See also: IRC log
<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.
The KEfED model https://wiki.birncommunity.org/display/NEWBIRNCC/KEfED+OWL+Model) - is a derivative from OBI - Allan Ruttenberg
Break down nanopub in several different types
Nanopub is an assertion, eg. mosquitoes cause malaria
Different types - see https://sites.google.com/site/beyondthepdf/home/program-draft/notes-from-the-breakout
<JoanneL> Hi, had trouble getting to IRC, would someone repost the link (if we're looking at slides) thanks!
<alex> same as me, where could I see the slides?
Joanne: Talking about nanopublication types- see https://sites.google.com/site/beyondthepdf/home/program-draft/notes-from-the-breakout
<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.
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]")
Very sorry about that David! We are victims of our own success... Need to check with W3C!
<Tim> What Anita said ! :-)
<JoanneL> David, are you able to press "operator" to ask W3C for assisitance?
<mscottm> Yes, there are 15 on the phone. That is apparently the reservation for Zakim (space for 15).
<Tim> Eric P - can you increase this limit on an ongoing basis?
Gully: looked at connections in the brain. Different bits of research - need to integrate.
<mscottm> I just asked him in another channel.
<mscottm> I'll cancel now. :)
Thnks Scott!!
<Tim> thx
<JoanneL> ABSOLUTELY - that the observations are different from the interpretation!
<Tim> Gully: observation vs. interpretation - interpretation depends (sometimes) on what observations you include / exclude
Most people focus on abstract interpretations vs. concrete observations. Need latter for metaanalysis
<Tim> This is reminiscent of Anita's ongoing points about "stories based upon data"
<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.
<Tim> interpretation being the "story part"
<Howard> There is a large literature on the theory-laden nature of observation, exp design, and interpretation; careful separating them
<Tim> Actually I think BOTH are pretty important. Look at what is published / not published - a lot depends upon the story-data relationship
I think there are 3 parts: data; observations; interpretations which correspond to 'stories that persuade (Interpretations) with data (observations and data)'
<Tim> story is very important too
<Tim> Anita, how would you distinguish data vs. observations?
Too bad Gully can't see this chat :-( will break in
Let me pull this into the phone call...
<Howard> Is "story" just another "type" of model, similar to a math model or causal model?
<Tim> We need a text to speeach robot for this call :-)
<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.
<Tim> Right, agree
<JoanneL> but meaning in different circumstances (contexts) is different.
<Tim> yup
To me data are non-textual, observations are textual representation of, er, observations, ie human view on data
Yes yes everyone reads every text differently - this is very important, take into account the mental space of the reader
So we have data - observations - interpretations - 'reader making sense of all this' = 4 levels?
<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
<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?
<JoanneL> Anita - and context too.
Ah yes that too! That's what Ed Hovy calls 'legal lifting': allowing the experimental context that a claim was made within
<Tim> the 4th level is what I would call "synthesis"
scribe: to be connected to the citation of that claim
<Tim> what you do when you read papers, ask questions, etc
Yes - which is also a type of annotation (to Tim)
<JoanneL> Yes, and this is what Gully's talking about now
<JoanneL> Capturing the context of the finding
<Tim> you mean, as in "my comments on your story>"
<Tim> ?
Yes! We'll open up the discussion to this topic now I think it'll be interesting to the group
"what you do when you read papers, ask questions, etc" = a type of annotation
<Tim> Another thing we might chat about is ramping
<Tim> separate topic
Ramping?
<Tim> Carole Goble: "on-ramps" to adoption - need to be simple
Gully: how do we break down reasoning into variables, etc.
<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)
<Tim> thanks Joanne, I see now
Yes so two contexts: writer's/researchers context, and reader's context.
Got it.
We should write a paper about this.
<JoanneL> Tim, it's like cultural context
Gully: how do we run analysis over this model e.g. using KEfED to improve reasoning over collections to allow predictions
Experimental design such that data can be put into data repository
<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)
Nanopub: how do we make an experimental prediction based on - ugh lost train of thought!
Gully: raw data, ie single animal; averaged data; representation in a figure or table
<Howard> Sorry; there are too many tracks here that need to be separated.
hi Howard can you make a stab? I think we're talking about levels of data now - all tracks seem to lead there?
<susanna> fyi, http://mibbi.org/index.php/Main_Page
Joanne: Context within which experiment was done needs to be preserved.
