15:06:20 <RRSAgent> RRSAgent has joined #hcls2
15:06:20 <RRSAgent> logging to http://www.w3.org/2011/02/07-hcls2-irc
15:07:07 <alex> alex has joined #hcls2
15:07:12 <mscottm> in general, it is simplest to dial directly to the MIT line if you can. It isn't as limited as the dial ins in U.K. and France.
15:07:14 <fresco> fresco has joined #hcls2
15:07:14 <Zakim> + +1.518.258.aakk
15:07:23 <Anita> The KEfED model https://wiki.birncommunity.org/display/NEWBIRNCC/KEfED+OWL+Model) - is a derivative from OBI - Allan Ruttenberg
15:07:50 <Anita> Break down nanopub in several different types
15:08:02 <Anita> Nanopub is an assertion, eg. mosquitoes cause malaria
15:09:21 <Anita> Different types - see https://sites.google.com/site/beyondthepdf/home/program-draft/notes-from-the-breakout
15:10:17 <marcelotallis> marcelotallis has joined #hcls2
15:10:23 <JoanneL> JoanneL has joined #hcls2
15:11:00 <JoanneL> Hi, had trouble getting to IRC, would someone repost the link (if we're looking at slides)  thanks!
15:11:33 <alex> same as me, where could I see the slides?
15:11:43 <Anita> Joanne: 	Talking about nanopublication types- see https://sites.google.com/site/beyondthepdf/home/program-draft/notes-from-the-breakout
15:12:32 <davidshotton> Sorry Guys.  On several attempts, both Paris and MIT numbers respond "The conference is full. No more parties can be added at this time.
15:13:08 <Anita> How can you get citations - hedging erodes (from Burns 2011:  'Results suggest that A >B' >> 'Burns suggests that A > B"  to "A>B [Burns, 2011]")
15:13:42 <Anita> Very sorry about that David! We are victims of our own success... Need to check with W3C!
15:14:16 <mscottm> Zakim, who is on the phone?
15:14:16 <Zakim> On the phone I see +1.617.768.aaaa, +1.619.252.aabb, +4238059aacc, ??P3, +1.310.279.aadd, +1.603.659.aaee, +1.617.993.aaff, +44.186.561.aagg, +1.714.292.aahh, [IPcaller],
15:14:20 <Zakim> ... +31.62.427.aaii, Joanne_Luciano, ??P19, +44.186.561.aajj, +1.518.258.aakk
15:14:33 <Tim> What Anita said ! :-)
15:14:49 <JoanneL> David, are you able to press "operator" to ask W3C for assisitance?
15:15:21 <mscottm> Yes, there are 15 on the phone. That is apparently the reservation for Zakim (space for 15).
15:15:45 <Tim> Eric P - can you increase this limit on an ongoing basis?
15:16:09 <Zakim> + +44.186.528.aall
15:16:19 <Anita> Gully: looked at connections in the brain. Different bits of research - need to integrate. 
15:16:24 <mscottm> I just asked him in another channel.
15:16:31 <mscottm> I'll cancel now. :)
15:16:32 <Anita> Thnks Scott!!
15:16:35 <Tim> thx
15:16:41 <Zakim> - +1.518.258.aakk
15:18:49 <JoanneL> ABSOLUTELY - that the observations are different from the interpretation!
15:19:15 <Tim> Gully: observation vs. interpretation - interpretation depends (sometimes) on what observations you include / exclude
15:19:52 <Anita> Most people focus on abstract interpretations vs. concrete observations. Need latter for metaanalysis
15:19:59 <Tim> This is reminiscent of Anita's ongoing points about "stories based upon data"
15:20:11 <JoanneL> (this is true in life too).   I agree with Gully 100% that you want to stick with observations and not interpretations - so they can be compared, etc.
15:20:12 <Tim> interpretation being the "story part"
15:20:18 <Howard> There is a large literature on the theory-laden nature of observation, exp design, and interpretation; careful separating them
15:21:09 <Tim> Actually I think BOTH are pretty important.  Look at what is published / not published - a lot depends upon the story-data relationship
15:21:16 <Anita> I think there are 3 parts: data; observations; interpretations which correspond to 'stories that persuade (Interpretations) with data (observations and data)'
15:21:18 <Tim> story is very important too
15:21:41 <Tim> Anita, how would you distinguish data vs. observations?
