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Novel Protein-Protein Interactions Inferred from Literature Context
2009
PLoS ONE
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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
2019
PLoS Computational Biology
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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
2011
BMC Bioinformatics
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The file type is application/pdf.
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]
2022
arXiv
pre-print
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2020 pre-print arXiv:2008.08727v2 fatcat:age6ohzmjfcszo56vypyhlbyumOther Versions
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
2019
Human Genomics
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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. biomedcentral.com/articles/supplements/volume-13-supplement-1. ...
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]
2011
arXiv
pre-print
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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
2002
International Journal of Medical Informatics
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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
2006
BMC Bioinformatics
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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
2019
PLoS ONE
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, 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
2010
PLoS Computational Biology
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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
2011
BMC Bioinformatics
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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 http://www.biomedcentral.com/1471-2105/12?issue=S8. ...
doi:10.1186/1471-2105-12-s8-s12
pmid:22151823
pmcid:PMC3269935
fatcat:s5f2j5ocnfcangzirxaplnuk6i
Recent progress in automatically extracting information from the pharmacogenomic literature
2010
Pharmacogenomics (London)
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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
2015
F1000Research
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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
2009
Interdisciplinary Sciences Computational Life Sciences
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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]
2019
arXiv
pre-print
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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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