<Anita> Did you dial into the UK or France? My colleagues are having problems dialing in
<pgroth> helena deus?
<pgroth> http://www.few.vu.nl/~pgroth/prov-overview-update-pg.pdf
<boycer> please repost link to slides for those of us who came in late to the chat
<Anita> prov-overview-update-pg.pdf [View next to chat]
<jodi> http://www.few.vu.nl/~pgroth/prov-overview-update-pg.pdf
<boycer> thanks!
[slide 2]
<Anita> Will also post to meeting wiki at http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20120220
<scribe> scribenick: ericP
[slide 3]
<Anita> ericP In 'note that the topic has the link to the slides' - where/what is this 'topic' that you speak of?
<Gully> repost slide location?
pgroth: Science needs repeatability and reproducability
<pgroth> http://www.few.vu.nl/~pgroth/prov-overview-update-pg.pdf
[slide 4]
pgroth: [timbl's quote about the "Oh yeah?" button] [actually comes from Dan Connolly, I believe]
[slide 5]
pgroth: many folks want prov representations immediately
... also, many implementations
<YolandaGil> We took Tim's quote from in his book as I recall
<Anita> ericP do you have the details on the 'other' way to dial in?
pgroth: the incubator group produced a literature review and a WG
[slide 8]
<pgroth> slide 8
pgroth: wide membership: industry, govornment, science
[slide 9]
pgroth: at the top of slide 8 are serializations of e.g. OWL encoding (Prov-O), XML (Prov-XML), JSON, ...
... these express the provenance data model (Prov-DM)
... one can access the DM via Prov-AQ
<Anita> Prov AQ = Provenance Accessing Query - how do I go from resource to Provenance
pgroth: we also have a provenance primer
[slide 10]
pgroth: DM has a small set of classes and relationships
[slide 11 - provenance example]
pgroth: [re: slide 11] we need a process to describe the chart which Alice produced
[slide 12]
pgroth: "Entity" describes a chart, CSV file, car, ...
[slide 13]
[slide 14]
pgroth: Prov helps us know who did what
<Anita> Agent takes an active role in an activity
<Anita> (Small thought: you could model the entire process of doing science in this model!)
pgroth: Prov talks about Entities, Agents and Activities
[slide 16]
pgroth: Activities can produce Entities
[slide 17]
<Anita> 'Generation is the production of a new entity by an activity' (by an agent, correct?)
pgroth: Usage is when an Activity consumes an entity
[slide 18]
pgroth: sometimes you want to describe the derivation without describing the exact process.
... e.g. "Chart1 was derived from Entity1" without going into details
[slide 19]
pgroth: want to link an Activity to an Agent
... e.g. "Alice is responsible for the Excel analysis"
[slide 20]
pgroth: responsibility of Alice. analysis used a CSV file, chart was derived from the CSV file
@@1: when you write out workflows for e.g. experiments, you have lots of intermediate activities
scribe: i found having an activity-to-activity relationship is useful
... do you have a representation of that intermediate structure. otherwise representation gets laborious
[slide 21]
pgroth: i think you're describing something we call wasInformedBy
... wasAttributedTo is fundamental
... we offer extra constructs.
... there may be many constructs which you want, but we need a small set to achieve interop
... that's a trade-off frequently discussed in the group
[slide 22]
pgroth: it's easy to write this in Turtle
[slide 23]
[slide 24]
pgroth: we're working on simplifying the explainations
... released a draft last year. got the feedback that we need a simpler explaination
... Ontology is available but volatile at this point
... we're working with Dublin Core on a document describing the relationship between Prov and DC
... preparing for deeper community feedback
... aiming for Rec by the end of 2012
[slide 25]
pgroth: want to hear how in HCLS you need to extend this model
... there are some implementations, and if you want to implement, we're anxious to work with you
<Anita> This is a good time to give feedback to teh PROV model
pgroth: feedback is useful now
1+
<pgroth> go ahead
Tim: please use a transcript of this presentation as documentation as it was very clear
<Anita> DavidShotton did you want to be added to the speaker queue?