15:21:45 <Anita> Too bad Gully can't see this chat :-( will break in
15:22:03 <Anita> Let me pull this into the phone call... 
15:22:11 <Howard> Is "story" just another "type" of model, similar to a math model or causal model?
15:22:11 <Tim> We need a text to speeach robot for this call :-)
15:22:13 <JoanneL> Tim, agree they are both important. What I'm stressing is that the DISTINCTION must be clear. Of course interpretation is important - otherwise there is NO MEANING.
15:22:25 <Tim> Right, agree
15:22:27 <JoanneL> but meaning in different circumstances (contexts) is different.
15:22:32 <Tim> yup
15:22:34 <Anita> To me data are non-textual, observations are textual representation of, er, observations, ie human view on data
15:23:07 <Anita> Yes yes everyone reads every text differently - this is very important, take into account the mental space of the reader
15:23:33 <Anita> So we have data - observations - interpretations - 'reader making sense of all this' = 4 levels? 
15:23:34 <JoanneL> well, it's also important to capture the context of the data (like "consider the source") because data isn't independent of the context eitehr
15:23:46 <Tim> So eg the data would be an image of a Western, observation would be description of what is happening on the Western, and interpretation would be placing it in context of biology?
15:23:56 <JoanneL> Anita - and context too.
15:24:09 <Anita> Ah yes that too! That's what Ed Hovy calls 'legal lifting': allowing the experimental context that a claim was made within
15:24:17 <Tim> the 4th level is what I would call "synthesis"
15:24:26 <Anita> ... to be connected to the citation of that claim
15:24:32 <Tim> what you do when you read papers, ask questions, etc
15:24:46 <Anita> Yes - which is also a type of annotation (to Tim)
15:25:07 <JoanneL> Yes, and this is what Gully's talking about now 
15:25:18 <JoanneL> Capturing the context of the finding
15:25:25 <Tim> you mean, as in "my comments on your story>"
15:25:28 <Tim> ?
15:25:36 <Anita> Yes! We'll open up the discussion to this topic now I think it'll be interesting to the group
15:25:48 <Anita> "what you do when you read papers, ask questions, etc" = a type of annotation
15:25:52 <Tim> Another thing we might chat about is ramping
15:25:58 <Tim> separate topic
15:26:00 <Anita> Ramping?
15:26:22 <Tim> Carole Goble: "on-ramps" to adoption - need to be simple
15:26:23 <Anita> Gully: how do we break down reasoning into variables, etc.
15:26:23 <JoanneL> no, i mean my story in my context, then you can pick it up and put it in your context, but you know where it comes from (in terms of how I obtained it)
15:26:47 <Tim> thanks Joanne, I see now
15:26:50 <Anita> Yes so two contexts: writer's/researchers context, and reader's context. 
15:26:55 <Anita> Got it.
15:27:03 <Anita> We should write a paper about this. 
15:27:07 <JoanneL> Tim, it's like cultural context 
15:27:47 <Anita> Gully: how do we run analysis over this model e.g. using KEfED to improve reasoning over collections to allow predictions
15:29:03 <Anita> Experimental design such that data can be put into data repository
15:29:06 <JoanneL> For example, now that you're at Manchester, I can understand certain references in/from that context (I was there for a few year), and may need to "translate" to make it relevant elsewhere (this may be too general, better discussed over beer)
15:30:11 <Anita> Nanopub: how do we make an experimental prediction based on - ugh lost train of thought!
15:32:55 <Anita> Gully: raw data, ie single animal; averaged data; representation in a figure or table
15:33:04 <Howard> Sorry; there are too many tracks here that need to be separated.
15:34:17 <Anita> hi Howard can you make a stab? I think we're talking about levels of data now - all tracks seem to lead there?
15:34:32 <susanna> fyi, http://mibbi.org/index.php/Main_Page
15:34:44 <Anita> Joanne: Context within which experiment was done needs to be preserved. 
