16:02:00 <RRSAgent> RRSAgent has joined #BioRDF
16:02:00 <RRSAgent> logging to http://www.w3.org/2008/01/07-BioRDF-irc
16:02:07 <ericP> Zakim, this is BioRDF
16:02:07 <Zakim> sorry, ericP, I do not see a conference named 'BioRDF' in progress or scheduled at this time
16:02:19 <Susie> Speaking to Josh to try to get it fixed...
16:02:20 <ericP> oops, is this hcls time?
16:02:21 <Don> I'm having trouble calling in...
16:02:29 <mscottm> was getting "this passcode is not valid".. trying again
16:02:32 <Don> it says that the code 246733 is not valid.
16:02:56 <BillBug> same here
16:02:57 <ericP> Susie, i'm next door -- can i help somehow?
16:03:38 <mscottm> Something to do with the new year? reschedule conferences?
16:04:02 <ericP> Don, mscottm, BillBug, our top scientists are working on it as we speak
16:04:26 <Don> Thank you Eric. Happy New Year everyone!
16:04:37 <BillBug> Very comforting :-)
16:04:39 <BillBug> Thanks, Eric.
16:04:54 <mscottm> "I'm doin the best I can Captain!"
16:05:00 <Susie> Things are being set up. It should just be another minute or so now.
16:05:23 <ericP> "damnit jim, i'm a doctor, not an operator"
16:06:04 <ericP> thanks should go to Susie who's actually dealing with the problem
16:06:15 <kei> kei has joined #BioRDF
16:06:17 <ericP> i'm just buying time by entertaining y'all
16:06:31 <ericP> Zakim, this is BioRDF
16:06:31 <Zakim> sorry, ericP, I do not see a conference named 'BioRDF' in progress or scheduled at this time
16:06:49 <kei> I have problem dialing in
16:06:58 <alanr> alanr has joined #biordf
16:07:04 <alanr> what's the call in code?
16:07:07 <ericP> kei, yes, we're working on that now
16:07:22 <ericP> alanr, zakim is ill. josh is working on it now
16:07:27 <alanr> k
16:07:42 <jar> as alan is on the call i think i'll pass today.  enjoy  -Jonathan
16:07:50 <jar> jar has left #biordf
16:07:54 <ericP> Zakim, if this was BioRDF, what would the code be?
16:07:54 <Zakim> I don't understand your question, ericP.
16:08:25 <ericP> Zakim, this is BioRDF
16:08:25 <Zakim> ericP, I see SW_HCLS(BioRDF)11:00AM in the schedule but not yet started.  Perhaps you mean "this will be BioRDF".
16:08:31 <ericP> Zakim, this will be BioRDF
16:08:31 <Zakim> ok, ericP; I see SW_HCLS(BioRDF)11:00AM scheduled to start 8 minutes ago
16:08:34 <Zakim> SW_HCLS(BioRDF)11:00AM has now started
16:08:34 <ericP> ok all
16:08:38 <Zakim> +Susie
16:08:48 <Zakim> +EricP
16:08:51 <Zakim> -Susie
16:08:53 <Zakim> +Susie
16:09:12 <Zakim> +M_Scott_Marshall
16:09:36 <Zakim> +Alan
16:09:44 <Zakim> +Don_Doherty
16:09:45 <Zakim> +Kei_Cheung
16:09:56 <BillBug> BillBug has joined #biordf
16:10:10 <Zakim> +??P16
16:10:24 <matthiassamwald> +??P16 is me.
