pavlopouloslab/onthefly repository overview

⁠OnTheFly^2.0

OnTheFly^2.0 is a web application to aid users collecting biological information from documents. With OnTheFly^2.0 one is able to:

• Extract bioentities from individual articles in formats such as plain text, Microsoft Word, Excel and PDF files.
• Scan images and identify terms by using Optical Character Recognition (OCR).
• Handle multiple files simultaneously.
• Isolate proteins, chemical compounds, organisms, tissues, diseases/phenotypes and gene ontology terms.
• Extract selected terms along with their identifiers in databases.
• Perform functional enrichment analysis on a selected group of terms.
• Generate and visualize protein-protein and protein-chemical interaction networks.

Online version: http://bib.fleming.gr:3838/OnTheFly/⁠, http://onthefly.pavlopouloslab.info⁠

GitHub repository: https://github.com/PavlopoulosLab/OnTheFly/⁠

Publication: 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) OnTheFly^2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. NAR Genomics and Bioinformatics, 2021, Vol. 3, No. 4. doi: 10.1093/nargab/lqab090⁠

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⁠How to run:

1. Pull the image to your machine:

1. Create a container for the image using a port of your choice, e.g. 3838: