Open source effort to bring all open biomedical data together


There is a vast amount of openly available biomedical information on the web in the form of open access journal publications, biomedical, gene or drug databases, drug labels and more. We are talking about millions of full text articles (i.e. indexed in PMC and possibly some in services such as Arxiv.org), tens of millions abstracts (MEDLINE), tens of thousands published drug labels (on DailyMed and some other drug databases such as DrugBank), hundrads of thousands clinical trials (ClinicalTrials.gov) and so on. However, they are all published by certain authority or institution, but they are not integrated. Imagine the data resource where you can get for free all accessible data integrated, text mined, semantically annotated, linked and infered at one place.  Imagine the system where you can get all publically available information about certain drug from drug labels to all clinical trials with extracted drug-drug interactions, adverse events and other things. Also, imagine if it is up to date all the time and all the tools doing mining are open source and available.

I believe this is what health reasearch and health informatics strive towards and what should be an open source community effort. An integrated data resource built with community created open source tools. 

What needs to be done

There are several things that need to be done. First of all, field experts need to be gathered in single open source organization that can be umbrella organization for the projects that strives towards this goal. It is easy to register organization, however, there are I believe plenty of small bio and health informatics organizations and institutes that are doing some effort, but they are not collaborating enough to make an unique single point of entry data resourse and accompaning tools available. Currently we have many organizations, each of them promoting their own standars or schemas, building tools, etc. But centralized effort will be of greater help. Some standards are relatively broad and a lot of researchers apply them, such as publishing resources as linked data and OWL, but even there, multiple endpoints, schemas and ontologies makes it not as useful as they would be integrated to each other.  And here I would not like to talk only about tools and schemas, but to actually build a resource with an endpoint where people can access all biomedical knowledge that is accessible freely.

This definitly is quite a bit task and requires a lot of resources, but these resources will be returned back to the public. In order to host fast service, REST API, website, mail server, and other things needed for such effort there is a need for money as well. Also, people working on integrating data, researching new approaches to extract data from literature, programming and maintaining tools and service needs to live out of something. I would welcome volonteers as well, but in order to be realistic, the most critical people need to be employed and physical infrastructure to be built. Money may come from Grants per projects or by industrial sponsors and supporters. However, they should be aware that all the built resources and tools will be open, free and vendor agnostic.

Projects and local efforts

Since I am part of OWASP and one of the project and chapter leader there, I would borrow organizational model from them. There has to be a number of different projects inside the organization, which would be led by one or more project leaders. The leaders would need to agree on general resource structure, but different people can work on integrating and maintaining some part of the resource or some tool.

Also, there should be a local chapter or local branches, which would hold a meetings at least 4 times per year and spread the word and awareness about the project, resource or lobby for the good laws and regulations in various countries that could make some annonimized biomedical data accessible through our resource.

What now

I am still doing my PhD at the University and my project is quite related to this topic and could be one of the projects under this umbrella organization. Doing a PhD does not let you to have too much time. However, if there is a critical mass of people who would like to start this type of effort, I would be happy to join or lead the effort. If you are interested, please let me know. If there is no critical mass, maybe it is still early, and this was just one of my shouts and opinion on what needs to be done for better quality of health, research and our community.

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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3 thoughts on “Open source effort to bring all open biomedical data together

  1. Would definitely suggest getting in touch with Debian Med to see if they can help you out with this effort.

    I’m just about to launch a Linked Data service for Debian and we already link software with related publications. I also remember in the past that we were exploring the use of an OWL ontology for describing biomedical software.


  2. GenBank and others have been centralizing sequence data. But with the advent of cheap sequencing data the database approach may soon be overwhelmed. MinION nanopore sequencer ($1000) may produce 100 million sequence base pairs. How will medical databases cope?

    Human transcriptomes and model animal transcriptomes may map immune systems throughout a life time.
    The sequence data per person will grow exponentially.

  3. I would encourage you to look into:
    created by Sage Bionetworks, which is an open science proponent and bioinformatics non-profit, with an open-source platform that you can contribute data or build the platform directly.
    I was an intern there, and Sage is a wonderful place to work with a powerful mission.

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