RE: Responses to public comments on primer (RE: PROV feedback)

Hi Bob,

I don't think we got a confirmation that you were happy with changes and responses to the W3C PROV Primer following an earlier review. We are preparing the final draft of the primer and other documents now, so could you say whether you are happy with the responses below?

thanks,
Simon

Dr Simon Miles
Senior Lecturer, Department of Informatics
Kings College London, WC2R 2LS, UK
+44 (0)20 7848 1166

Efficient Multi-Granularity Service Composition:
http://eprints.dcs.kcl.ac.uk/1396/
________________________________
From: Freimuth, Robert, Ph.D. [Freimuth.Robert@mayo.edu]
Sent: 13 November 2012 15:13
To: Miles, Simon
Subject: RE: Responses to public comments on primer (RE: PROV feedback)

Hi,

I will be happy to review the changes and responses.  However, I may not have time until later this week.  I think there are some other changes pending my review as well.  I will try to get through them as soon as possible.


Thanks,
Bob



________________________________
From: Miles, Simon [mailto:simon.miles@kcl.ac.uk]
Sent: Tuesday, November 13, 2012 8:46 AM
To: Freimuth, Robert, Ph.D.
Cc: public-prov-comments@w3.org
Subject: Responses to public comments on primer (RE: PROV feedback)

Dear Robert,

Among the comments you sent in your review of the PROV specifications were some on the primer document. We believe we have now addressed these comments and have written two responses describing the changes we've made.

I copy the responses below. Could you let us know whether you are satisfied with these?

The updated primer can be seen at the link below.
http://dvcs.w3.org/hg/prov/raw-file/default/primer/Primer.html

ISSUE-561: Primer Section 2 figure
=====
Tracker: http://www.w3.org/2011/prov/track/issues/561
Group Response
 - Since (and partly prompted by) the reviewer comment, the Working Group has discussed the best form for the primer overview diagram.
 - It was decided to change so that the overview image used by primer is no longer to be a copy of the one from the PROV-DM. This is because the intention is different: the primer aims to give just a very few concepts and relations to give an intuition ahead of the rest of the introduction.
 - The figure has been changed to be a reduced version of the one used in the PROV-O specification, and no link between the diagrams in specs is now claimed.
References:
 - For a history of the debates: see http://www.w3.org/2011/prov/track/issues/574
Changes to the document:
 - Removed the claim in the primer text that the image is the same as the one in PROV-DM.
 - Changed the primer key concepts (overview) image to be one with a reduced set of concepts and relations giving an introductory intuition.
ISSUE-562, 563 and 564: Specialization and alternates
=====
Tracker: http://www.w3.org/2011/prov/track/issues/561, http://www.w3.org/2011/prov/track/issues/562, http://www.w3.org/2011/prov/track/issues/563
Group Response
- In ISSUE-562 and ISSUE-563, the comment is that the primer text implies particular things which the reviewer believes to be untrue, but are actually correct implications.
- First, it is correct that specialization implies that the child entity inherits all of the attributes of the parent entity. It is the reviewer's counter-example that is an incorrect use of PROV: the "parent" entity of one version of a document is not the prior version of the document, but the document in general, i.e. independent of version. All versions of a document share the attributes of the document in general.
- Second, the fact that two specializations of a single general entity are alternates of each other is a common case that fits the PROV definition of "alternate", and the implication is again correct.
- The fact that the reviewer believed the implications to be incorrect suggests that the primer did not adequately explain the concepts.
- ISSUE-564 relates to the reviewer finding the listed possible uses of the alternate relation confusingly distinct. Again, this is probably due to an inadequate explanation of the alternate and specialization relations.
- The conclusion of the group is that the previous explanation of the concepts was not adequately clear.
References:
- The revised text is partly informed by the discussion in response to another reviewer's public comment: http://www.w3.org/2011/prov/track/issues/569
- Clarifying the meaning of alternate and its relation to specialization: http://lists.w3.org/Archives/Public/public-prov-wg/2012Oct/0091.html
Changes to the document:
- The intuitive introduction to specialization and alternate relations, Section 2.9, has been completely rewritten based around a few use cases each with more detail than present before. Specialization is introduced before alternate, as it more clearly gives the overall motivation for the relations. We believe this gives a clearer indication of what the relations mean, and in what cases they should be used.
- See http://dvcs.w3.org/hg/prov/raw-file/default/primer/Primer.html#alternate-entities-and-specialization
Thanks,
Simon

Dr Simon Miles
Senior Lecturer, Department of Informatics
Kings College London, WC2R 2LS, UK
+44 (0)20 7848 1166

Modelling the Provenance of Data in Autonomous Systems:
http://eprints.dcs.kcl.ac.uk/1264/

________________________________
From: Freimuth, Robert, Ph.D. [Freimuth.Robert@mayo.edu]
Sent: 24 July 2012 19:38
To: public-prov-comments@w3.org
Subject: PROV feedback


To the W3C PROV working group:

This email is in response to the call for comment and feedback on the current working draft of the PROV model.  I reviewed the PROV documentation following a recommendation from Jim McCusker.

I am impressed with the volume of PROV documentation.  I did not have time to thoroughly review all of the documents that comprise the PROV spec, but I was able to review the Primer, Notation, and Data Model.  I found PROV to be relatively complete and well-documented.  Thank you for all of the effort the working group has put into this.

I have attached a document that contains my detailed comments and feedback.  Thanks to Tim Lebo and Jim McCusker for answering some of my early questions via email.

As part of my review and learning process, I also created a UML model of PROV.  This allowed me to actively understand the model and see the effects of change proposals.  I attached a document that summarizes my proposed changes and a series of images from the model that I created (which incorporates the proposed changes), which I hope will help make the proposed changes more clear to the work group.  This is done in the spirit of offering ideas and solutions, not just complaints.

I would be happy to discuss these documents with the work group if my comments are unclear (which is likely).  I am interested in your response to these suggestions and I look forward to seeing the final PROV spec.

Finally, some context for my interest in this work.  I am looking for a provenance model to use for pharmacogenomics.  Now that I feel like I have a decent understanding of the model I will evaluate it for use in this scenario.  I suspect I will need to extend the model to capture more information about why changes were made, not just when and how they were made.  This may be outside the scope of PROV.

Regards,

Robert R. Freimuth, Ph.D.
Associate Consultant
Division of Biomedical Statistics and Informatics
Assistant Professor of Medical Informatics
_______________________________
Mayo Clinic
200 First Street SW
Rochester, MN 55905
www.mayoclinic.org<file://www.mayoclinic.org>

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