15:35:39 <JessT> in neuroimaging data sharing we call this "meta-data"
15:35:52 <Howard> I spent time with philosopher Fred Suppe who has book "Semantic conceptualization of scientific theory"; "data" is theory laden
15:35:59 <Anita> Gully: Methods nanopub: 1) Lab notebook; 2) information you need to interpret the data
15:36:03 <JessT> well that is part of the problem (Howard)
15:37:48 <Tim> it is unavoidable - from a basic neuropsych point of view, actually
15:38:44 <Howard> At NASA, we wanted to get satellite imagery of Earth actually *used* so we could justify paying for its maintenance; made federation gov-academic-private sector
15:40:11 <Anita> Howard: started in neuroscience, PET scan image analysis in humans, then got into NASA Earth understanding
15:41:07 <Anita> Howard: Context for understanding Earth science data - three types of understanding: Government, academics, private sector
15:42:17 <Anita> Howard: spent some time on Semantic conceptualisation of scientific theory - observation is an act of attention; you excerpt values that you give meaning to
15:42:34 <JoanneL> We humans have a hard time with observation - we are so easy to interpret
15:42:41 <JoanneL> and to judge
15:44:17 <JoanneL> Agree w/ what Anita says - that people see different things (when looking at a scene)
15:44:31 <JessT> Or when interpreting results
15:44:49 <JoanneL> Radial Category - take an instance and elaborate differently
15:45:55 <Anita> Anita: Champlain basin project: http://www.lcbp.org/ - data has very different interpretations between scientists (and different scientists, at that!), foresters/farmers, and people governing both
15:46:07 <Anita> Joanne is a different her than she was a week ago
15:46:11 <Anita> :-)
15:46:29 <paoloC> paoloC has joined #hcls2
15:46:32 <Anita> Howard: categories are context-based; person based
15:46:34 <JoanneL> I am alive, I move through time (we all do)
15:46:50 <Anita> Panta rhei, ouden menei. 
15:47:01 <Tim> Howard - have you read Lakoff's _Where Mathematics COmes From_?
15:47:24 <JoanneL> It's really cool, being human and going forward every day to experience a new day (life).  A day is a little life, I think the saying goes
15:47:28 <Tim> JL - can't step into the same river twice?
15:47:37 <JoanneL> can you Tim?
15:47:43 <Tim> course not
15:47:44 <Anita> πάντα χωρεῖ καὶ οὐδὲν μένει
15:47:50 <JoanneL> isn't tis fun!
15:48:04 <Tim> <attack of the classicists>
15:48:06 <Anita> http://en.wikipedia.org/wiki/Heraclitus#Ta_Panta_rhei.2C_.22everything_flows.22
15:48:32 <JessT> The question will be whether we can ever get out of the "domain-specific" context, given the theory-laden nature of language
15:48:44 <JessT> But it is worth a try.
15:48:55 <Tim> A monk asked Zhaozhou, "What is the living meaning of Zen?."   Zhaozhou said,     "The cypress tree in the courtyard." -  Mumonkan, Case 37
15:48:56 <Anita> Just giving a citation to Joanne's statement! From my context :-)
15:49:13 <JessT> :) Tim
15:49:13 <Tim> (to JL)
15:50:13 <Anita> Howard: need to have a story that you're trying to make sense of; that influences how you see the dataset; how to interpret it.
15:51:26 <JessT> Anita re: Champlain project and dfferent groups needing different things: Faceted ontologies might help?
15:53:11 <JoanneL> The other ares don't know what the preconceived notions are.
15:53:28 <david_newman> This sounds very much like Boundary Objects - http://en.wikipedia.org/wiki/Boundary_object
15:54:05 <david_newman> This was part of the inspiration for research objects within myExperiment and other projects
15:54:06 <Zakim> - +1.714.292.aahh
15:54:22 <Anita> Joanne: working with National Oceanographic Network - facilitate technology transfer to nonscientists
15:54:30 <Zakim> - +4238059aacc
15:54:43 <Anita> David - can you unmute and share thoughts?