16:10:25 <Zakim> +??P17
16:10:48 <Susie> Zakim, pick a scribe
16:10:48 <Zakim> Not knowing who is chairing or who scribed recently, I propose EricP
16:10:55 <ericP> Zakim, +??P17 is BillBug 
16:10:55 <Zakim> sorry, ericP, I do not recognize a party named '+??P17'
16:10:59 <ericP> Zakim, ??P17 is BillBug 
16:10:59 <Zakim> +BillBug; got it
16:11:06 <ericP> sribe: ericP
16:11:12 <ericP> chair: Susie
16:11:21 <alanr> scribe: ericP
16:11:23 <ericP> meeting: BioRDF
16:11:54 <ericP> Susie: focus on documentation
16:12:07 <ericP> agenda + KB documentation
16:12:12 <ericP> Zakim, take up agendum 1
16:12:12 <Zakim> agendum 1. "KB documentation" taken up [from ericP]
16:12:28 <Zakim> + +049681aaaa
16:12:29 <ericP> mscottm: had goal of draft by end of year
16:12:48 <ericP> ... didn't work out, but a lot has happened on the doc
16:13:29 <ericP> ... up 'till the 22nd, several of us met on the HCLS telecon slot and made decisions about the doc
16:13:35 <ericP> ... most of that stuff has been edited in
16:13:46 <ericP> ... i've been on vacation and just returned
16:14:13 <ericP> ... Eric documented an issue
16:14:43 <mscottm> http://www.w3.org/2001/sw/hcls/notes/kb/
16:14:55 <BillBug> scott: everyone review current doc?
16:15:08 <mscottm> lost connection
16:15:19 <ericP> -> http://www.w3.org/2001/sw/hcls/notes/kb/#empty-protein-set Empty Protein Set issue
16:15:32 <Zakim> +M_Scott_Marshall.a
16:15:52 <BillBug> eric: forward closure - extra triples that we'd normally use OWL to infer
16:16:20 <mscottm> forward chaining or transitive closure, I believe
16:16:21 <alanr> unbound query?
16:16:24 <BillBug> eric: AlanR has put them in named graphs - when including name graphs, you get the "inferred" classes
16:17:07 <BillBug> eric: I can write up a description of why the query would be unbound - Alan thinks there are higher priority tasks.
16:17:53 <BillBug> AlanR: There is a way to be more precise - the problem could be better addressed in a triple store supporting inferencing.  Not a trivial task. 
16:18:21 <BillBug> AlanR: Some of the bnodes are essentially implementing OWL syntax as opposed to being real "things".
16:19:13 <BillBug> susie: you said problem is unbounded query, but if inferencing done outside of KB, then inferred classes added to KB, then it becomes bounded?
16:19:37 <alanr> it wouldn't really be a problem, even if the query was in owl. But there are different ways of asking questions in OWL.
16:20:03 <BillBug> ericP: yes - wondering if we could tweak query a bit so the same query WOULD work in an OWL triple store.  Think can be done by adding one more triple to the query
16:20:20 <BillBug> AlanR: That's where I had issues
16:20:57 <BillBug> ericP: Alan, you seemed to be looking to use a query language other than SPARQL (Alan: yes).  I'm trying to work out a way to do this in SPARQL
16:21:18 <Zakim> +??P20
16:21:45 <BillBug> AlanR: Since SPARQL doesn't directly support inferencing, any proposal would be purely speculative.  Similar problem in OWL, since there is not now a specified OWL query language?
16:22:58 <BillBug> AlanR: There are OWL query options BUT none are a part of an excepted W3C spec.
16:23:33 <BillBug> EricP: So there are essentially design patterns that have arisen to help make such inference-dependent queries bounded in SPARQL
16:23:38 <alanr> http://clarkparsia.com/files/pdf/sparqldl.pdf
16:25:11 <BillBug> EricP: Why would this not work in Pellet?
16:25:13 <BillBug> AlanR: Not clear it won't work, just more complicated than Pellet can contend with now.  May work in the Jena model (AQL) where there might be support for this sort of query.  The general problem is NOT ALL QUERIES ARE DECIDABLE - i.e., there are queries you can express in SPARQL that are not decideable.
16:26:30 <BillBug> EricP: Agreed.  However, there are ways of defining a virtual graph that can make unbounded queries work.
16:26:31 <BillBug> AlanR: True but the range of virtual graphs expressible in OWL would certainly allow you to express undecideable queries
16:27:49 <BillBug> EricP: True - but you can still define a virtual graph in SPARQL that would make this particular query bounded.  I was just proposing a way of creating extra triples that essentially exist as a Rule that sits outside the query and helps to make it decideable.
16:28:40 <BillBug> EricP: Still having a hard time documenting the current query that explains how we've created a intersection that could be THEORETICALLY EMPTY, but is not so because of the way we've populated our KB triple store.
