IRC log of hcls on 2010-12-02
Timestamps are in UTC.
- 15:55:37 [RRSAgent]
- RRSAgent has joined #hcls
- 15:55:37 [RRSAgent]
- logging to http://www.w3.org/2010/12/02-hcls-irc
- 16:04:15 [Susie]
- Susie has joined #hcls
- 16:05:14 [Joanne]
- Joanne has joined #hcls
- 16:05:33 [Joanne]
- I couldn't get on the mbit client
- 16:07:29 [mscottm]
- Zakim, pick a victim
- 16:07:29 [Zakim]
- sorry, mscottm, I don't know what conference this is
- 16:07:35 [mscottm]
- zakim, this is hcls
- 16:07:35 [Zakim]
- ok, mscottm; that matches SW_HCLS()11:00AM
- 16:07:36 [mscottm]
- Zakim, pick a victim
- 16:07:36 [Zakim]
- Not knowing who is chairing or who scribed recently, I propose +1.610.651.aacc
- 16:07:48 [ericP]
- Zakim, please dial ericP-office
- 16:07:48 [Zakim]
- ok, ericP; the call is being made
- 16:07:50 [Zakim]
- +EricP
- 16:08:26 [ericP]
- Zakim, who is here?
- 16:08:26 [Zakim]
- On the phone I see +1.860.440.aabb, mscottm, +1.610.651.aacc, epichler, +1.518.276.aadd, ??P7, EricP
- 16:08:31 [Zakim]
- On IRC I see Joanne, Susie, RRSAgent, Zakim, mscottm, ericP
- 16:08:40 [Zakim]
- +Bob_Powers
- 16:08:48 [Susie]
- Scott gives update on BioRDF
- 16:08:50 [Joanne]
- I'm 518
- 16:09:02 [Zakim]
- + +1.617.947.aaee
- 16:09:16 [ericP]
- Zakim, please mute +1.617.947.aaee
- 16:09:16 [Zakim]
- +1.617.947.aaee should now be muted
- 16:09:41 [Susie]
- Presentation from Adrian Coulet
- 16:09:56 [Susie]
- Did work on text mining using PharmGKB
- 16:10:01 [Bob]
- Bob has joined #hcls
- 16:10:08 [michel]
- michel has joined #HCLS
- 16:10:12 [Susie]
- And created an ontology from that data
- 16:10:32 [Susie]
- Also presentation from Dietrich RS on SESL
- 16:10:45 [Zakim]
- - +1.617.947.aaee
- 16:10:47 [Susie]
- It has many ties to what we are doing
- 16:11:07 [Zakim]
- + +1.617.947.aaff
- 16:11:37 [Susie]
- Using microarrays in both projects
- 16:11:53 [Susie]
- We've been looking at federation with SPARQL
- 16:12:06 [Susie]
- Will give tutorial on this topic at SWAT4LS next week
- 16:12:06 [ericP]
- Zakim, please mute +1.617.947.aaff
- 16:12:06 [Zakim]
- +1.617.947.aaff should now be muted
- 16:12:19 [Susie]
- EricP will dial in remotely for this
- 16:12:21 [michel1]
- michel1 has joined #HCLS
- 16:12:57 [Susie]
- Will use Uniprot and GO annotations from UCSC
- 16:13:30 [Susie]
- Similar to what we started to do with the microarray data
- 16:14:11 [Susie]
- Continue to work on type of RDF to represent microarray data
- 16:14:32 [Susie]
- Will work with scientific discourse and array express
- 16:15:06 [ericP]
- Zakim, unmute +1.617.947.aaff
- 16:15:06 [Zakim]
- +1.617.947.aaff should no longer be muted
- 16:15:20 [Susie]
- Tim talks about scientific discourse
- 16:16:02 [Susie]
- one thread align swan, obi and myexperiment with microarray representation
- 16:16:09 [Susie]
- using mged and obi for that
- 16:16:41 [Susie]
- set up relationship with Susanna Santone at University of Oxford, and Philippe
- 16:17:01 [Susie]
- being done with swan, myexperiment and obi
- 16:17:25 [Susie]
- will be able to represent experiments using genetic epidemiology or population studies
- 16:17:48 [Susie]
- Have the data in private db and then release publicly when ready
- 16:17:52 [mscottm]
- ISATAB - ISATools, ISACreator, etc.
