14:59:49 <RRSAgent> RRSAgent has joined #hcls
14:59:49 <RRSAgent> logging to http://www.w3.org/2010/06/09-hcls-irc
15:00:01 <mscottm> Zakim, this is lodd
15:00:01 <Zakim> ok, mscottm; that matches SW_HCLS(LODD)11:00AM
15:00:10 <Zakim> +[IPcaller]
15:00:27 <mscottm> Zakim, who is here?
15:00:27 <Zakim> On the phone I see +1.412.623.aaaa, mscottm, [IPcaller]
15:00:31 <Zakim> On IRC I see RRSAgent, janos, mscottm, egonw, matthias_samwald, Zakim, trackbot, ericP
15:01:00 <ericP> Zakim, please dial ericP-office
15:01:01 <Zakim> ok, ericP; the call is being made
15:01:01 <Zakim> +EricP
15:01:29 <mscottm> Zakim, +1.412.623.aaaa is Richard_Boyce
15:01:29 <Zakim> +Richard_Boyce; got it
15:01:31 <janos> janos has joined #HCLS
15:01:39 <mscottm> Zakim, who is here?
15:01:39 <Zakim> On the phone I see Richard_Boyce, mscottm, [IPcaller], EricP
15:01:44 <Zakim> On IRC I see janos, RRSAgent, mscottm, egonw, matthias_samwald, Zakim, trackbot, ericP
15:01:44 <egonw> lovely... french number does not pick up the conf code :(
15:01:45 <rboyce> rboyce has joined #HCLS
15:01:54 <rboyce> hi
15:02:02 <matthias_samwald> zakim, [IPcaller] is matthias_samwald
15:02:03 <mscottm> Zakim, [IPcaller] is matthias_samwald
15:02:06 <Zakim> +matthias_samwald; got it
15:02:10 <Zakim> sorry, mscottm, I do not recognize a party named '[IPcaller]'
15:02:22 <Zakim> +janos
15:02:33 <mscottm> Zakim, who is here?
15:02:33 <Zakim> On the phone I see Richard_Boyce, mscottm, matthias_samwald, EricP, janos
15:02:35 <Zakim> On IRC I see rboyce, janos, RRSAgent, mscottm, egonw, matthias_samwald, Zakim, trackbot, ericP
15:02:45 <egonw> grmph...
15:02:48 <mscottm> Zakim, Richard_Boyce is rboyce
15:02:48 <Zakim> +rboyce; got it
15:02:57 <egonw> calling in with skype is not working... :(
15:03:04 <egonw> it does not pick up the conference code
15:03:29 <ericP> not an unusual problem
15:03:52 <ericP> the dtmf coming from skype's dialout is borderline
15:04:03 <egonw> I have used it so far without problems
15:04:16 <egonw> ericP: ok, will try again
15:04:40 <Zakim> +??P17
15:05:01 <mscottm> Zakim, who is here?
15:05:01 <Zakim> On the phone I see rboyce, mscottm, matthias_samwald, EricP, janos, ??P17
15:05:01 <Zakim> On IRC I see rboyce, janos, RRSAgent, mscottm, egonw, matthias_samwald, Zakim, trackbot, ericP
15:05:04 <Zakim> +??P18
15:05:50 <egonw> Zakim: help
15:06:00 <mscottm> Zakim, +??P17 is bin_chen
15:06:00 <Zakim> sorry, mscottm, I do not recognize a party named '+??P17'
15:06:04 <mscottm> Zakim, ??P17 is bin_chen
15:06:04 <Zakim> +bin_chen; got it
15:06:10 <egonw> Zakim: ??P18 is egonw
15:06:19 <egonw> Zakim, ??P18 is egonw
15:06:21 <Zakim> +egonw; got it
15:06:24 <egonw> cool :)
15:07:29 <egonw> student of David Wild
15:07:34 <egonw> working in chem2bio2rdf
15:08:16 <egonw> I could scribe here too
15:08:32 <rboyce> rboyce has joined #HCLS
15:08:40 <mscottm> scribenick: egonw
15:08:49 <egonw> ok :)
15:08:55 <egonw> egonw will cover on IRC
15:09:10 <egonw> agenda 1. ontology alignment initiative
15:09:39 <egonw> Francois Scharffe joined us earlier about OAEI
15:09:50 <mscottm> http://oaei.ontologymatching.org/
15:09:59 <egonw> also see these minutes: http://www.w3.org/2010/05/26-hcls-minutes.html (I think)
15:10:10 <Bin> Bin has joined #HCLS
15:10:24 <egonw> they are considering LODD data for next years challenge
15:10:40 <egonw> not just aligning classes, but also on instance similarity