16:28:49 <mscottm> my connection has been dropped again (!)
16:29:08 <BillBug> AlanR: This is where I don't quite get it.
16:29:18 <Zakim> +M_Scott_Marshall.aa
16:29:23 <alanr> Current example returns pairs of classes and instances
16:29:29 <Zakim> -M_Scott_Marshall.aa
16:29:31 <mscottm> and again..
16:29:52 <alanr> SPARQL effectively returns only instances (or classes viewed as instances)
16:29:57 <BillBug> Kei: Current example is you are using a GO process.  If we try another example, would we still be able to find intersection sets?
16:30:04 <alanr> OWL considers this kind of query to be complicated
16:30:17 <alanr> because of the mix of return values
16:30:33 <BillBug> Kei: Also - are there other ways of connecting SenseLab data to other data sets?
16:31:02 <BillBug> Susie: Make sense for AlanR & EricP to have another call to resolve this?
16:31:03 <BillBug> EricP: Yes - we have a call coming up later today
16:31:04 <alanr> I will be in at 1, not 12, as discussed previously
16:31:25 <Zakim> +M_Scott_Marshall.aa
16:31:40 <BillBug> Susie: I beleive we decided we'd write up things up as they are, and also separately descirbe enhancements 
16:32:42 <BillBug> EricP: I just felt there was an outstanding issue in describing the current state of the KB - and wanted to make certain we truly understood the issue.
16:32:44 <BillBug> AlanR: A key aspect to clearly specifying which BNODES represent OWL syntax.  (EricP: agreed)
16:33:01 <ericP> Susie: would like to get to WD and solicit feedback
16:33:34 <alanr> In fact, these bnodes could be replaces by constants without changing the OWL-DL meaning (but the OWL-Full meaning would change)
16:33:41 <ericP> ericP: happy to publish as it is
16:34:06 <Zakim> +Scott_Marshall
16:34:30 <alanr> I don't have a lot of time until the end of the week
16:34:31 <BillBug> Susie: Eric - do you have a date in mind for soliciting feedback one more time?
16:34:33 <BillBug> EricP: I'm happy to publish at any point, since the IG has agreed to do so.  I'm happy to go as is
16:34:34 <BillBug> Susie: What about asking for additional review by end of this week.
16:34:36 <BillBug> EricP: Rather not wait too much - if we push it off 'til next Friday, that's fine - or get others to review in next few days for publishing by this Friday?
16:34:57 <alanr> need to get names
16:35:03 <alanr> and assign actions
16:35:08 <BillBug> Susie: Think it would be good to aim for the 18th with folks passing their comments to Scott
16:35:27 <ericP> reviewers: Susie, BillBug
16:35:55 <alanr> 24 hours from now
16:36:10 <BillBug> EricP: what would your time frame be, Scott
16:36:11 <BillBug> Scott: 24 hrs
16:36:18 <BillBug> All: OK
16:36:32 <ericP> Susie: how goes the SenseLab note?
16:36:32 <BillBug> Eric - can I pass the minutes baton back to you?
16:36:44 <ericP> matthiassamwald: quite close to completion IMO
16:37:10 <ericP> ... need to reformat citations and change pictures
16:37:13 <matthiassamwald> http://www.w3.org/2001/sw/hcls/notes/senselab/
16:37:30 <ericP> Susie: can be done by when?
16:37:35 <BillBug> For those of us who have been out of the loop, could all document URLs be listed on the IRC please
16:37:37 <ericP> matthiassamwald: during the next few days
16:37:52 <Zakim> -M_Scott_Marshall.aa
16:37:54 <Zakim> -M_Scott_Marshall
16:37:55 <Zakim> -M_Scott_Marshall.a
16:37:58 <ericP> Susie: ready for review by next Mon's BioRDF call?
16:38:09 <ericP> matthiassamwald: reviewable now
16:38:57 <ericP> ericP: would like them reviewed and published simultaneously
16:39:07 <ericP> Susie: do you need a pub req?
