lovely... french number does not pick up the conf code :(

<rboyce> hi

grmph...

calling in with skype is not working... :(

it does not pick up the conference code

<ericP> not an unusual problem

<ericP> the dtmf coming from skype's dialout is borderline

I have used it so far without problems

ericP: ok, will try again

Zakim: help

Zakim: ??P18 is egonw

cool: )

student of David Wild

working in chem2bio2rdf

I could scribe here too

<mscottm> scribenick: egonw

ok: )

egonw will cover on IRC

agenda 1. ontology alignment initiative

Francois Scharffe joined us earlier about OAEI

<mscottm> http://oaei.ontologymatching.org/

also see these minutes: http://www.w3.org/2010/05/26-hcls-minutes.html (I think)

they are considering LODD data for next years challenge

not just aligning classes, but also on instance similarity

so looking for many instances

possible outcome: we get better aligned and cleaned up data

Scott asked Egon about thoughts

(indeed :)

<mscottm> egon: would like to use InChi identifiers for the linking

<mscottm> scott: notes from last time: http://www.w3.org/2010/05/26-hcls-minutes.html

<mscottm> egon: compare based on similarity in addition to identifiers

SCOP

<mscottm> ..can use BLAST to compare protein sequences

http://scop.mrc-lmb.cam.ac.uk/scop/

chEMBL and SIDER are both available as RDF within LODD

drug activity and side effect

we can further look at how SIDER is already hooked up with other LODD data sets...

SIDER: http://www4.wiwiss.fu-berlin.de/sider/snorql/

chEMBL: http://rdf.farmbio.uu.se/chembl/snorql/

<mscottm> janos: DrugBank also has InChi

<mscottm> egon: Prefer to use InChi number to InChi key

InChI preferred over InChIKey

DrugBank: http://www4.wiwiss.fu-berlin.de/drugbank/snorql/

at this moment I do not see InChI in SIDER yet

so, we are to define a data set for the challenge where the people will work on...

instead of use + Francois actually competing in the challenge...

mscottm: sorry, that I misunderstood that

so, that would imply that we could not do such linking ourself...

we'll follow up on this next time

we need confirmation that Francois is participating, rather than organizing

janos is working on a LOD database of ... what? (did not get it exactly)

<janos> http://link.informatics.sunysb.edu/sparql/

using CAS registry number to link to, e.g. DrugBank

<mscottm> janos: linking RxNorm to DrugBank

mscottm: thanx

janos: has access to the latest version

disease info recently added

different licenses for different parts

level 0:

public domain, can republish

egonw asks about CC0 waiver... might be possible...

janos will look at it for the RDF translation

<janos> http://link.informatics.stonybrook.edu/rxnorm/RXCUI/88249

much data is openly available

but egonw likes to know what that means, but that is (as usual) not completely clear

janos: no worries about that... common situation :)

mscottm: asked about the content

janos was looking at linking to DailyMed but could not find a common identifier

there seems to be ID in the source data to do this

<mscottm> mscottm: might want to check with Anja to see if she has a script handy: Anja Jentzsch <anja@anjeve.de>

discussion ongoing on active compound vs medication

talk about using generic names as linking...

that was richard

== rboyce?

<mscottm> yes

<rboyce> rdb20@pitt.edu

http://link.informatics.stonybrook.edu/rxnorm/RXAUI/687117

http://link.informatics.stonybrook.edu/rxnorm/ATN#SRC J Pharm Biomed Anal 1995 Feb;13(2):155-8

egonw asks about using citation information to link LODD data sets

suggestion to use PubMed ...

for linking LODD to literature

many databases have references to literature

chEMBL does, so does rxNORM

what about curation...

talk about boosting confidence of data...

also, data from various LODD sources from 1 paper with same generic link, might complement each other

<rboyce> http://sourceforge.net/projects/loddproject/forums/forum/910130/topic/3719723

rboyce invites people to comment on that question

rboyce: http://www.linkedin.com/in/boycer <- that's you?

mscottm: refers rboyce to anja who is not here today

<rboyce> yes

<rboyce> out of date

:)

next item on agenda:

<scribe> new data sources?

what are best practicaes for sources for us to report our LODD data sets?

<rboyce> http://ihi2010.sighi.org/

mscottm: asks if there are data updates?

rboyce: mentiones the sighi link for a recent ACM conf paper on their work

that's an abstract; acceptence reported in August

<rboyce> scott - can I cc you in an email to anja? what is your address?

<mscottm> mscottmarshall@gmail.com

egonw mentions CC0 data source for malaria research recently released...

see: http://blog.rguha.net/?p=591

"GSK released an approximately 13,000 member compound library (using the CC0 license) that had been tested for activity against P. falciparum."

mscottm: moving to the outreach agenda item

http://chem-bla-ics.blogspot.com/2010/05/three-acs-rdf-sessions.html

there is talk about a special issue for that meeting

LODD has a talk at that meeting

<janos> This is should be correct link for the Sparql endpoint http://link.informatics.stonybrook.edu/sparql/

janos: have you seen SNORQL?

<mscottm> http://ws.adaptivedisclosure.org/search/

snorql is a web frontend to sparql end points

some of the links today were snorql... easier to use than the Virtuoso SPARQL end point

<mscottm> http://hcls.deri.org/sparql

mscottm: shows AIDA, but it does not seem to work with the data from janos

<mscottm> janos: mentions RelFinder

mscottm: closed meeting, thanx all

This is scribe.perl Revision: 1.135  of Date: 2009/03/02 03:52:20  
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        <dbooth> Present: dbooth jonathan mary
        <dbooth> Present+ amy


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Got date from IRC log name: 09 Jun 2010
Guessing minutes URL: http://www.w3.org/2010/06/09-hcls-minutes.html
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