<JessT> in neuroimaging data sharing we call this "meta-data"
<Howard> I spent time with philosopher Fred Suppe who has book "Semantic conceptualization of scientific theory"; "data" is theory laden
Gully: Methods nanopub: 1) Lab notebook; 2) information you need to interpret the data
<JessT> well that is part of the problem (Howard)
<Tim> it is unavoidable - from a basic neuropsych point of view, actually
<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
Howard: started in neuroscience,
PET scan image analysis in humans, then got into NASA Earth
understanding
... Context for understanding Earth science data - three types
of understanding: Government, academics, private sector
... spent some time on Semantic conceptualisation of scientific
theory - observation is an act of attention; you excerpt values
that you give meaning to
<JoanneL> We humans have a hard time with observation - we are so easy to interpret
<JoanneL> and to judge
<JoanneL> Agree w/ what Anita says - that people see different things (when looking at a scene)
<JessT> Or when interpreting results
<JoanneL> Radial Category - take an instance and elaborate differently
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
Joanne is a different her than she was a week ago
:-)
Howard: categories are context-based; person based
<JoanneL> I am alive, I move through time (we all do)
Panta rhei, ouden menei.
<Tim> Howard - have you read Lakoff's _Where Mathematics COmes From_?
<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
<Tim> JL - can't step into the same river twice?
<JoanneL> can you Tim?
<Tim> course not
πάντα χωρεῖ καὶ οὐδὲν μένει
<JoanneL> isn't tis fun!
<Tim> <attack of the classicists>
http://en.wikipedia.org/wiki/Heraclitus#Ta_Panta_rhei.2C_.22everything_flows.22
<JessT> The question will be whether we can ever get out of the "domain-specific" context, given the theory-laden nature of language
<JessT> But it is worth a try.
<Tim> A monk asked Zhaozhou, "What is the living meaning of Zen?." Zhaozhou said, "The cypress tree in the courtyard." - Mumonkan, Case 37
Just giving a citation to Joanne's statement! From my context :-)
<JessT> :) Tim
<Tim> (to JL)
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.
<JessT> Anita re: Champlain project and dfferent groups needing different things: Faceted ontologies might help?
<JoanneL> The other ares don't know what the preconceived notions are.
<david_newman> This sounds very much like Boundary Objects - http://en.wikipedia.org/wiki/Boundary_object
<david_newman> This was part of the inspiration for research objects within myExperiment and other projects
Joanne: working with National Oceanographic Network - facilitate technology transfer to nonscientists
David - can you unmute and share thoughts?
<JoanneL> NEONINC.ORG
<david_newman> accidentally just hung up rather than unmuted
<david_newman> just calling back in
Ok!
<JoanneL> has anyone in the group heard things talked in terms of "data publishing"?
A lot of domain knowledge has to do with what a typical data finding looks like
David Shotton: what is a model, what does it look like?
DavidN are you back on?
<JoanneL> Re: David Shotton's comment about looking at a cell in an electron microsope
<Howard> That was part of the ESIP Federation work with Peter Fox and Deborah McGuinness (sp) (Joanne)
<JoanneL> Seeing vs perceiving
Joanne: difference between seeing and perceiving
DavidS: we learn what to ignore.
Hi DavidN!
<JoanneL> Learning what to ignore (someone said) --- and that's what statistics are used for
<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
So, wrapping up: how do we stick this into a formalism to wrap around scientific discourse?
Gully: have to start with parameters; Joanne: also the assumptions!
<Howard> I'm trying a spatial model with landmarks in space.
<Tim> or - how does one take this understanding forwardinto something useful to research scientists?
Sorry that was the project - the Ontology of Assumptions (for the Champlain model)
Yes - what Tim said.
<Tim> that is not too aboscure, opaque, byzantine or difficult to incorporate into existing practice
Howard can you talk about your work more next week?
Gully: nanopublications and domains they operate in?
<Howard> two weeks?
Howard yes please! Thank you!
Tim: DEXI model - http://esw.w3.org/HCLSIG/SWANSIOC/Actions/SWANmyExpArray
... Bestiary of nanopublications; can be simple, complex
things; makes them 'sticky', help people adopt it. That is a
boundary object; they are polymorphous
<Howard> let me do it in terms of Gully's notes on research objects; and maybe F0RC?
Yes wonderful; what about FoRC?
Joanne - next couple weeks pretty flat out but not to drop off;
David Newman - can you perhaps give some more data on your work on research objects and MyExperiment?
