IRC log of HCLS on 2012-02-14

Timestamps are in UTC.

15:55:42 [RRSAgent]
RRSAgent has joined #HCLS
15:55:42 [RRSAgent]
logging to
15:56:18 [michel]
Meeting: W3C HCLS – Life Sciences Forum
15:56:21 [ericP]
Zakim, this will be hcls
15:56:21 [Zakim]
ok, ericP; I see SW_HCLS()11:00AM scheduled to start in 4 minutes
15:56:23 [michel]
Chair: michel
15:56:33 [Zakim]
SW_HCLS()11:00AM has now started
15:56:34 [michel]
zakim, this is hcls
15:56:34 [Zakim]
michel, this was already SW_HCLS()11:00AM
15:56:35 [Zakim]
15:56:35 [Zakim]
ok, michel; that matches SW_HCLS()11:00AM
15:57:36 [Zakim]
15:57:46 [michel]
zakim, [IPcaller] is michel
15:57:46 [Zakim]
+michel; got it
16:00:32 [amrapali]
amrapali has joined #hcls
16:00:37 [jun]
jun has joined #hcls
16:01:38 [Zakim]
+ +1.510.541.aaaa
16:01:45 [Helena]
Helena has joined #hcls
16:01:53 [Zakim]
+ +1.832.386.aabb
16:02:16 [Zakim]
16:02:26 [Zakim]
16:02:33 [JP]
JP has joined #HCLS
16:02:44 [Zakim]
+ +1.215.239.aacc
16:02:51 [iker]
iker has joined #hcls
16:03:03 [ericP]
Zakim, aacc is iker
16:03:03 [Zakim]
+iker; got it
16:03:04 [michel]
zakim, +1.215.239.aacc is iker
16:03:05 [Zakim]
sorry, michel, I do not recognize a party named '+1.215.239.aacc'
16:03:15 [Zakim]
16:03:24 [jun]
zakim, [IPcaller] is jun
16:03:24 [Zakim]
+jun; got it
16:03:34 [ericP]
Zakim, who is here?
16:03:34 [Zakim]
On the phone I see EricP, michel, +1.510.541.aaaa, +1.832.386.aabb, Joseph_Scheuhammer, ScottB, iker, jun
16:03:36 [mscottm2]
mscottm2 has joined #hcls
16:03:37 [Zakim]
On IRC I see iker, JP, Helena, jun, amrapali, RRSAgent, Zakim, michel, MacTed, egonw_, ericP
16:03:38 [epichler]
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16:03:50 [Helena]
zakim, +1.832.386.aabb is me
16:03:50 [Zakim]
+Helena; got it
16:04:34 [matthias_samwald]
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16:05:22 [Zakim]
16:05:35 [matthias_samwald]
zakim, [IPcaller] is matthias_samwald
16:05:35 [Zakim]
+matthias_samwald; got it
16:05:38 [Helena]
16:05:51 [mscottm2]
Have been trying to dialin but keep getting "This passcode is not valid."
16:06:29 [Zakim]
+ +31.62.427.aadd
16:06:51 [mscottm2]
Zakim, +31.62.427.aadd is mscottm2
16:06:51 [Zakim]
+mscottm2; got it
16:06:53 [matthias_samwald]
"hcls" passcode worked for me
16:07:11 [matthias_samwald]
oh, you made it by now.
16:07:37 [mscottm2]
Yeah, 4x a charm. :)
16:08:39 [Zakim]
16:08:43 [Zakim]
16:08:57 [mscottm2]
16:10:02 [michel]
lena: can use provenance model on tcga dataset
16:11:04 [Zakim]
+ +1.514.864.aaee
16:13:16 [mscottm2]
Zakim, who is making noise?
16:13:32 [Zakim]
mscottm2, listening for 13 seconds I heard sound from the following: michel (65%), ericP (7%)
16:16:52 [mscottm2]
From Richard Boyce: For the SciDisc Use Case, we have created a set of web pages that show a very basic demo of one way that a drug package insert might be flagged to claims present in the other knowledge sources on the semantic web.
16:16:52 [mscottm2]
16:16:52 [mscottm2]
Each web page shows DailyMed Structured Product Label sections (posted on the new linkedSPL endpoint <>) that have been linked to 1) claims present in the linked data version of the Drug Interaction Knowledge Base ( and 2) published results from studies involving the drug's active ingredient that have been registered in (via LinkedCT). I will discuss the use case and demo at
16:17:39 [michel]
16:18:02 [michel]
16:18:19 [junz]
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16:19:05 [jun]
that link works fine for me. just tested it
16:20:29 [michel]
mscottm2: biordf group - expression rdf w3c note
16:21:32 [michel]
... gives guidelines for producing rdf on differentially expressed genes, experimental conditions
16:22:00 [michel]
... getting people around the table fged, arrayexpress, more confidence in rdf created
16:22:23 [michel]
... workshop article shows show to interconvert between representations
16:23:27 [michel]
... tutorial aspect needs to be developed in the note - R script from jim mccusker to generate the rdf; python scripts from io informatics; other tools
16:24:11 [michel]
... rdf representation + how to use it with other tools to perform analysis; take the results and do something with it
16:25:09 [Zakim]
16:25:15 [michel]
... looking at putting a SPARQL interface to synapse (API from sage bionetworks)
16:26:18 [michel]
... includes snp data, patient data
16:27:15 [michel]
matthias: seems that main access is now api, no file download
16:28:18 [michel]
mscottm2: are they interested in linked open data? further discussion required
16:28:40 [michel]
... focus on network biology
16:28:52 [michel]
... goals are close; should be possible to work together
16:29:23 [michel]
... stephen friend has raised some $16M in a years time, sage bionetworks have many partners in pharma
16:30:42 [mscottm2]
i did get a chance to talk with mike about synapse and the semantic web.
