Open source effort to bring open biomedical data together – anyone interested? • Hacker News Board

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

#21

Post by x1k » Mon, Dec 14, 2015, 2:29 AM UTC

eggie wrote: post #17

dekhn wrote: post #12

Earlier quoted context omitted.

I don't think that GA4GH is literally using CORBA. The data model is not implicit, it's explicit (there is a schema). The "data silos can communicate some things ... but not personally identifiable information" is a constraint placed on the alliance by legal system. As for the semantic web, every bio project I've seen which adopted the semantic web ultimately failed -- the semantic web seems like a great idea, but at…

> I don't think that GA4GH is literally using CORBA. It's not literally CORBA, but people who spent time implementing literal CORBA in a bioinformatics context (for instance, the original author of https://github.com/bioperl/bioperl-corba-server ) have noted that the design pattern and discussions followed by the GA4GH are pretty similar to those had in the EBI when they attempted to unify everything using CORBA. > T…

For NN, we have a clear target: for example, beat HMM on speech recognition. To achieve that, you write a tool on some standard test data sets. You don't need to interact with many parties. NN is only technically hard. For GA4GH, things are quite different. Technically, it is hard, but it is much simpler than NN in my view. What is hard is 1) we lack a target and 2) the communications between developers and users. People don't know what we need, don't know what is the right approach and don't know how to evaluate the success. They have changed course back and forth, and still have clashes between programmers and those with more biological background.

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

#22

Post by heuermh » Tue, Dec 15, 2015, 11:26 PM UTC

eggie wrote: post #9

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…

Curious of your affiliation, if you're willing to provide it. I recently joined the Big Data Genomics team at UC Berkeley AMPLab, a GA4GH contributor.

I was initially quite impressed with the GA4GH effort, because it was transparent and producing useful things, in terms of schema and code in github repositories. I am afraid now it has all gone working groups and private email threads and very little is happening in the open any more.

I wish I understood semantic web. I've built more than one system on it but have never found a use case that sells it for me.

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

#23

Post by nikolamilosevic » Fri, Dec 18, 2015, 5:47 PM UTC

Since this sparked quite an interest, I have created a mailing list and wiki. For more information about idea, you can read here http://inspiratron.org/blog/2015/12/18/starting-an-effort-to... where you can find the links to mailing list and wiki. I believe that would be the more appropriate place to collect all efforts that currently exist, index them and maybe try to integrate them and make them interoperable. Please join the mailing list.