15:10:48 <egonw> so looking for many instances
15:11:32 <egonw> possible outcome: we get better aligned and cleaned up data
15:11:41 <egonw> Scott asked Egon about thoughts
15:11:44 <egonw> (indeed :)
15:13:00 <mscottm> egon: would like to use InChi identifiers for the linking
15:13:16 <mscottm> scott: notes from last time: http://www.w3.org/2010/05/26-hcls-minutes.html
15:15:44 <mscottm> egon: compare based on similarity in addition to identifiers
15:16:18 <egonw> SCOP
15:16:21 <mscottm> ..can use BLAST to compare protein sequences
15:16:30 <egonw> http://scop.mrc-lmb.cam.ac.uk/scop/
15:17:54 <egonw> chEMBL and SIDER are both available as RDF within LODD
15:18:02 <egonw> drug activity and side effect
15:19:23 <egonw> we can further look at how SIDER is already hooked up with other LODD data sets...
15:19:53 <egonw> SIDER: http://www4.wiwiss.fu-berlin.de/sider/snorql/
15:20:10 <egonw> chEMBL: http://rdf.farmbio.uu.se/chembl/snorql/
15:22:18 <mscottm> janos: DrugBank also has InChi
15:22:49 <mscottm> egon: Prefer to use InChi number to InChi key
15:22:49 <egonw> InChI preferred over InChIKey
15:23:16 <egonw> DrugBank: http://www4.wiwiss.fu-berlin.de/drugbank/snorql/
15:23:51 <egonw> at this moment I do not see InChI in SIDER yet
15:26:07 <egonw> so, we are to define a data set for the challenge where the people will work on...
15:26:18 <egonw> instead of use + Francois actually competing in the challenge...
15:26:26 <egonw> mscottm: sorry, that I misunderstood that
15:26:39 <egonw> so, that would imply that we could not do such linking ourself...
15:29:15 <egonw> we'll follow up on this next time
15:29:36 <egonw> we need confirmation that Francois is participating, rather than organizing
15:30:01 <egonw> janos is working on a LOD database of ... what? (did not get it exactly)
15:30:12 <janos> http://link.informatics.sunysb.edu/sparql/
15:30:53 <egonw> using CAS registry number to link to, e.g. DrugBank
15:30:58 <mscottm> janos: linking RxNorm to DrugBank
15:31:05 <egonw> mscottm: thanx
15:31:34 <egonw> janos: has access to the latest version
15:31:43 <egonw> disease info recently added
15:32:08 <egonw> different licenses for different parts
15:32:10 <egonw> level 0:
15:32:18 <egonw> public domain, can republish
15:33:10 <egonw> egonw asks about CC0 waiver... might be possible...
15:33:17 <egonw> janos will look at it for the RDF translation
15:35:18 <Zakim> -rboyce
15:36:06 <janos>  http://link.informatics.stonybrook.edu/rxnorm/RXCUI/88249
15:36:09 <Zakim> +rboyce
15:36:17 <egonw> much data is openly available
15:36:34 <egonw> but egonw likes to know what that means, but that is (as usual) not completely clear
15:36:47 <egonw> janos: no worries about that... common situation :)
15:37:03 <egonw> mscottm: asked about the content
15:37:38 <egonw> janos was looking at linking to DailyMed but could not find a common identifier
15:38:13 <egonw> there seems to be ID in the source data to do this
15:39:21 <mscottm> mscottm: might want to check with Anja to see if she has a script handy: Anja Jentzsch <anja@anjeve.de>
15:40:41 <egonw> discussion ongoing on active compound vs medication
15:41:40 <mscottm> Zakim, who is speaking?
15:41:41 <egonw> talk about using generic names as linking...
15:41:50 <Zakim> mscottm, listening for 10 seconds I heard sound from the following: rboyce (19%), janos (20%), egonw (14%)
15:42:03 <egonw> that was richard
15:42:06 <egonw> == rboyce?
