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

Research output: Contribution to journalJournal articlepeer-review

Standard

OnTheFly2.0 : a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. / Baltoumas, Fotis A; Zafeiropoulou, Sofia; Karatzas, Evangelos; Paragkamian, Savvas; Thanati, Foteini; Iliopoulos, Ioannis; Eliopoulos, Aristides G; Schneider, Reinhard; Jensen, Lars Juhl; Pafilis, Evangelos; Pavlopoulos, Georgios A.

In: NAR Genomics and Bioinformatics, Vol. 3, No. 4, lqab090, 2021.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Baltoumas, FA, Zafeiropoulou, S, Karatzas, E, Paragkamian, S, Thanati, F, Iliopoulos, I, Eliopoulos, AG, Schneider, R, Jensen, LJ, Pafilis, E & Pavlopoulos, GA 2021, 'OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis', NAR Genomics and Bioinformatics, vol. 3, no. 4, lqab090. https://doi.org/10.1093/nargab/lqab090

APA

Baltoumas, F. A., Zafeiropoulou, S., Karatzas, E., Paragkamian, S., Thanati, F., Iliopoulos, I., Eliopoulos, A. G., Schneider, R., Jensen, L. J., Pafilis, E., & Pavlopoulos, G. A. (2021). OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. NAR Genomics and Bioinformatics, 3(4), [lqab090]. https://doi.org/10.1093/nargab/lqab090

Vancouver

Baltoumas FA, Zafeiropoulou S, Karatzas E, Paragkamian S, Thanati F, Iliopoulos I et al. OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. NAR Genomics and Bioinformatics. 2021;3(4). lqab090. https://doi.org/10.1093/nargab/lqab090

Author

Baltoumas, Fotis A ; Zafeiropoulou, Sofia ; Karatzas, Evangelos ; Paragkamian, Savvas ; Thanati, Foteini ; Iliopoulos, Ioannis ; Eliopoulos, Aristides G ; Schneider, Reinhard ; Jensen, Lars Juhl ; Pafilis, Evangelos ; Pavlopoulos, Georgios A. / OnTheFly2.0 : a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. In: NAR Genomics and Bioinformatics. 2021 ; Vol. 3, No. 4.

Bibtex

@article{92862067dfc04f35873c2b298ec4201d,
title = "OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis",
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 analyzing 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 analyzed, 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://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info.",
author = "Baltoumas, {Fotis A} and Sofia Zafeiropoulou and Evangelos Karatzas and Savvas Paragkamian and Foteini Thanati and Ioannis Iliopoulos and Eliopoulos, {Aristides G} and Reinhard Schneider and Jensen, {Lars Juhl} and Evangelos Pafilis and Pavlopoulos, {Georgios A}",
note = "{\textcopyright} The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.",
year = "2021",
doi = "10.1093/nargab/lqab090",
language = "English",
volume = "3",
journal = "NAR Genomics and Bioinformatics",
issn = "2631-9268",
publisher = "Oxford University Press",
number = "4",

}

RIS

TY - JOUR

T1 - OnTheFly2.0

T2 - a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis

AU - Baltoumas, Fotis A

AU - Zafeiropoulou, Sofia

AU - Karatzas, Evangelos

AU - Paragkamian, Savvas

AU - Thanati, Foteini

AU - Iliopoulos, Ioannis

AU - Eliopoulos, Aristides G

AU - Schneider, Reinhard

AU - Jensen, Lars Juhl

AU - Pafilis, Evangelos

AU - Pavlopoulos, Georgios A

N1 - © The Author(s) 2021. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.

PY - 2021

Y1 - 2021

N2 - 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 analyzing 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 analyzed, 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://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info.

AB - 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 analyzing 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 analyzed, 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://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info.

U2 - 10.1093/nargab/lqab090

DO - 10.1093/nargab/lqab090

M3 - Journal article

C2 - 34632381

VL - 3

JO - NAR Genomics and Bioinformatics

JF - NAR Genomics and Bioinformatics

SN - 2631-9268

IS - 4

M1 - lqab090

ER -

ID: 282189822