biohackathon2024-paper

BioHackrXiv paper from BioHackathon Europe 2024 Project #16

TO DO LIST

Erik - relevant background and references + method and results from exact string matching/"naive" approach for the baseline

Rob - Venn diagrams for mentions of comet, mascot and maxquant, in OA and non-OA literature

Tess - methods and results from the machine learning (with input from others involved)

Aleks - co-mention and co-citation matrices, network construction with igraph? Interested in making this a paper of your PhD?

Ana - Cytoscape visualization with py4cytoscape - explore possibilities to make an interactive visualization with Cytoscape.js or put a network up on NDEx, silimar to the Bioregistry network?

Vedran - Jupyter notebooks, GitHub repositories and data repositories

Magnus - Discussion and Conclusion (first draft, for input by everyone)

Veit - Clean up general stats and find some interesting cases, co-writing

TIMELINE

Have first versions of all of the above before the end of November (Aleks, Ana, Magnus and Veit will meet December 2 in Odense)

Future tasks

• Finalize BioHackrXiv paper

• Integrate ML results into pipeline for stats and co-mentioning graphs

• Make networks openly (interactively) available?

• Create comprehensive diagram of the conceptional background: what are tools, what type of connections, how is the entire thing organized and developed?

• Two different networks: a) co-mentioned tools (through other papers), b) which tools mentions/cites which other tool

• Collect concrete use cases for where these graphs can be used