Tim: Roles would be useful
<pgroth> err… actually...
<Anita> Tim: Can you add roles to the (core) model?
Tim: I reallize that Roles don't belong in the Core
... e.g. role as a presenter, convener, etc.
... need it for a project
<Anita> TIm; I have a project I need that in
<DavidShotton> We are developing role ontologies
<Anita> pgroth: roles are in the spec
pgroth: we do have roles. i should add to this explaination
... we have a placeholder for entities with respect to activites
<Anita> pgroth: have a placeholder - entities wrt activity: e.g. chart plays-role-of output
<Anita> pgroth: but we don't define any roles
pgroth: we have a construct called prov:Role, but don't supply any kinds of Role
<pgroth> http://dvcs.w3.org/hg/prov/raw-file/default/primer/Primer.html
<DavidShotton> I would distinguish the STATUS of a document as an output from the ROLE of an AGENT
pgroth: you'll find Roles in the primer
Tim
<Anita> Tim: implementations: we started working with Susanna Sansone on an OWL model to encapsulate ISA-TAB data for experiments;
Tim: re: implementations and use use, we're working with Susana S on the ISA representation of genetic experiments
... we started saying "we need to subclass OBI" but migrated to Prov
<Anita> Tim: incorporating provenance as a motivator for that; much more useful to take Provenance as a motivator for experiments
<Zakim> ericP, you wanted to ask about Prov-AQ vs. SPARQL over the RDF representation
<Anita> So - if you have a question please type in 'q+' and then your question
pgroth: Prov-AQ tells you how to go from a resource to it's associated provenance
... we have a number of ways
<Anita> EricP asks question about Prov-AQ
pgroth: .. what metadata you need to embed in HTML to get to the provenance
... .. use of HTTP protocol to look up a prov service or set of data
<Anita> Are there other questions?
pgroth: another part of Prov-AQ is an query endpoint
... .. you POST or GET and we give you back some prov info
... also discusses SPARQL patterns
DavidShotton: excellent work. the simplicity is the key thing
... people have tried to capture e.g. time-dependent Roles, but that complicates things
pgroth: we've seen two broad uses:
... .. i've got a web doc or publication and i want to assign some prove info.
<Anita> paulG 1) web document, want to assign Provenance information; need simple document
pgroth: .. i want to track in a detailed fashion provenance in an automated system
<Anita> paulG: 2) You want to track in lots of detail provenance in automated system, fixed or time-dependent things, Paul on Feb 20th at 16:43 in Amsterdam
pgroth: in latter, i want to talk about e.g. "Paul at 4:21 while he's in Europe"
... supporting both of these views has been a challenge to the group
... we think we've got it with this model of starting with a simple model but having additions you can use
<Zakim> Anita, you wanted to say current implementations anywhere? Also: publishers can apply somehow?
Anita: there might be provenance stored in workflow tools
... could the prov model expose that in e.g. supplementary material in a publication?
<Anita> Sorry really two questions: first what are implementations? Second can we store workflow data in publication as Prov?
pgroth: Workflow4Ever (Taverna) provenance info is exposed via the Prov model
... there are some tools for mapping from OPN to Prov
<DavidShotton> For encoding time-related roles, see http://imageweb.zoo.ox.ac.uk/pub/2012/cerif/Shotton&Peroni_PRO-and-PSO.ppt
pgroth: not many implementation yet, still in a bit of flux
<pgroth> http://www.w3.org/2011/prov/wiki/TavernaProvenance
<pgroth> ack, I forgot about wings!