15:54:43 <JoanneL> NEONINC.ORG
15:55:07 <david_newman> accidentally just hung up rather than unmuted 
15:55:11 <david_newman> just calling back in
15:55:14 <Anita> Ok! 
15:56:23 <JoanneL> has anyone in the group heard things talked in terms of "data publishing"?
15:56:46 <Anita> A lot of domain knowledge has to do with what a typical data finding looks like
15:57:02 <Anita> David Shotton: what is a model, what does it look like?
15:57:08 <Anita> DavidN are you back on?
15:57:18 <JoanneL> Re: David Shotton's comment about looking at a cell in an electron microsope
15:57:21 <Howard> That was part of the ESIP Federation work with Peter Fox and Deborah McGuinness (sp) (Joanne)
15:57:23 <JoanneL> Seeing vs perceiving
15:57:25 <Anita> Joanne: difference between seeing and perceiving
15:58:23 <Anita> DavidS: we learn what to ignore.
15:58:25 <Zakim> + +44.238.059.aamm
15:58:31 <Anita> Hi DavidN!
15:58:39 <JoanneL> Learning what to ignore (someone said) --- and that's what statistics are used for
15:58:55 <Howard> One trouble is that none of this is "edgy"; it is an analog world very difficult to capture with balls and sticks or ER diagrams
15:59:15 <Anita> So, wrapping up: how do we stick this into a formalism to wrap around scientific discourse?
15:59:37 <Anita> Gully: have to start with parameters; Joanne: also the assumptions!
15:59:58 <Howard> I'm trying a spatial model with landmarks in space.
16:00:01 <Tim> or - how does one take this understanding forwardinto something useful to research scientists?
16:00:09 <Anita> Sorry that was the project - the Ontology of Assumptions (for the Champlain model)
16:00:21 <Anita> Yes - what Tim said. 
16:00:28 <Tim> that is not too aboscure, opaque, byzantine or difficult to incorporate into existing practice
16:01:04 <Zakim> - +31.62.427.aaii
16:02:22 <Anita> Howard can you talk about your work more next week? 
16:02:33 <Anita> Gully: nanopublications and domains they operate in?
16:02:55 <Howard> two weeks?
16:03:11 <Anita> Howard yes please! Thank you!
16:03:26 <Anita> Tim: DEXI model - http://esw.w3.org/HCLSIG/SWANSIOC/Actions/SWANmyExpArray
16:04:23 <Anita> Tim: Bestiary of nanopublications; can be simple, complex things; makes them 'sticky', help people adopt it. That is a boundary object; they are polymorphous
16:04:38 <Howard> let me do it in terms of Gully's notes on research objects;  and maybe F0RC?
16:04:51 <Anita> Yes wonderful; what about FoRC?
16:05:58 <Anita> Joanne - next couple weeks pretty flat out but not to drop off; 
16:06:38 <Anita> David Newman - can you perhaps give some more data on your work on research objects and MyExperiment?
