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OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

View ORCID ProfileFotis A. Baltoumas, Sofia Zafeiropoulou, View ORCID ProfileEvangelos Karatzas, View ORCID ProfileSavvas Paragkamian, Foteini Thanati, Ioannis Iliopoulos, View ORCID ProfileAristides G. Eliopoulos, View ORCID ProfileReinhard Schneider, View ORCID ProfileLars Juhl Jensen, View ORCID ProfileEvangelos Pafilis, View ORCID ProfileGeorgios A. Pavlopoulos
doi: https://doi.org/10.1101/2021.05.14.444150
Fotis A. Baltoumas
1Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, Vari, 16672, Greece
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  • For correspondence: pavlopoulos@fleming.gr baltoumas@fleming.gr
Sofia Zafeiropoulou
1Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, Vari, 16672, Greece
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Evangelos Karatzas
1Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, Vari, 16672, Greece
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Savvas Paragkamian
2Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
3Department of Biology, University of Crete, Voutes University Campus, P.O.Box 2208, 70013, Heraklion, Crete, Greece
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Foteini Thanati
1Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, Vari, 16672, Greece
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Ioannis Iliopoulos
4Department of Basic Sciences, School of Medicine, University of Crete, Heraklion 71003, Crete, Greece
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Aristides G. Eliopoulos
5Department of Biology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
6Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
7Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
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Reinhard Schneider
8University of Luxembourg, Luxembourg Centre for Systems Biomedicine, Bioinformatics Core, Esch-sur-Alzette, Luxembourg
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Lars Juhl Jensen
9Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Evangelos Pafilis
2Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Former U.S. Base of Gournes P.O. Box 2214, 71003, Heraklion, Crete, Greece
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Georgios A. Pavlopoulos
1Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, Vari, 16672, Greece
6Center for New Biotechnologies and Precision Medicine, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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  • ORCID record for Georgios A. Pavlopoulos
  • For correspondence: pavlopoulos@fleming.gr baltoumas@fleming.gr
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ABSTRACT

Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analysing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, Office documents, PDF files or images. OnTheFly2.0 can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform Named Entity Recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and Gene Ontology terms. Multiple files can be analysed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein-protein and protein-chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0 currently supports 197 species and is available at http://onthefly.pavlopouloslab.info.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/PavlopoulosLab/OnTheFly/tree/main/Supplementary_Material

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted May 17, 2021.
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OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Savvas Paragkamian, Foteini Thanati, Ioannis Iliopoulos, Aristides G. Eliopoulos, Reinhard Schneider, Lars Juhl Jensen, Evangelos Pafilis, Georgios A. Pavlopoulos
bioRxiv 2021.05.14.444150; doi: https://doi.org/10.1101/2021.05.14.444150
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OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis
Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Savvas Paragkamian, Foteini Thanati, Ioannis Iliopoulos, Aristides G. Eliopoulos, Reinhard Schneider, Lars Juhl Jensen, Evangelos Pafilis, Georgios A. Pavlopoulos
bioRxiv 2021.05.14.444150; doi: https://doi.org/10.1101/2021.05.14.444150

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