15:42:11 <mscottm> yes
15:42:11 <rboyce> rdb20@pitt.edu
15:42:31 <egonw> http://link.informatics.stonybrook.edu/rxnorm/RXAUI/687117
15:43:14 <egonw> http://link.informatics.stonybrook.edu/rxnorm/ATN#SRC	J Pharm Biomed Anal 1995 Feb;13(2):155-8
15:43:52 <egonw> egonw asks about using citation information to link LODD data sets
15:44:15 <egonw> suggestion to use PubMed ...
15:44:32 <egonw> for linking LODD to literature
15:44:43 <egonw> many databases have references to literature
15:44:50 <egonw> chEMBL does, so does rxNORM
15:44:57 <egonw> what about curation...
15:46:59 <egonw> talk about boosting confidence of data...
15:47:26 <egonw> also, data from various LODD sources from 1 paper with same generic link, might complement each other
15:48:40 <rboyce> http://sourceforge.net/projects/loddproject/forums/forum/910130/topic/3719723
15:49:46 <egonw> rboyce invites people to comment on that question
15:52:33 <egonw> rboyce: http://www.linkedin.com/in/boycer <- that's you?
15:52:50 <egonw> mscottm: refers rboyce to anja who is not here today
15:53:28 <rboyce> yes
15:53:38 <rboyce> out of date
15:54:06 <egonw> :)
15:54:10 <egonw> next item on agenda:
15:54:14 <egonw> new data sources?
15:55:17 <egonw> what are best practicaes for sources for us to report our LODD data sets?
15:55:35 <rboyce> http://ihi2010.sighi.org/
15:55:42 <egonw> mscottm: asks if there are data updates?
15:55:58 <egonw> rboyce: mentiones the sighi link for a recent ACM conf paper on their work
15:56:34 <egonw> that's an abstract; acceptence reported in August
15:57:27 <rboyce> scott - can I cc you in an email to anja? what is your address?
15:57:39 <mscottm> mscottmarshall@gmail.com
15:57:49 <egonw> egonw mentions CC0 data source for malaria research recently released...
15:58:02 <egonw> see: http://blog.rguha.net/?p=591
15:58:16 <egonw> "GSK released an approximately 13,000 member compound library (using the CC0 license) that had been tested for activity against P. falciparum."
15:58:31 <egonw> mscottm: moving to the outreach agenda item
16:00:08 <egonw> http://chem-bla-ics.blogspot.com/2010/05/three-acs-rdf-sessions.html
16:00:19 <egonw> there is talk about a special issue for that meeting
16:00:22 <Zakim> -bin_chen
16:00:29 <egonw> LODD has a talk at that meeting
16:00:56 <janos> This is should be correct link for the Sparql endpoint http://link.informatics.stonybrook.edu/sparql/
16:01:18 <egonw> janos: have you seen SNORQL?
16:02:04 <mscottm> http://ws.adaptivedisclosure.org/search/
16:02:09 <egonw> snorql is a web frontend to sparql end points
16:02:25 <egonw> some of the links today were snorql... easier to use than the Virtuoso SPARQL end point
16:02:29 <mscottm> http://hcls.deri.org/sparql
16:03:38 <egonw> mscottm: shows AIDA, but it does not seem to work with the data from janos
16:04:09 <mscottm> janos: mentions RelFinder
16:04:28 <Zakim> -rboyce
16:04:29 <Zakim> -janos
16:04:31 <Zakim> -EricP
16:04:34 <Zakim> -mscottm
16:04:36 <Zakim> -egonw
16:04:44 <egonw> mscottm: closed meeting, thanx all
16:04:49 <mscottm>   RRSAgent, please draft minutes
16:04:49 <RRSAgent> I have made the request to generate http://www.w3.org/2010/06/09-hcls-minutes.html mscottm
16:04:57 <mscottm>   RRSAgent, please make log world-visible
16:05:36 <Zakim> -matthias_samwald
16:05:37 <Zakim> SW_HCLS(LODD)11:00AM has ended
16:05:38 <Zakim> Attendees were mscottm, EricP, matthias_samwald, janos, rboyce, bin_chen, egonw
16:05:43 <egonw> neat :)
16:05:56 <egonw> that saves me some work..
16:06:06 <egonw> I always find it hard to take notes of conf calls...
16:06:23 <egonw> good, /me is off for dinner now