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Starting an open source effort to bring biomedical data and tools together

Motivation from the community

A week ago I posted an blog post about my idea of creating Open Source organization that would have an goal to bring biomedical data and tools together to a single place. The original post can be read found here: http://inspiratron.org/blog/2015/12/12/open-source-effort-to-bring-all-open-biomedical-data-together/.

Since I posted it, quite large number of people contacted me, either by email or by social media, telling me that that would like to help. This quite motivated me and I believe validated this idea, so I decided to kick start it.

Community

In order to facilitate and coordinate the efforts of the community towards our goal of integrating, indexing and make data and tools accessible from the single source, I have created an mailing list and a wiki.

Mailing list

I believe mailing list is a best resource to coordinate efforts of the community and to encourage discussion and collaboration between people, especially in the open source community. I have created an open Google group mailing list, where anyone can join and be part of the team and the effort. If interested, please join mailing list on the following address: https://groups.google.com/forum/#!forum/obditf . Here, all the archives of the discussion from the list will also be available.

Wiki

I have also installed as a subdomain of this site an Wiki to facilitate this effort. I have heard comments over the internet, that the project is very ambitious, which it certainly is and there are many technical issues, I still don’t know how to solve, neither I have resource currently to do that. I am completely aware that I will be unable to store too much data on my hosting, because it is not too large and we will need other solution for that. However, to kick start it, I have made the wiki, which will certainly help for the time being. Later, when we finally chose a right name, domain and hosting for the whole effort, we may clone and transfer there wiki as well.

The main purpose of the wiki is to build common knowledge source for the effort. As an objective of the wiki, I would recommend to index openly accessible data resources and tools. For each tool or data source we can have couple of sentences on what it does, how it work, how to obtain data, how to use a tool and a link to the resource. We can have also a full page for the resources that needs it or deserves it. Once we got all the resources mapped and indexed and we have the infrastructure for the integration, we will see the great benefit of the wiki. The other use of the wiki could be to facilitate local efforts, such as local chapter meetings, conferences, workshops, etc.

You can register on the Wiki, however, for the security reasons, I will need to approve the new users in order to edit. Please, build some profiles and include some data in it, so I can unambiguously distinguish people from scam bots and vandals.

Currently the wiki is quite empty, but you will get the idea, and hopefully, soon, with community help, we will populate it with all available tools and data sources in biomedicine.

The address of the wiki is http://biomed.inspiratron.org/

Name and logo

Because of the lack of better ideas, I have named the effort “Open Biomedical Data Integration Task Force”. However, on the mailing list, we can decide to change it and make some more creative name the official name. However, this needs to be done relatively soon, since it might affect the branding and the image of the community. That’s why, I would suggest it to be done, while the community is still young.

obmditf logo
Open Biomedical Data Integration Task Force Logo

Yesterday evening, I have created some logo, containing caduceus and a acronym of the proposed name (OBDITF). It didn’t took long and does not look super professional, since I am not a designer, so I will be open to change it for better logo. Logo can be here on the left and is part of the wiki.

 

Let the collaboration start

So I would like to invite again, all interested people interested in the subject to join us. More people can archive more and be more productive. There are great challenges ahead (organization, legal, hardware, funding, etc.), but once we start, we can archive some big steps towards the goal and by doing it help the healthcare, biology, biomedicine, and humanity as a whole.

Born in Bratislava, Slovakia, but he lived in Belgrade, Serbia. Now he is doing a PhD in natural language processing at the University of Manchester. Great enthusiast of AI, natural language processing, machine learning, web application security (founder of OWASP local chapter in Serbia, currently one of the leaders of OWASP Manchester chapter and OWASP Seraphimdroid project), open source, mobile and web technologies. Looking forward to create future. Nikola wants to teach machines to feel and understand. Always finding way for dreams to come true.

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