Table 1.
OnTheFly1.0 versus OnTheFly2.0
| Functionality | OnTheFly1.0 | OnTheFly2.0 |
|---|---|---|
| Named Entity Recognition | Genes, proteins, chemical compounds | Genes/proteins, chemical compounds, organism names, environments, tissues, diseases, phenotypes, gene ontology terms |
| Supported files in textual formats | PDF (.pdf), Office texts (.doc), Flat text (.txt, .tsv, .csv) | PDF (.pdf) Microsoft Word (.doc and .docx) OpenOffice Writer(.odt) Microsoft Excel (.xls, .xlsm and .xlsx) OpenOffice Calc (.ods) XML (.xml) Flat text (.txt, .tsv, .csv) |
| Image files with the use of OCR | N/A | Images (.bmp, .png, .jpg, .tif), PostScript (.ps, .eps) |
| tesseract-ocr package | ||
| Interaction networks | STRING | STRING, STITCH |
| Infrastructure | Windows-based server | Unix-based (Linux) server and standalone package, compatible with Windows through WSL (Windows Subsystem for Linux) |
| File Converters | Commercial converters: ultrashareware, verypdf (PDF layout loss) | Freely available, open-source converters: pdf2htmlEX, LibreOffice, ImageMagick (PDF, Text, spreadsheet & image layout preservation with minimal losses) |
| Tagging service | REFLECT | EXTRACT |
| GUI Implementation | Java Applet (obsolete) | R/Shiny, JavaScript |
| Functional Enrichment | Link to BioCompendium (outdated and Human/Mouse only) | In-house analysis based on g:Profiler and aGOtool. Enrichment terms include Gene Ontology, biological pathways, regulatory motifs, protein databases, human phenotype ontology etc. |
| Organisms | Human and Mouse | 197 species |
| Combination of files and entity selection | N/A | Offered |
| Parameterization | N/A | Offered (e.g. functional enrichment options) |
| Browser Compatibility | Java Applets are not supported anymore | Safari, Tor, Firefox, Chrome, Microsoft Edge, Operaa |
aTested on the following browser versions: Chrome: 93.0.4577.63, Firefox: 92.0, Microsoft Edge: 93.0.961.38, Safari: 14.1.2, Opera: 78.0.4093.184, Tor: 10.5.5.