OnTheFly 2.0 main functionality: A) A document file containing an Nf-kB regulatory network description B) Reflected Button Document annotation through the Reflect service C) Network Button: Protein(s)/chemical(s) interaction network generation through the STITCH database D) Knowledge Button: Collection of relevant knowledge from public resources via the Biocompendium service E) Summary Button: Enriched summaries containing short descriptions about the bioentities of a set of documents

OnTheFly 2.0 architecture: An overview of the architecture of OnTheFly. OnTheFly central sever in Greece and its information exchange with other servers (Reflect server based in Dennmark, Stitch server in Germany and Biocompendium server in Luxembourg)

OnTheFly 2.0 API: Currently, OnTheFly comes with its own Application Programming Interface (API). For each session, OnTheFly 2.0 assigns an identifier and a folder named with the same name as the identifier is created. For each of the files of the running sessions, a set of subfolders named as the filenames is further created. After annotating all of the files, users can access the relevant information for each of the uploaded article through public URLs as shown here. Several options are currently offered:

• "http://onthefly.embl.de/sessionID/filename/entities"
• "http://onthefly.embl.de/sessionID/filename/stitch.input"
• "http://onthefly.embl.de/sessionID/filename/biocompendium.input".

Supplementary methos are available:

• "http://onthefly.embl.de/Session"
• "http://onthefly.embl.de/Organisms"

A Perl API can be downloaded here

The list of organisms with their taxonomy Ids is available here