openTECR

Project Leads:
- Robert Giessmann (IGNORE) This email address is being protected from spambots. You need JavaScript enabled to view it.
- Elad Noor (Weizmann Institute) This email address is being protected from spambots. You need JavaScript enabled to view it.

Abstract:
Databases are of fundamental importance to research in the life sciences, and the development of custom-made infrastructure, workflows, tools, and guidelines by database teams is common. But wouldn’t it be great, if it was all open and ready to be re-used for new databases, too? We are interested in achieving this, working on our open database on thermodynamics of enzyme-catalyzed reactions. But don’t fear, you don’t have to have a science background in this to participate!

Our community of coders, experimentalists and modellers met at the previous BioHackathon Germany in 2023 for an online-only, globe-spanning week of work. Back then, we created prototypes of curation-supporting web apps and submission forms and laid the foundation for curating real data (see slide deck here: https://docs.google.com/presentation/d/1TFQVtOUAlswK5xkh0TZG590tL3Pm5Sp7u_FIiJhKdkM/edit?usp=sharing). In the next months following the hackathon, we organized a community-curation effort to bring 280 pages of PDFs filled with tables into a machine-readable data structure.

In this hackathon project, participants can choose (and switch) between different perspectives on the data and the community behind it: 

  • curation of new data

  • quality control of existent data, integration with other databases

  • backend and/or frontend development for our search web service

  • community management, including website improvement

  • advancing the (basic) science behind thermodynamic networks

  • improving existing prediction tools for thermodynamics of enzyme-catalyzed reactions

– About the data – 

Our dataset contains ~5500 data points on collected apparent equilibrium constants and enthalpies of enzyme-catalyzed reactions. The data bridges a wide field from chemicals, enzymes, metabolism, literature references, and physics. It can be seen here: https://docs.google.com/spreadsheets/d/1jLIxEXVzE2SAzIB0UxBfcFoHrzjzf9euB6ART2VDE8c/edit?gid=952025966#gid=952025966 

We developed basic and advanced search functionality, which aims to empower end users to search the data. This can be found here: https://w3id.org/opentecr/tecrdb 

The existing data is partly well curated (with room to improvement…) and can e.g. be integrated with further databases. Some cross-references to Rhea and PubMed / DOIs were created already.

– What to expect – 

In the last year, we managed to integrate people with no previous knowledge of either thermodynamics or IT, and had a good time working together on our individual interests. 

So, no matter your background, we are sure to find a task which you like and for which you have the skills!

If you like, you can have a look at a list of tasks we could think of: https://docs.google.com/document/d/1UFTLCb9QeDxPBj_j29_Tx1d-om2dKlVdqkhcGboit8I

But all of your suggestions are very welcome, too! Everyone is free to work on whatever they like during our hackathon.

We would be happy to have you on board! :)