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GA4GH Beacon specification.
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Extend the query language to support data use #60

Open mcupak opened 8 years ago

mcupak commented 8 years ago

After adding consent codes and ADA-M, we should consider supporting them at the level of the query language, for example allow to filter for results that can be used for clinical purposes.

antbro commented 8 years ago

Absolutely! I have always argued that we could use these formal data use models to support resources [databases, datasets, biosamples, subjects, etc] with respect to

a) communicating data use conditions b) querying/discovery actions c) automation of sharing actions (simple cases only)

Beacon can do (a) immediately, and (b) soon afterwards, as a general extension of our query scope and language. This latter item is something which we really must start some serious work on, but it will open a can of worms in terms ethics, governance and the question of when discovery becomes a form of sharing/access.

Cheers Tony

Professor Anthony J Brookes Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK Tel: +44 (0)116 2523401 Mbl: +44 (0)777 0620396 Fax: +44 (0)116 2523378 mailto: ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.uk

* Where is the wisdom we have lost in knowledge? * Where is the knowledge we have lost in information? \ T.S. Eliot

From: Miro Cupak [notifications@github.com] Sent: 27 July 2016 19:47 To: ga4gh/beacon-team Subject: [ga4gh/beacon-team] Extend the query language to support data use (#60)

After adding consent codes and ADA-M, we should consider supporting them at the level of the query language, for example allow to filter for results that can be used for clinical purposes.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI_EVAqNOkHQHyGRpLUuLBWtjEKdYMNoks5qZ6fcgaJpZM4JWgSF.

ghost commented 8 years ago

FYI, the permission-management system that Genetic Alliance’s Platform for Engaging Everyone Responsibly (PEER) http://www.geneticalliance.org/programs/biotrust/peer system uses has such formal models in place that consider far more than data use. The permission-management system is driven by an ontology that considers the interrelationships among a number of factors, including legal regulations, institutional policies, and individual permissions. The technology is provided by Private Access, which has been building the system, and the ontology behind it, for nearly a decade. So it’s quite mature at this point (though we all know that ontologies are living entities).

In full disclosure, I am a consultant to both Private Access and Genetic Alliance. However, I wanted to make sure you knew that this capability currently exists and has been deployed by over 40 health advocacy groups.

-Dixie

Dixie B. Baker, Ph.D. Senior Partner Martin, Blanck and Associates Office (Redondo Beach, CA): 310-791-9671 Mobile: 310-279-2579

On Jul 27, 2016, at 6:29 PM, antbro notifications@github.com<mailto:notifications@github.com> wrote:

Absolutely! I have always argued that we could use these formal data use models to support resources [databases, datasets, biosamples, subjects, etc] with respect to

a) communicating data use conditions b) querying/discovery actions c) automation of sharing actions (simple cases only)

Beacon can do (a) immediately, and (b) soon afterwards, as a general extension of our query scope and language. This latter item is something which we really must start some serious work on, but it will open a can of worms in terms ethics, governance and the question of when discovery becomes a form of sharing/access.

Cheers Tony

Professor Anthony J Brookes Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK Tel: +44 (0)116 2523401 Mbl: +44 (0)777 0620396 Fax: +44 (0)116 2523378

mailto: ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.uk

* Where is the wisdom we have lost in knowledge? * Where is the knowledge we have lost in information? \ T.S. Eliot

From: Miro Cupak [notifications@github.commailto:notifications@github.com] Sent: 27 July 2016 19:47 To: ga4gh/beacon-team Subject: [ga4gh/beacon-team] Extend the query language to support data use (#60)

After adding consent codes and ADA-M, we should consider supporting them at the level of the query language, for example allow to filter for results that can be used for clinical purposes.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI_EVAqNOkHQHyGRpLUuLBWtjEKdYMNoks5qZ6fcgaJpZM4JWgSF.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60#issuecomment-235741336, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKQxHR6mO0_5_dZ38GQcWndc2BD6fQUcks5qZ9uvgaJpZM4JWgSF.

