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qiita-spots / qiita

Qiita - A multi-omics databasing effort
http://qiita.microbio.me
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Create a gold standard portal #1391

Closed ElDeveloper closed 7 years ago

ElDeveloper commented 9 years ago

This portal will have a list (see proposed studies below) of studies that are commonly useful for meta-analyses and that have metadata that has gone extensive care:

Human associated:

While this list is subject to change and we certainly may be missing a few studies here, we should consider this a starting point.

antgonza commented 9 years ago

Will these be portals or simply a meta-analysis predefined selection? For the former the user will need to upload their study in the given portal and will be limited to only that portal and for the latter you could have a button that says select samples from predefined selection and those studies/samples will be selected. I like the latter more but I might be missing something.

ackermag commented 9 years ago

I like the idea of the second option as Antonio says. I think we could add additional studies from the EMP for other environmental packages so it is more comprehensive and includes other host-associated studies, fresh water, marine samples etc. Clearly having studies that are from well-known publications (like HMP) is important, as well as including studies across platforms - 454 and Illumina.

On Tue, Aug 18, 2015 at 3:55 AM, Antonio Gonzalez notifications@github.com wrote:

Will these be portals or simply a meta-analysis predefined selection? For the former the user will need to upload their study in the given portal and will be limited to only that portal and for the latter you could have a button that says select samples from predefined selection and those studies/samples will be selected. I like the latter more but I might be missing something.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/1391#issuecomment-132171186.

Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu

rob-knight commented 9 years ago

I think it needs to be a portal because people will want to do their own meta-analysis from this subset? Or I suppose we could do what they do in GNPS where it’s an attribute of a dataset and you can filter?

On Aug 18, 2015, at 5:22 AM, Gail Ackermann notifications@github.com wrote:

I like the idea of the second option as Antonio says. I think we could add additional studies from the EMP for other environmental packages so it is more comprehensive and includes other host-associated studies, fresh water, marine samples etc. Clearly having studies that are from well-known publications (like HMP) is important, as well as including studies across platforms - 454 and Illumina.

On Tue, Aug 18, 2015 at 3:55 AM, Antonio Gonzalez notifications@github.com wrote:

Will these be portals or simply a meta-analysis predefined selection? For the former the user will need to upload their study in the given portal and will be limited to only that portal and for the latter you could have a button that says select samples from predefined selection and those studies/samples will be selected. I like the latter more but I might be missing something.

— Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/1391#issuecomment-132171186.

Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu ackermag@ucsd.edu — Reply to this email directly or view it on GitHub https://github.com/biocore/qiita/issues/1391#issuecomment-132190546.

antgonza commented 9 years ago

Just to be clear, a portal is a "virtual" space where users can create/manage/etc their study but is limited to the studies that are in that portal.

Now, my idea was to add a new feature where you have a list of environments (human, built environment, etc) and each one has a predefined list of studies (admin managed, similar to a portal). The the user will simply click on that link (all those samples will get added to their metaanalysis) and they can add their own or other studies, including from other environments ...

ackermag commented 8 years ago

here is the gold standard discussion - we will need to add some in

antgonza commented 7 years ago

Resolution: a better solution might be to create a "tagging" system where we can add labels to studies. The first tag will be Gold and selecting this will filter studies to just show you the ones that have it. I though a button "Show me the gold!!!", will be appropriate.

Note that this now became a duplicate of: https://github.com/biocore/qiita/issues/969, closing.