W3C PROV-O

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S James Parsons Jr

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Apr 21, 2022, 10:46:45 AMApr 21
to bioprotocols
I’m confident I understand the core features of PAML, but I’m having difficulty understanding the W3C Prov-O part.  I’ve read the site, I’ve watched some videos on YouTube, and I’m still kind of unsure on how this feature is implemented in PAML. Could you ELI5?


Jake Beal

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Apr 21, 2022, 11:02:42 AMApr 21
to S James Parsons Jr, bioprotocols
Hi, James:

PROV-O is a way of describing how things were created from other things. For example, we might want to say:
-  "this metabolomics data was produced by running this measurement protocol on these samples" or 
- "these samples were produced by running this culturing protocol on these strains" or 
- "these strains were produced by running this transformation protocol to put these genetic constructs into these organisms"

PROV-O describes this with "Activity" objects and "wasGeneratedBy" links. So we could take the metabolomics dataset and say it "wasGeneratedBy" running a particular protocol with particular inputs, etc. This, in turn, is described by a PAML BehaviorExecution (which is a type of PROV-O Activity), which in turn links to a description of the protocol and to the strains that were used. Together, these say how the metabolomics data was produced.

Finally, we can also describe which persons or machines ran the protocol by linking from the BehaviorExecution (Activity) to PROV-O "Agent" objects.

Thanks,
-Jake 

On Thu, Apr 21, 2022 at 9:46 AM S James Parsons Jr <sjamesp...@gmail.com> wrote:
I’m confident I understand the core features of PAML, but I’m having difficulty understanding the W3C Prov-O part.  I’ve read the site, I’ve watched some videos on YouTube, and I’m still kind of unsure on how this feature is implemented in PAML. Could you ELI5?


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