antbro commented 8 years ago

...and to add to this, with information provided by Dixie I looked at the PEER system in detail, and it is indeed very powerful and built for a particular use case. That said, it is also worth mentioning that ADA-M and (to a degree) Consent Codes also go considerably beyond 'Data Use Conditions'. We merely use that as a convenient label. But ADA-M, for example, actually covers areas of subject consent, researcher and institutional requirements, protection for sensitive groups, etc, relating to items as broad ranging as research and clinical domains of use, contracts, publication, timeline restrictions, data security, data withdrawal/destruction or return of any subject data, data linking, subject recontact, IP, reporting back, collaboration and fees. So the scope is similar to PEER, but it is designed to be more generally applicable which implies less detail and ontology control than a targeted system like PEER.

PEER and I have floated the idea of exploring interoperability on the level of discovery via the two systems, but time and funding are major obstacles.

Cheers Tony

From: bakerdb [notifications@github.com] Sent: 28 July 2016 02:35 To: ga4gh/beacon-team Cc: Brookes, Anthony J. (Prof.); Comment Subject: Re: [ga4gh/beacon-team] Extend the query language to support data use (#60)

FYI, the permission-management system that Genetic Alliance’s Platform for Engaging Everyone Responsibly (PEER) http://www.geneticalliance.org/programs/biotrust/peer system uses has such formal models in place that consider far more than data use. The permission-management system is driven by an ontology that considers the interrelationships among a number of factors, including legal regulations, institutional policies, and individual permissions. The technology is provided by Private Access, which has been building the system, and the ontology behind it, for nearly a decade. So it’s quite mature at this point (though we all know that ontologies are living entities).

In full disclosure, I am a consultant to both Private Access and Genetic Alliance. However, I wanted to make sure you knew that this capability currently exists and has been deployed by over 40 health advocacy groups.

-Dixie

Dixie B. Baker, Ph.D. Senior Partner Martin, Blanck and Associates Office (Redondo Beach, CA): 310-791-9671 Mobile: 310-279-2579

On Jul 27, 2016, at 6:29 PM, antbro notifications@github.com<mailto:notifications@github.com> wrote:

Absolutely! I have always argued that we could use these formal data use models to support resources [databases, datasets, biosamples, subjects, etc] with respect to

a) communicating data use conditions b) querying/discovery actions c) automation of sharing actions (simple cases only)

Beacon can do (a) immediately, and (b) soon afterwards, as a general extension of our query scope and language. This latter item is something which we really must start some serious work on, but it will open a can of worms in terms ethics, governance and the question of when discovery becomes a form of sharing/access.

Cheers Tony

Professor Anthony J Brookes Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK Tel: +44 (0)116 2523401 Mbl: +44 (0)777 0620396 Fax: +44 (0)116 2523378

mailto: ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.uk

* Where is the wisdom we have lost in knowledge? * Where is the knowledge we have lost in information? \ T.S. Eliot

From: Miro Cupak [notifications@github.commailto:notifications@github.com] Sent: 27 July 2016 19:47 To: ga4gh/beacon-team Subject: [ga4gh/beacon-team] Extend the query language to support data use (#60)

After adding consent codes and ADA-M, we should consider supporting them at the level of the query language, for example allow to filter for results that can be used for clinical purposes.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI_EVAqNOkHQHyGRpLUuLBWtjEKdYMNoks5qZ6fcgaJpZM4JWgSF.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60#issuecomment-235741336, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKQxHR6mO0_5_dZ38GQcWndc2BD6fQUcks5qZ9uvgaJpZM4JWgSF.

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60#issuecomment-235772266, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI_EVAlGrNdi_Lv-OkcheU66Tf8dRdfMks5qaAdFgaJpZM4JWgSF.

ghost commented 8 years ago

You're right in saying that PEER is a specific use case of privacy technology. The privacy technology is Private Access. John Mattison is quite familiar with Private Access, as is the CEO and founder, Robert Shelton. I've brought both into this conversation.