<JoanneL> I'm getting involved in 'data publishing' which is relevant and overlaps with our discussions. (the domain is earth and env sciences)
David: yes, if you could do that next week? 10 minutes would be great
David next week, Howard 2 weeks, possibly Joanne in 3 weeks (or otherwise 4)
Sorry that's DavidN next week, Howard 2 weeks, possibly JoanneL in 3 weeks (or otherwise 4)
Joanne: teaching course to turn students into researchers
<johnM> +1.31.288.aaaa is narciso
<mscottm> Hi John - sorry I'm late. BioRDF is running over.
<johnM> +1.301.827.aabb is mary
<johnM> I'd like some feedback related to our last week's discussion.
<johnM> Imagine the Description section of the report contains the
<johnM> following statement:
<johnM> "There are scattered amorphous microcalcifications in both breasts."
<johnM> So we have several ways to model this statement.
<johnM> Let's say we've created handles for theRightBreast and theLeftBreast.
<johnM> Maybe we even have decided on some handle for bothBreasts, though this is
<johnM> more difficult to decide how to do.
<johnM> Example:
<johnM> theRightBreast = [a Breast; has laterality Right; anatomicPartOf thePatient].
<johnM> (You could do this differently, say by making a restriction class).
<johnM> +20416aacc is mscottm
<johnM> I'd like some feedback related to our last week's discussion.
<johnM> Imagine the Description section of the report contains the
<johnM> following statement:
<johnM> "There are scattered amorphous microcalcifications in both breasts."
<johnM> So we have several ways to model this statement.
<johnM> Let's say we've created handles for theRightBreast and theLeftBreast.
<johnM> Maybe we even have decided on some handle for bothBreasts, though this is
<johnM> more difficult to decide how to do.
<johnM> Example:
<johnM> theRightBreast = [a Breast; has laterality Right; anatomicPartOf thePatient].
<johnM> (You could do this differently, say by making a restriction class).
<johnM> Comparison is made to exams dated: 1/1/2007 ultrasound biopsy and
<johnM> 1/1/2008 mammogram - Acme Breast Imaging.
<johnM> There are scattered fibroglandular elements in both breasts.
<johnM> There is an irregular mass with a spiculated margin in the left breast
<johnM> at 9 o'clock. This is seen in additional views. This correlates as
<johnM> palpated and with breast MRI findings.
<johnM> There also is a new 3.1 cm area of grouped fine linear and pleomorphic
<johnM> calcifications in the left breast at 1 o'clock posterior depth. These
<johnM> are seen in additional views. This correlates with breast MRI findings.
<johnM> No other suspicious masses or calcifications are seen in either breast.
<johnM> ,,,
<johnM> There are scattered fibroglandular elements in both breasts.
<johnM> *****
<johnM> bothBreast have finding [a FibroglandularElements].
<johnM> bothBreasts haveFinding [a Finding; = theFinding].
<johnM> theFinding consistsOf [a FibroglandularElement].
<johnM> rightBreast = [a Breast; anatomicPartOf thePatient].
<johnM> bothBreasts = (rightBreast, leftBreast).
<johnM> rightBreast hasFinding theFinding.
<johnM> leftBreast hasFinding theFinding.
<johnM> (rightBreast, leftBreast) hasFinding theFinding.
<johnM> rightBreast has [a FibroglandularElement].
<ericP> +1
<johnM> theFinding = {rightBreast has [a FibroglandularElement]}.
<johnM> Option 1: every single fact in the document is viewed individually as a "finding"
<johnM> Option 2: the entire document is a named graph, an inside the named graph we just state facts
<ericP> <testX> { <testX> a <PathologyText> ; :subject <breastSample7> . }
<ericP> <findingy> { <findingY> a <InterventionFlag>, <PathologyFinding> ; :resultOf <testX> }
<ericP> <findingy> { <findingY> a <PathologyFinding> ; :resultOf <testX> ; :indicator [ :location "0900"^^xsd:time ; :margin :Spiculated ] }
<johnM> {rightBreast has [a FibroglandularElement]} is a n3:falsehood.
<ericP> <findingZ> { <findingZ> a <PathologyFinding> ; :resultOf <testX> ; :indicator [ :location "0100"^^xsd:time ; :size 3.1 ; a :Calcificiation ] }
<johnM> "No microcalcifications are seen."
<johnM> We're going to have be able say this!
<johnM> thingsNotSeen = (microcalcifiations).
<mscottm> breaking up
<mscottm> ericP your sound is breaking up
<mscottm> better now
<ericP> <report11> :finding <findingY> , <findingZ> .
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