Anita: we've been talking with many folks about capturing workflows
<pgroth> sorry yolanda :-)
<david_r_newman> http://www.wf4ever-project.org/
Anita: and presenting in a way which can be easily used
<DavidShotton> Workflows 4 Ever http://www.wf4ever-project.org/
Anita: prov model is generic enough that it could be used in many domain
Tim: i expected another use case:
... .. when you guys publish, there's workflow applied to treating the manuscript
Anita: good point, we don't have good ways of capturing that
<pgroth> https://github.com/lucmoreau/ProvToolbox
Anita: could start earlier at e.g. figures and charts
... i don't know of any publisher who has that
<DavidShotton> Simple post hoc capture of publishing workflows: The Publishing Workflows Ontology http://purl.org/spar/pwo/
Tim: this is a goal of ISA-RDF
... .. define metadata in a way which standardizes workflow and provenance
<pgroth> https://github.com/INCF/ProvenanceLibrary
<Anita> Tim: say if you publish something and you have a figure - be able to click on it and go to a data repository that has primary data, steps and provenance
Tim: we're hoping by having a standard model, you could be able to e.g. click on a heatmap and get back to the source data
YolandaGil: i thought Tim was discussing the e.g. review process
... there's also the processing to generate a certain figure
<Anita> YolandaGil: Tim is capturing review process, is one workflow; other one is kind of processing that took place to generate a certain figure
YolandaGil: or the lab experiments and steps you took to obtain the data in the first place
... these are different steps, but they are connected
<Anita> Or link to gully's work: steps taken in the lab, observational assertions, interpretational assertions...
YolandaGil: reviewers often don't have a good way to check the work that they are reviewing
... this could help the reviewer inspect and detect errors
<Anita> YolandaGil: easier to inspect errors and insufficiencies in the papers; helps us review (and reproduce! - Anita) what was done
YolandaGil: the issue of credit is crucial to scientists
<Anita> YolandaGil credit is intertwined with provenance - different people do different things: who did what?
YolandaGil: with today's level of collaboration/re-use, they want to assign credit with precise detail
<Anita> ORCID is interested in developing a taxonomy of microcredit attribution
YolandaGil: if we were able to easily record prov on a dataset, samples, etc, we'd end up with extensive provenance records
... gives us the movie-level credits
<Anita> It would be interesting to link this - Amy Brand at Harvard is leading this, my colleague Mike Taylor is working on it in practice
Anita: Orchid is working on a model for micro-credit for authors working on a paper
... use case came from Provost, the evaluation side
<Anita> http://about.orcid.org/
YolandaGil: you may not be able to anticipate the credits you want to include
... prov model would provide a substrate
Tim: there's a little workshop on this
<Anita> http://about.orcid.org/civicrm/event/info?id=4&reset=1 ORCID workshop
<Anita> Tim: Yolanda can you attend the ORCID event?
<jodi> definitely a good time to hear about this!
Anita: many thanks. you'll hear from us
<boycer> one sec
<YolandaGil> Thank you for inviting us to talk about provenance!
<pgroth> thanks everyone
boycer: on track wrt milestones
<Anita> Use case 1: developing demo: https://docs.google.com/document/d/1QpW-axtGL7Tuhd_Zcaf30a4-s4S_lveIJtpKL5QBLfQ/edit?hl=en_US
boycer: Anita, Joey and Anita, we've developed a proof-of-concept of the product inserts
<pgroth> If you have any questions, let us know. We really want feedback
boycer: linked to claims at clinical trials.gov, medical pathways, and drug-drug interactions
<Anita> Use case 2: Boycer is presenting at C-SHALS this week about Use Case 1 - http://www.iscb.org/cshals2012-program/
DavidShotton: no progress since last meeting
<Anita> Sorry that's Use case 1: Boycer is presenting at C-SHALS this week about Use Case 1 - http://www.iscb.org/cshals2012-program/
<Anita> DavidShotton: no news on UC 2, need to talk to TIm
<Anita> Tim: we have model we've been developing with classes and object properties, not yet datatype props get started on discussions, happy to chat
Tim: i can share with you the latest and greatest, added object properties and starting on data properties
Anita: joanne and I have been developing UC3 for a class which Deb McGuinness teacing
... students will provide a portal to link adolescent antidepressants to drug interaction and some proprietary Elsevier data
DavidShotton: there are two meetings in Cambrige MA related Roles:
... Welcome Trust and then ORCHID the next day
... 16 and 17 May
Tim: they are specifically joined
Anita: next joint meeting in 4 weeks
... soliciting thoughts for presentations