16:30:42 [mscottm2]
if i understood him right, currently he doesn't believe there really is a
16:30:42 [mscottm2]
good use case to making the data available as a sparql end point. i kind
16:30:42 [mscottm2]
of agree that HCLS hasn't made a compelling case for this yet. but, on
16:30:42 [mscottm2]
the other hand, mike is working with NCBO in developing an ontology that
16:30:43 [mscottm2]
describes and drives how synapse works, which will be published via
16:30:45 [mscottm2]
bioportal. this concept is like what i worked on with mike at teranode,
16:30:47 [mscottm2]
where our customers (who, sadly, never came to be) would describe their
16:30:49 [mscottm2]
business process (how the drug pipeline worked, who reported to who,...)
16:30:51 [mscottm2]
and that would drive the UI and what options users had.
16:31:18 [mscottm2]
16:31:23 [mscottm2]
16:32:07 [Zakim]
- +1.514.864.aaee
16:34:43 [mscottm2]
re:eric's comments - I was hoping for a database connector (as usual :) )
16:34:52 [ericP]
16:35:23 [michel]
mscottm2: lodd
16:36:02 [michel]
... paper in journal of web semantics - should be published soon
16:36:17 [michel]
... w3c note derived from this without the use cases
16:36:28 [michel]
... solicited comments, got a few
16:37:15 [michel]
... pretty close to being done
16:37:19 [michel]
... more comments welcome
16:37:45 [michel]
... next discussion will be about future work
16:37:51 [michel]
... and approval
16:37:55 [iker]
@scott, could you send the link to the note please?
16:38:20 [michel]
16:38:25 [iker]
16:39:56 [michel]
mscottm2: biohackathon 2011 got some people together to come up with a vocabulary to describe datasets (beyond void, etc)
16:40:22 [Helena]
(i think the document is ready for publication as a working draft or something of the sort )
16:42:39 [Helena]
(that would actually push us to finalize it, I think :) )
16:43:02 [iker]
16:44:19 [michel]
16:44:37 [michel]
ack iker
16:46:17 [mscottm2]
16:47:45 [Helena]
16:48:25 [Helena]
16:48:41 [Helena]
(never mind, was going to mention void, but now i saw it there in the document :) )
16:49:11 [Zakim]
16:51:25 [michel]
lena: signaling pathway leads to death; take list of proteins, go in tcga by exposing the data as rdf, snps/expression. idea is to look at what is happening in the pathway at several layers of biological info, see if the changes are localized
16:51:41 [michel]
... gene, protein, snps, epigenetics
16:52:18 [ericP]
agenda+ bio-hackathon around BOS
16:53:14 [michel]
... patterns were previously uncovered; 1st layer epigenetics, 2nd layer snps, 3rd layer gene expression
16:53:32 [michel]
... 4th layer protein expression
16:54:48 [michel]
... lots of data (terabytes?), better to target specific data
16:55:47 [Helena]
16:56:08 [iker]
IMO sounds really interesting!!
16:56:45 [iker]
@michel, do you have a couple of minutes after the call?
16:56:45 [mscottm2]
Persons who discover new tools relevant to the HCLSIG can Tweet it using the hashtag #hclstool and I will periodically aggregate tweets with that hashtag and add these tools to the HCLSIG wiki <>.
16:57:40 [michel]
ericP: biohackathon in Boston in June?
16:58:45 [Helena]
16:59:56 [jun]
Will try if I can get the visa for another meeting in June in USA
17:00:44 [iker]
@ericP could you send a link to the Biohackathon website?
17:01:48 [jun]
How about having one in Europe too?:)
17:02:12 [mscottm2]
Ideas for experts: Paul Groth -
17:02:27 [mscottm2]
Lee Harland (Pistoia, OpenPHACTS tech lead)
17:02:33 [Zakim]
- +1.510.541.aaaa
17:02:37 [Zakim]
17:02:41 [Zakim]
17:02:43 [Zakim]
17:02:43 [Zakim]
17:08:39 [mscottm2]
17:09:14 [michel]
rrsagent, draft minutes
17:09:14 [RRSAgent]
I have made the request to generate michel
17:09:20 [michel]
rrsagent, make log world-visible
17:12:47 [Zakim]
17:12:48 [Zakim]
17:12:48 [Zakim]
17:12:50 [Zakim]
SW_HCLS()11:00AM has ended
17:12:50 [Zakim]
Attendees were EricP, michel, +1.510.541.aaaa, Joseph_Scheuhammer, ScottB, +1.215.239.aacc, iker, jun, Helena, matthias_samwald, mscottm2, +1.514.864.aaee
18:32:05 [egonw]
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18:59:18 [matthias_samwald]
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20:24:03 [matthias_samwald]
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22:19:35 [matthias_samwald]
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23:34:54 [Reiner]
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