khmer tools, protocols, and pipelines should generate PROV-compliant provenance data

[mr-c]

http://www.w3.org/TR/prov-primer/

[ctb]

On Mon, Oct 21, 2013 at 11:38:16AM -0700, Michael R. Crusoe wrote:

http://www.w3.org/TR/prov-primer/

Old fuddy duddies' network expresses skepticism.

[mr-c]

About tracking provenance, the value of it, this particular standard?

This would be an optional feature. For example upon discovering
${input}.prov we consume that information and add it plus our own to
${output}.prov

On Tue, Oct 22, 2013 at 2:14 PM, C. Titus Brown [email protected]:

On Mon, Oct 21, 2013 at 11:38:16AM -0700, Michael R. Crusoe wrote:

http://www.w3.org/TR/prov-primer/

Old fuddy duddies' network expresses skepticism.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/189#issuecomment-26827794
.

[ctb]

On Tue, Oct 22, 2013 at 11:21:29AM -0700, Michael R. Crusoe wrote:

About tracking provenance, the value of it, this particular standard?

This particular standard.

--t

[mr-c]

Noted.

It would be useful to (optionally) output provenance receipts.
Implementation of reading one standard or another could wait.

Do you know of other provenance standards? This is the one used by Sage
Synapse / TCGA Pancancer Project

http://www.nature.com/ng/journal/v45/n10/full/ng.2761.html

On Tue, Oct 22, 2013 at 2:25 PM, C. Titus Brown [email protected]:

On Tue, Oct 22, 2013 at 11:21:29AM -0700, Michael R. Crusoe wrote:

About tracking provenance, the value of it, this particular standard?

This particular standard.

--t

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/189#issuecomment-26828716
.

[mr-c]

Or perhaps provenance tracking is the job of Galaxy, DiscoveryEnvironment, and so forth?

That would leave out those who run things by hand. One might say that they would have the most to gain from app-level support.

[ctb]

Out of scope for khmer, I think, at least for now. If we get a request for it or find that there are tools that integrate well with it, we can reconsider.