Dixie Baker Office: 310-791-9671 Cell: 310-279-2579

On Jul 28, 2016, at 6:00 AM, antbro notifications@github.com<mailto:notifications@github.com> wrote:

...and to add to this, with information provided by Dixie I looked at the PEER system in detail, and it is indeed very powerful and built for a particular use case. That said, it is also worth mentioning that ADA-M and (to a degree) Consent Codes also go considerably beyond 'Data Use Conditions'. We merely use that as a convenient label. But ADA-M, for example, actually covers areas of subject consent, researcher and institutional requirements, protection for sensitive groups, etc, relating to items as broad ranging as research and clinical domains of use, contracts, publication, timeline restrictions, data security, data withdrawal/destruction or return of any subject data, data linking, subject recontact, IP, reporting back, collaboration and fees. So the scope is similar to PEER, but it is designed to be more generally applicable which implies less detail and ontology control than a targeted system like PEER.

PEER and I have floated the idea of exploring interoperability on the level of discovery via the two systems, but time and funding are major obstacles.

Cheers Tony

From: bakerdb [notifications@github.commailto:notifications@github.com] Sent: 28 July 2016 02:35 To: ga4gh/beacon-team Cc: Brookes, Anthony J. (Prof.); Comment Subject: Re: [ga4gh/beacon-team] Extend the query language to support data use (#60)

FYI, the permission-management system that Genetic Alliance's Platform for Engaging Everyone Responsibly (PEER) http://www.geneticalliance.org/programs/biotrust/peer system uses has such formal models in place that consider far more than data use. The permission-management system is driven by an ontology that considers the interrelationships among a number of factors, including legal regulations, institutional policies, and individual permissions. The technology is provided by Private Access, which has been building the system, and the ontology behind it, for nearly a decade. So it's quite mature at this point (though we all know that ontologies are living entities).

In full disclosure, I am a consultant to both Private Access and Genetic Alliance. However, I wanted to make sure you knew that this capability currently exists and has been deployed by over 40 health advocacy groups.

-Dixie

Dixie B. Baker, Ph.D. Senior Partner Martin, Blanck and Associates Office (Redondo Beach, CA): 310-791-9671 Mobile: 310-279-2579

On Jul 27, 2016, at 6:29 PM, antbro notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> wrote:

Absolutely! I have always argued that we could use these formal data use models to support resources [databases, datasets, biosamples, subjects, etc] with respect to

a) communicating data use conditions b) querying/discovery actions c) automation of sharing actions (simple cases only)

Beacon can do (a) immediately, and (b) soon afterwards, as a general extension of our query scope and language. This latter item is something which we really must start some serious work on, but it will open a can of worms in terms ethics, governance and the question of when discovery becomes a form of sharing/access.

Cheers Tony

Professor Anthony J Brookes Department of Genetics University of Leicester University Road Leicester, LE1 7RH, UK Tel: +44 (0)116 2523401 Mbl: +44 (0)777 0620396 Fax: +44 (0)116 2523378

mailto: ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.ukmailto:ajb97@leicester.ac.uk

* Where is the wisdom we have lost in knowledge? * Where is the knowledge we have lost in information? \ T.S. Eliot

From: Miro Cupak [notifications@github.commailto:notifications@github.commailto:notifications@github.com] Sent: 27 July 2016 19:47 To: ga4gh/beacon-team Subject: [ga4gh/beacon-team] Extend the query language to support data use (#60)

After adding consent codes and ADA-M, we should consider supporting them at the level of the query language, for example allow to filter for results that can be used for clinical purposes.

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI_EVAqNOkHQHyGRpLUuLBWtjEKdYMNoks5qZ6fcgaJpZM4JWgSF.

You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60#issuecomment-235741336, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKQxHR6mO0_5_dZ38GQcWndc2BD6fQUcks5qZ9uvgaJpZM4JWgSF.

You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60#issuecomment-235772266, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AI_EVAlGrNdi_Lv-OkcheU66Tf8dRdfMks5qaAdFgaJpZM4JWgSF.

You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/ga4gh/beacon-team/issues/60#issuecomment-235852746, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AKQxHSsG-vParuprv3P2jCoXuvsWEZqUks5qaH3EgaJpZM4JWgSF.

jrambla commented 8 years ago

+1 to add it to the query language. Not sure about if it should happen in v.0.4...