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Open source effort to bring open biomedical data together – anyone interested?

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Re: Open source effort to bring open biomedical data together – anyone interested?

#2

Post by jerven »

I am very supportive of the idea in general. I think that the author underestimates some of the reasons for the diversity in the data sources schemas etc... They are different often because of the data being different.

The linked data/semantic web approaches are slowly eating away at the unneeded data diversity. With small shared standards for common data, and unique schemas for unique data. The single endpoint solution unfortunately does not scale; it would be the AOL of biomedical data or entrez as you prefer. To be truly open and free anyone should be able to contribute their data and tools. This means decentralized infrastructure which means confusion and difficult to find information. However, as acedemia and research is decentralized their IT infrastructure must match that reality. This leads to infrastructure that can integrate on demand, such as made possible by the SPARQL service keyword.

Open source has always been an important part of bio-IT and that is not going to change. But a single source is not the answer to our problems. We need to make it easier to find information, but most importantly need to make it easier to answer questions with the data that is available.

Re: Open source effort to bring open biomedical data together – anyone interested?

#3

Post by crypt1d »

jerven wrote: post #2

I am very supportive of the idea in general. I think that the author underestimates some of the reasons for the diversity in the data sources schemas etc... They are different often because of the data being different. The linked data/semantic web approaches are slowly eating away at the unneeded data diversity. With small shared standards for common data, and unique schemas for unique data. The single endpoint solut…

I have no knowledge of the field, so apologizes in advance if this idea does not make sense.

Would it be possible to make a compromise here? Perhaps by maintaining the decentralized structure, but at the same time introducing standards to categorize data on a global level and allow it to be 'mined' by a centralized entity that has API access to this data. Kind of like Google does indexing and searching, just with more cooperation of those being indexed.

Re: Open source effort to bring open biomedical data together – anyone interested?

#4

Post by nikolamilosevic »

jerven wrote: post #2

I am very supportive of the idea in general. I think that the author underestimates some of the reasons for the diversity in the data sources schemas etc... They are different often because of the data being different. The linked data/semantic web approaches are slowly eating away at the unneeded data diversity. With small shared standards for common data, and unique schemas for unique data. The single endpoint solut…

Linked data and SPARQL are definitely very possible solution and infrastructure can be decentralized. There is a bit of resistance in one part of the community from these technologies, because people are not used to them and compared to some other data storages they tend to be a bit slower, but thats other discussing. I do not have anything against these technoogies. What I currently don't like is that there are a lot of resources that are technically open source and free, but they are burried somewhere on the internet and sometimes hard to find and it takes quite a lot of time to review all existing resources. What I wanted to recommend is one central umbrella organization that will be (1) platform for collaboration in biomedical field, (2) central endpoint to all major existing project, possibly with some maturity level of projects and internal review in order to arrange projects into maturity levels, so it can be relatively easy to review how much you can "trust" that project of data, (3) central repository for open source NLP, data curation and semantic web tools, (4) some relevant body that would be able to propose and work on standards for data curation that would take in account all field specific needs.

Re: Open source effort to bring open biomedical data together – anyone interested?

#5

Post by nikolamilosevic »

crypt1d wrote: post #3
jerven wrote: post #2

I am very supportive of the idea in general. I think that the author underestimates some of the reasons for the diversity in the data sources schemas etc... They are different often because of the data being different. The linked data/semantic web approaches are slowly eating away at the unneeded data diversity. With small shared standards for common data, and unique schemas for unique data. The single endpoint solut…

I have no knowledge of the field, so apologizes in advance if this idea does not make sense. Would it be possible to make a compromise here? Perhaps by maintaining the decentralized structure, but at the same time introducing standards to categorize data on a global level and allow it to be 'mined' by a centralized entity that has API access to this data. Kind of like Google does indexing and searching, just with mor…

Yes, this is kinda what I wanted to propose. An umbrella organization that would make an infrastructure using which it would be possible to query, index and integrate data acros the web. And I am not running away from decentralized structure or infrastructure.

Re: Open source effort to bring open biomedical data together – anyone interested?

#7

Post by michaelmachine »

Hey, Mike from DrugBank here. Send me an email at mike@drugbank.ca to chat more. You should take a look at https://www.openphacts.org/ which has a similar goal to this project. I think one problem is this: http://xkcd.com/927/

Re: Open source effort to bring open biomedical data together – anyone interested?

#8

Post by eggie »

I'm curious if the author knows about DisGeNET: https://en.m.wikipedia.org/wiki/DisGeNET.

The whole idea of the semantic web is exactly what the author is getting at. I'm curious why this is rarely regarded as a serious basis for such an effort like that which the author is promoting.

Re: Open source effort to bring open biomedical data together – anyone interested?

#9

Post by eggie »

nairboon wrote: post #6

Quite an interesting idea, so it'd be like extending the scope of GA4GH beyond 'just' genomics? https://genomicsandhealth.org/work-products-demonstration-pr...

The global alliance for genomics and health is a similar idea but not designed to be completely open nor linked. They don't acknowledge the semantic web. Practically, it is implemented as CORBA using JSON. Everything is an API and after that an implicit data model (in JSON) is being produced for each type of concept. AFAIK security is a huge limitation here. The idea of GA4GH is data silos can communicate some things with each other, but not personally identifiable information.

I work on the project but find it pretty uninspiring. It presents a dark image of the future in which a handful of large tech companies control all of our biomedical data and we have to beg them to allow us to share it. I guess that sounds pretty similar to the present. Just switch bio and social and here we are.

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