16:39:31 <ericP> ACTION: ericP to send 1st WD transition req to webreq
16:39:42 <ericP> Topic DSE Note
16:40:03 <ericP> Susie: haven't read the DSE note yet
16:40:18 <BillBug> Can a drug be efficacious but not safe?
16:40:26 <ericP> ... got write-lock from EricN on Fri
16:40:40 <ericP> ... alanr, did you want write lock?
16:40:49 <ericP> alanr: yes, but not today
16:41:06 <ericP> Susie: is there a word version?
16:41:44 <ericP> alanr: Rachel had one, but don't know the normative one
16:41:52 <mscottm> Here's one that I know of: http://www.w3.org/2001/sw/hcls/Note_DSE_20071108.html
16:43:12 <Zakim> -??P20
16:44:42 <ericP> ... this is working in GoogleDocs
16:44:46 <ericP> Susie: works for me
16:46:42 <alanr> Your document is publicly viewable at: http://docs.google.com/Doc?id=dthvctw_5fwwwprc3 
16:46:47 <ericP> -> http://docs.google.com/Doc?id=dthvctw_5fwwwprc3 DSE Note, editor's draft
16:47:51 <ericP> Susie: were Rachel's edits obvious to you?
16:48:42 <ericP> ACTION: alanr to ask Rachel to edit the google doc, and barring that, will integrate Rachel's comments
16:48:48 <ericP> Topic: URI Note
16:49:02 <ericP> alanr: gave the note a rest for this month
16:49:10 <ericP> ... discussing issues informally
16:49:17 <ericP> ... will take up editing 1 Feb
16:50:04 <ericP> Topic: Demo (Alan and Kavitha and Holger)
16:50:17 <ericP> holger: not much update due to xmass
16:50:53 <ericP> ... would like to demo Semantic Web Search Engine and Semantic Web Pipes
16:51:00 <ericP> ... matthiassamwald has been working on these
16:51:20 <ericP> matthiassamwald: new release in the next two weeks
16:51:44 <ericP> holger: will jump back into demo work tomorrow
16:51:53 <ericP> ... expect proper update next week
16:52:02 <ericP> Susie: proposal submission deadline?
16:52:35 <ericP> alanr: due 11Jan
16:52:37 <alanr> http://www.eswc2008.org/calldemos.html
16:53:07 <ericP> Susie: you were going to pull out some old abstracts (Society for Neuroscience) and re'use
16:53:17 <ericP> holger: are they publicly available?
16:53:35 <BillBug> Matthias had the ISMB abstract from last summer, I believe
16:54:09 <matthiassamwald> Holger, here is the link to the ISMB poster: http://neuroscientific.net/res/ismb2007/poster.svg
16:54:26 <ericP> ACTION: Don to send the abstract to alanr and matthiassamwald
16:55:39 <ericP> Topic: Misc
16:55:43 <BillBug> Alan - there is also the PPT for the biocurator presentation we gave - which has at least a few slides that are probably relevant.  I believe you have a copy of this, though it is available here on line - http://genome-www.stanford.edu/biocurator/IBCM2007/abshtml/abstract-table.html
16:55:58 <ericP> Susie: Scott will be presenting at infotech forum in March
16:56:11 <alanr> bye
16:56:18 <alanr> take care...
16:56:21 <Zakim> -BillBug
16:56:23 <Zakim> -Don_Doherty
16:56:24 <Zakim> -Alan
16:56:24 <Zakim> -Susie
16:56:26 <Zakim> -Kei_Cheung
16:56:30 <BillBug> bye
16:56:36 <Zakim> -??P16
17:03:18 <Zakim> - +049681aaaa
17:03:51 <holger> holger has left #BioRDF
17:37:50 <Zakim> SW_HCLS(BioRDF)11:00AM has ended
17:37:51 <Zakim> Attendees were Susie, EricP, M_Scott_Marshall, Alan, Don_Doherty, Kei_Cheung, BillBug, +049681aaaa, Scott_Marshall
18:19:49 <alanr> rrsagent, please draft minutes
18:19:49 <RRSAgent> I have made the request to generate http://www.w3.org/2008/01/07-BioRDF-minutes.html alanr
18:20:09 <alanr> rrsagent, please make log world-readable