16:07:09 <JoanneL> I'm getting involved in 'data publishing' which is relevant and overlaps with our discussions. (the domain is earth and env sciences)
16:07:14 <Anita> David: yes, if you could do that next week? 10 minutes would be great
16:07:46 <Zakim> -??P19
16:07:51 <Zakim> - +44.186.561.aagg
16:08:13 <Anita> David next week, Howard 2 weeks, possibly Joanne in 3 weeks (or otherwise 4)
16:08:18 <Zakim> - +1.617.768.aaaa
16:08:43 <Anita> Sorry that's DavidN next week, Howard 2 weeks, possibly JoanneL in 3 weeks (or otherwise 4)
16:09:13 <Anita> Joanne: teaching course to turn students into researchers 
16:10:58 <Zakim> - +44.186.561.aajj
16:11:08 <Zakim> - +44.186.528.aall
16:11:09 <Zakim> - +1.310.279.aadd
16:11:15 <Zakim> - +44.238.059.aamm
16:11:22 <Zakim> - +1.603.659.aaee
16:11:23 <Zakim> -??P3
16:11:23 <Zakim> - +1.617.993.aaff
16:11:24 <Zakim> - +1.619.252.aabb
16:11:28 <Zakim> -[IPcaller]
16:11:41 <marcelotallis> marcelotallis has left #hcls2
16:11:54 <Zakim> -Joanne_Luciano
16:11:55 <Zakim> SW_HCLS(Disc)10:00AM has ended
16:11:57 <Zakim> Attendees were +1.617.768.aaaa, +1.619.252.aabb, +4238059aacc, +1.310.279.aadd, +1.603.659.aaee, +1.617.993.aaff, +44.186.561.aagg, +1.714.292.aahh, [IPcaller], +31.62.427.aaii,
16:11:59 <Zakim> ... Joanne_Luciano, +44.186.561.aajj, +1.518.258.aakk, +44.186.528.aall, +44.238.059.aamm
16:53:56 <johnM> johnM has joined #hcls2
16:54:05 <johnM> johnM has joined #hcls2
16:54:19 <johnM> zakim, this will be TERM
16:54:19 <Zakim> ok, johnM; I see SW_HCLS(TERM)12:00PM scheduled to start in 6 minutes
17:03:07 <Zakim> SW_HCLS(TERM)12:00PM has now started
17:03:13 <Zakim> +John_Madden
17:03:16 <Zakim> + +1.312.288.aaaa
17:03:47 <Zakim> + +1.301.827.aabb
17:04:03 <johnM> +1.31.288.aaaa is narciso
17:04:37 <mscottm> Hi John - sorry I'm late. BioRDF is running over.
17:04:39 <johnM> +1.301.827.aabb is mary
17:05:54 <johnM> I'd like some feedback related to our last week's discussion.
17:05:54 <johnM> Imagine the Description section of the report contains the 
17:05:54 <johnM> following statement:
17:05:54 <johnM>      "There are scattered amorphous microcalcifications in both breasts."
17:05:54 <johnM> So we have several ways to model this statement.
17:05:55 <johnM> Let's say we've created handles for theRightBreast and theLeftBreast.
17:05:57 <johnM> Maybe we even have decided on some handle for bothBreasts, though this is
17:05:59 <johnM> more difficult to decide how to do.
17:06:01 <johnM> Example: 
17:06:03 <johnM> theRightBreast = [a Breast; has laterality Right; anatomicPartOf thePatient].
17:06:05 <johnM> (You could do this differently, say by making a restriction class).
17:14:19 <ericP> Zakim, please dial ericP-office
17:14:19 <Zakim> ok, ericP; the call is being made
17:14:21 <Zakim> +EricP
17:14:49 <Zakim> + +20416aacc
17:15:38 <johnM> +20416aacc is mscottm
17:18:16 <johnM> I'd like some feedback related to our last week's discussion.
17:18:16 <johnM> Imagine the Description section of the report contains the 
17:18:17 <johnM> following statement:
17:18:17 <johnM>      "There are scattered amorphous microcalcifications in both breasts."
17:18:17 <johnM> So we have several ways to model this statement.
17:18:17 <johnM> Let's say we've created handles for theRightBreast and theLeftBreast.
17:18:19 <johnM> Maybe we even have decided on some handle for bothBreasts, though this is
17:18:23 <johnM> more difficult to decide how to do.
17:18:25 <johnM> Example: 
17:18:27 <johnM> theRightBreast = [a Breast; has laterality Right; anatomicPartOf thePatient].
17:18:29 <johnM> (You could do this differently, say by making a restriction class).
17:19:20 <johnM> Comparison is made to exams dated: 1/1/2007 ultrasound biopsy and
17:19:20 <johnM> 1/1/2008 mammogram - Acme Breast Imaging.
17:19:20 <johnM> There are scattered fibroglandular elements in both breasts.
17:19:21 <johnM> There is an irregular mass with a spiculated margin in the left breast
17:19:21 <johnM> at 9 o'clock. This is seen in additional views. This correlates as
17:19:21 <johnM> palpated and with breast MRI findings.
