Τίτλος:
OnTheFly(2.0): a text-mining web application for automated biomedical
entity recognition, document annotation, network and functional
enrichment analysis
Γλώσσες Τεκμηρίου:
Αγγλικά
Περίληψη:
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 OnTheFly(2.0), a web application for extracting biomedical
entities from individual files such as plain texts, office documents,
PDF files or images. OnTheFly(2.0) 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. OnTheFly(2.0)
currently supports 197 species and is available at
http://bib.fleming.gr:3838/OnTheFly/and
http://onthefly.pavlopouloslab.info.
Συγγραφείς:
Baltoumas, Fotis A.
Zafeiropoulou, Sofia
Karatzas, Evangelos and
Paragkamian, Savvas
Thanati, Foteini
Iliopoulos, Ioannis and
Eliopoulos, Aristides G.
Schneider, Reinhard
Jensen, Lars Juhl
and Pafilis, Evangelos
Pavlopoulos, Georgios A.
Περιοδικό:
NAR GENOMICS AND BIOINFORMATICS
Εκδότης:
Oxford University Press
DOI:
10.1093/nargab/lqab090
