Hatz, Scott Spangler, Andrew Bender, Matthew Studham, Philipp Haselmayer, Alix M. B. Lacoste, Van C. Willis, Richard L. Martin, Harsha Gurulingappa, Ulrich Betz, Jianjun Hu
2019 PLoS ONE  
, requiring only an initial determination of a specific target-disease relationship.  ...  A biological pathway network typically includes entities (e.g. genes, proteins and chemicals/drugs) as well as the relationships between these and is typically curated or mined from structured databases  ...  Protein-Protein interactions Performance evaluation of different text mining scoring systems.  ... 
doi:10.1371/journal.pone.0214619 pmid:30958864 pmcid:PMC6453528 fatcat:qamjegiikncmrplaggakgwesn4

A Comprehensive Benchmark of Kernel Methods to Extract Protein–Protein Interactions from Literature

Domonkos Tikk, Philippe Thomas, Peter Palaga, Jörg Hakenberg, Ulf Leser, Andrey Rzhetsky
2010 PLoS Computational Biology  
Extraction of proteinprotein interactions (PPIs) reported in scientific publications is one of the core topics of text mining in the life sciences.  ...  The most important way of conveying new findings in biomedical research is scientific publication.  ...  Acknowledgments We thank all authors of the kernel methods we discuss for providing code and numerous hints on how to install and use the systems.  ... 
doi:10.1371/journal.pcbi.1000837 pmid:20617200 pmcid:PMC2895635 fatcat:qdq7b4efsfeoloh4rkkq74biai

A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature

Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M Rocha
2011 BMC Bioinformatics  
We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge.  ...  Conclusions: For the ACT, we show that the use of named entity recognition tools leads to a substantial improvement in the ranking and classification of articles relevant to protein-protein interaction  ...  The full contents of the supplement are available online at  ... 
doi:10.1186/1471-2105-12-s8-s12 pmid:22151823 pmcid:PMC3269935 fatcat:s5f2j5ocnfcangzirxaplnuk6i

Recent progress in automatically extracting information from the pharmacogenomic literature

Yael Garten, Adrien Coulet, Russ B Altman
2010 Pharmacogenomics (London)  
Full text, figure captions & tables Because of the accessibility of scientific abstracts, most biomedical text mining research has used abstracts to extract information from publications.  ...  of full text pharmacogenomic articles [19, 20] .  ...  Includes table comparing existing tools for information retrieval and information extraction across many attributes. 22 Jensen LJ, Saric J, Bork P: Literature mining for the biologist: from information  ... 
doi:10.2217/pgs.10.136 pmid:21047206 pmcid:PMC3035632 fatcat:7g3jwc4hjfetbb5phmzstzhjeu

Detecting miRNA Mentions and Relations in Biomedical Literature

Shweta Bagewadi, Tamara Bobić, Martin Hofmann-Apitius, Juliane Fluck, Roman Klinger
2015 F1000Research  
PubMed Abstract | Publisher Full Text | Free Full Text 15. Czarnecki J, Nobeli I, Smith A, et al.: A text-mining system for extracting metabolic reactions from full-text articles.  ...  PubMed Abstract | Publisher Full Text | Free Full Text Source 23. Murray BS, Choe SE, Woods M, et al.: An in silico analysis of microRNAs: mining the miRNAome. Mol Biosyst. 2010; 6(10): 1853-62.  ...  Acknowledgements We would like to thank Heinz-Theo Mevissen for all the support during implementation of the dictionaries and regular expressions in ProMiner.  ... 
doi:10.12688/f1000research.4591.3 pmid:26535109 pmcid:PMC4602280 fatcat:bazcjsqnsrddbhdicmpek73wdi

Text mining biomedical literature for constructing gene regulatory networks

Yong-Ling Song, Su-Shing Chen
2009 Interdisciplinary Sciences Computational Life Sciences  
Most text mining systems can extract information from the collection of abstracts. Full-length texts analysis is more complicated and difficult.  ...  First, the text mining biomedical literature subsystem can extract the strain number and genotype, and the phenotype information from the full-length text.  ... 
doi:10.1007/s12539-009-0028-7 pmid:20640836 fatcat:5bnptxze4vfk3gck2wywg4zeum

Modeling of negative protein-protein interactions: methods and experiments [article]

Andrea Moscatelli
2019 arXiv   pre-print
These systems have to face two main problems: the high incompleteness of the human interactome and the lack of high-quality negative protein-protein interactions (i.e. proteins that are known to not interact  ...  Protein-protein interactions (PPIs) are of fundamental importance for the human body, and the knowledge of their existence can facilitate very important tasks like drug target developing and therapy design  ...  interactions from the literature through text mining [42, 47] .  ... 
arXiv:1910.04709v1 fatcat:rqqcz5qmivdkhnj2tamsh2vrzm
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