17:19:23 <johnM> There also is a new 3.1 cm area of grouped fine linear and pleomorphic
17:19:25 <johnM> calcifications in the left breast at 1 o'clock posterior depth. These
17:19:27 <johnM> are seen in additional views. This correlates with breast MRI findings.
17:19:29 <johnM> No other suspicious masses or calcifications are seen in either breast.
17:20:03 <johnM> ,,,
17:20:05 <johnM> There are scattered fibroglandular elements in both breasts.
17:20:08 <johnM> *****
17:21:34 <johnM> bothBreast have finding [a FibroglandularElements].
17:22:02 <johnM> bothBreasts haveFinding [a Finding; = theFinding].
17:22:39 <johnM> theFinding consistsOf [a FibroglandularElement].
17:23:24 <johnM> rightBreast = [a Breast; anatomicPartOf thePatient].
17:24:03 <johnM> bothBreasts = (rightBreast, leftBreast).
17:24:40 <johnM> rightBreast hasFinding theFinding.
17:24:51 <johnM> leftBreast hasFinding theFinding.
17:25:09 <johnM> (rightBreast, leftBreast) hasFinding theFinding.
17:26:17 <johnM> rightBreast has [a FibroglandularElement].
17:26:28 <ericP> +1
17:28:12 <johnM> theFinding = {rightBreast has [a FibroglandularElement]}.
17:31:41 <johnM> Option 1: every single fact in the document is viewed individually as a "finding"
17:32:18 <johnM> Option 2: the entire document is a named graph, an inside the named graph we just state facts
17:32:21 <ericP> <testX> { <testX> a <PathologyText> ; :subject <breastSample7> . }
17:32:21 <ericP> <findingy> { <findingY> a <InterventionFlag>, <PathologyFinding> ; :resultOf <testX> }
17:36:49 <ericP> <findingy> { <findingY> a <PathologyFinding> ; :resultOf <testX> ; :indicator [ :location "0900"^^xsd:time ; :margin :Spiculated ] }
17:37:15 <johnM> {rightBreast has [a FibroglandularElement]} is a n3:falsehood.
17:40:21 <ericP> <findingZ> { <findingZ> a <PathologyFinding> ; :resultOf <testX> ; :indicator [ :location "0100"^^xsd:time ; :size 3.1 ; a :Calcificiation ] }
17:41:21 <johnM> "No microcalcifications are seen."
17:41:34 <johnM> We're going to have be able say this!
17:43:30 <johnM> thingsNotSeen = (microcalcifiations).
17:47:52 <mscottm> breaking up
17:48:12 <mscottm> ericP your sound is breaking up
17:48:23 <mscottm> better now
17:56:43 <ericP> <report11> :finding <findingY> , <findingZ> .
18:00:10 <Zakim> - +1.301.827.aabb
18:02:28 <Zakim> -John_Madden
18:02:49 <johnM> rrsagent, draft minutes.
18:02:49 <RRSAgent> I'm logging. I don't understand 'draft minutes.', johnM.  Try /msg RRSAgent help
18:03:01 <johnM> rrsagent, make minutes public
18:03:01 <RRSAgent> I'm logging. I don't understand 'make minutes public', johnM.  Try /msg RRSAgent help
18:03:30 <mscottm>   RRSAgent, please draft minutes
18:03:30 <RRSAgent> I have made the request to generate http://www.w3.org/2011/02/07-hcls2-minutes.html mscottm
18:03:31 <johnM> Eric/Scott -- can you tell rrsagent to do its thing? I always forget the commands
18:03:36 <mscottm>   RRSAgent, please make log world-visible
18:12:04 <mscottm> http://www.w3.org/blog/hcls
18:19:43 <Zakim> - +1.312.288.aaaa
18:19:47 <Zakim> - +20416aacc
18:19:48 <Zakim> -EricP
18:19:49 <Zakim> SW_HCLS(TERM)12:00PM has ended
18:19:51 <Zakim> Attendees were John_Madden, +1.312.288.aaaa, +1.301.827.aabb, EricP, +20416aacc
19:48:57 <Zakim> Zakim has left #hcls2
20:34:22 <ericP> RRSAgent, bye
20:34:22 <RRSAgent> I see no action items