View source for HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20110321

=== Agenda March 21 Scientific Discourse call ===
* Talk by Barend Mons: [http://www.slideshare.net/anitawaard/barend-mons-nanopublications-as-nanopublications "Nanopublications in nanopublications"]
* Ontologies update: Dexi/Bibo/ORB/others
* AOB 

==== Dial-in & IRC Information ====
* Time: 15:00 GMT / 10am EST / 7am PST
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* Participant Access Code: 42572 ("HCLS2") 
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* Mibbit quick start: Click on mibbit for instant IRC access
* Duration: 1hr

==== IRC Transcript: ====
 09:56		*** paoloC joined #hcls2
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 09:59	Anita	HI all! Can you all dail in?
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 09:59	Anita	Details here...http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/201 10321
 10:01	Anita	Hi Paolo, Barend and Scott - are you on the phone?
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 10:06	david_r_newman	Is anyone else having problems with the conference bridge. I am gettting "All lines are busy" on the UK bridge number
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 10:08	Anita	Hi David Newman did you get in?
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 10:08	Anita	Anyone else having problems on accessing the phone lines?
 10:08	Anita	Barend: now start measuring actual citations of nanopublications
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 10: 09	david_r_newman	Anita: No I am using Skype from the US number
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 10: 09	RRSAgent	logging to http://www.w3.org/2011/03/21-hcls2-irc
 10: 09	Anita	Thanks - that's working ok then?
 10: 09	david_r_newman	Anita: But I am now in
 10: 10	Howard	Very nice sequence from slide 5 to 6 showing how nanoPubs solve current problems with strictly narrative papers
 10: 10	Joanne	it's hard to hear Barend, but am getting most of it. ... would be useful, once he goes throught he overview to go into a specific example and walk us through something
 10: 10	Anita	If you want to describe the variants in the underlying databases there are hundreds of thousands - easily mine 40.000 nanopublications from an abstract but there are really only 600 in them (Scott/Barnd did I get that right?)
 10: 10	david_r_newman	Yes, I hopefully won't drop out from lack on credit. Think I have enough for this call.
 10:11	Anita	No - paper is textual review of LOPDs mine text manually  100.000 nanopubs; only 40.000 make it into the paper
 10:12	Anita	If you look in general for variants: in literature frequency of variants is very low - is only in the databases
 10:12	mscottm	BareBarend was referring to LOVD - Leiden Open Variant Database
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 10:12	Anita	Scott can you pse (co-)scribe - I'm not sure I'm catching all the nuances - thanks!
 10:13	Anita	Good David glad you're here - nr should be toll-free though??
 10:13	mscottm	I'll do my best. I find it also difficult to hear Barend even though he's about a 20 min walk away. !
 10:13	Joanne	Someone (Gully?) is asking how the nanopublicaions are structured
 10:13	Anita	Gully: how is nanopub represented? Barend: we're just making that - Scott will explain details!
 10:14	mscottm	http://www.mendeley.com/research/the-anatomy-of-a-nanopublication/
 10:14	Gully	nanopub.org is the site where this will be put
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 10:16	matthias_samwald	(just joined the call)
 10:18	Anita	Details of RDF is to be determined - Herman Verhagen did mining of LOVD - Leiden Open Variant Database: http://www.lovd.nl/2.0/
 10:19	Gully	Scott: do you have a group on Mendeley for nanopublication developers?
 10:20	Anita	A certain SNP has a variation frequency in a population - "cognitive deficits relate to BACA-1 gene" - see many things that refer to this core assertion
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 10:20	Anita	Joanne: can we get a bit of background? What makes something a nanopublication?
 10:22	Anita	Eric (LastName?) - nanopub is an assertion, with provenance and context, which defines when it is true or not true -
 10:22	Anita	Is there a difference between provenance and context?
 10:23	Anita	Typical things you reference in a research paper - Author, journal, date, DOI - are different from conditions critical to understanding of the data and the assertions
 10:23	Anita	Or: this SNP has a frequency of 2.5% only in a given population
 10:24	Anita	Does this mean that the reference is the provenance?
 10:26	Anita	Anita: do you take the opinion of the author or the experimental data as the context?
 10:27	Anita	Eric: either the data or the opinion - so nanopublication has no hedging: "Protein A interacts with Protein B"
 10:27	Howard	I like finer grained sciDiscourse; is there a good way to link claim to warrant?
 10:28	Anita	Provenance and context will tell you how believable this is -
 10:29	Howard	I am not clear on the link from P&C to warrant: the warrant is theory or model dependent.
 10:36	Anita	Joanne - yes, so is this like fine-grained structure?
 10:36	Anita	Anita: yes-ish: I'm not clear on how nanopub comes out of a paper. Is it only for databases?
 10:37	Anita	Eric: much more exposed data in databases than in papers - easier than text-mining literature. So: with high-throughput biology and unambiguous data, we want to make a system for publishing data points.
 10:38	Anita	Eric: create a system that is recognised by e.g. Nature and Thompson to publish thier *data* as nanopublications
 10:40	mscottm	Erik Schultes
 10:40	Anita	Like to get rid of the idea of 'supplemental data': but publish data as a first-order citizen and then publish paper as an afterthought
 10:40	Howard	The paper is the pre-thought: what made the data count as data
 10:41	Anita	Joanne: went to earth science data conference: they publish data all the time! Let's not duplicate efforts.
 10:41	mscottm	Re: Gully's question "Scott: do you have a group on Mendeley for nanopublication developers?" - it sounds like a suggestion. Should we start one?
 10:44	Anita	Joanne are you still talking next week about the GeoData stuff?
 10:45	Gully	Re: Mendeley group. Yes, would you like to start it or shall I?
 10:46	Joanne	Anita -- I'm not sure that I will have time to prepare (sorry to keep putting this off, but am working through a backlog created by travel and moving)
 10:46	Joanne	http://www.sciencemag.org/content/331/6018/705.abstract (this is the science article I was talking about -- it's focus is on data visualization). I'll post the link next to the GeoData2011 workshop
 10:49	Joanne	GeoData 2011 -Geo-Data Informatics: Exploring the Life Cycle, Citation and Integration of Geo-Data http://tw.rpi.edu/web/Workshop/Community/GeoData2011
 10:49	Howard	Erik: nanoPubs have "flavors" or semantic types: these types may vary within biology domains
 10:49	Joanne	Note- the term citation is used instead of publication here - but we're talking about the same thing
 10:50	Howard	Erik: microCitations within a hemoglobin database can be used to track usage of the dataset
 10:51	paoloC	Anita: I have to drop out in a minute, just wanted to say that if nobody else has further remarks/comments about ORB, the draft is ready to go.
 10:51	Anita	LODD just published data publishing provenance recommendations - just been submitted; now a paper
 10:52	mscottm	http://www.w3.org/blog/hcls
 10:55	mscottm	mscottmarshall@gmail.com
 10:56	Gully	thanks
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 10:57	david_r_newman	Creative Commons is a good starting point for licensing - http://creativecommons.org/ns#
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 10:58	paoloC	Nanopublications and SWAN: http://www.slideshare.net/paolociccarese/alzswan-hyque-and-nanopublications
 11:00	Gully	http://www.w3.org/wiki/HCLSIG/SWANSIOC/Nanopublications-Subtask
 11:01	Anita	List of ontologies is here: http://www.w3.org/wiki/HCLSIG/SWANSIOC