- 16:18:11 [Susie]
- columns are aligned to identifiers in ontologies
- 16:18:23 [Susie]
- excel workbook with tabs for entities
- 16:18:38 [mscottm]
- http://www.slideshare.net/proccaserra/hcls-sci-discisa2rdf
- 16:19:24 [Susie]
- also working on rhetorical document structure which is lead by Anita de Waard
- 16:19:34 [Susie]
- Has sub-comments, 1 is orb
- 16:19:54 [Susie]
- Tudor Groza is working on an HCLS note on that topic
- 16:20:10 [Susie]
- Also a mid-grain ontology in a draft form, which was proposed by Elsevier
- 16:20:22 [Susie]
- Fine grained ontology by David Shotton and others
- 16:20:41 [Susie]
- Moving towards supporting the text mining community
- 16:21:11 [Bob]
- Tim: supporting the text-mining community is a good way to advance linked data
- 16:23:32 [Susie]
- Ontologies are beginning to form a nice dense web of models
- 16:25:00 [Susie]
- Scott talks about terminology
- 16:25:11 [Susie]
- Progress on mamagram use case
- 16:25:47 [Susie]
- Talk about ways to prototype ideas relating to discrepancies between reports
- 16:26:05 [Susie]
- John Madden has reports in XML that he's seeing if we can start with
- 16:26:32 [Susie]
- Aiming to put in an NIH grant, but will need to have finished prototyping in order to write it up
- 16:26:47 [Susie]
- Eric gives update on COI
- 16:27:24 [Susie]
- NCI work on adding semantics to web services is happening in COI wiki space
- 16:27:40 [Susie]
- Hasn't started his contract there yet
- 16:28:07 [Susie]
- NCBO seminar yesterday that referenced this work
- 16:29:01 [Susie]
- Susie update on LODD
- 16:29:05 [Bob]
- "Google it up" is now a verb.
- 16:29:11 [mscottm]
- scribenick: mscottm
- 16:29:17 [ericP]
- -> http://www.bioontology.org/webinar-series NCBO webinar list
- 16:29:30 [mscottm]
- Susie: We're working to finish the paper for J. of Cheminformatics
- 16:29:48 [mscottm]
- ..will refer to recent RDF data, and the Allen Brain Atlas work.
- 16:30:13 [mscottm]
- ..Still interested in writing a Best Practices document. We'll move to that as soon as the paper is done.
- 16:30:18 [ericP]
- -> http://www.bioontology.org/sites/default/files/NCBO_Webinar_20101201_caBIG_DavidHau.pdf slides for Dav Hau's NCI webinar at NCBO
- 16:30:47 [mscottm]
- ..We will also consider the role of LODD. One role: LODD could be a useful place for people to publish their data.
- 16:31:02 [Joanne]
- thanks Eric (you're faster than I am - I was just back to the window to paste!)
- 16:31:07 [mscottm]
- ..With time, I think that there should be more effective search mechanisms but this is a good start.
- 16:31:45 [mscottm]
- ..With my role in PRISM, we are interested in creating a document about our data needs for distribution to NCI, NCBI, and Pistoia.
- 16:32:10 [mscottm]
- ..Interested in working with other organizations to create quality standards for linked data.
- 16:32:33 [mscottm]
- Joanne: RPI is involved with U.S. and UK gov linked data.
- 16:33:00 [mscottm]
- Susie: PRISM is interested in creating quality standards for Pharma.
- 16:33:01 [michel]
- question: what does "high quality" mean
- 16:33:24 [mscottm]
- scott's definition: annotated with provenance
- 16:33:51 [mscottm]
- Joanne: RPI would be interested in any service of URIs and linked data.
- 16:33:52 [ericP]
- -> https://stanford.webex.com/stanford/lsr.php?AT=pb&SP=MC&rID=46376657&rKey=21d56b8b169a3a31 WEBEX recording on Dav Hau's NCI webinar at NCBO
- 16:34:17 [mscottm]
- Susie: We'll keep you posted on our progress.
- 16:34:59 [Bob]
- Susie: Quality = make sure data are linked together so makes sense
- 16:35:58 [Bob]
- ...quality also means a service level of availability
- 16:36:00 [mscottm]
- Susie: Make sure that there are links between things that are supposed to be the same.
- 16:36:25 [mscottm]
- scribenick: Susie
- 16:36:31 [Susie]
- Michel updates on TMO
- 16:36:39 [Susie]
- Submitted paper on J. Biomedical Semantics
- 16:36:44 [Susie]
- Lead by Jim and Joanne
- 16:37:01 [Susie]
- Nice section by EricP on unit testing for ontology development
- 16:37:34 [Susie]
- Considering next areas of work
- 16:37:45 [Susie]
- Representing genetic variations is of intrest
- 16:37:58 [Susie]
- Want to represent htis information accurately
- 16:38:06 [Susie]
- Want to do more work to integrate with other ontologies
- 16:38:14 [Susie]
- Want working eHR system
- 16:38:36 [Susie]
- Should look at options that are free and available, that have web interface, support for terminology
- 16:39:09 [ericP]
- Zakim, who is making noise?
- 16:39:13 [mscottm]
- Zakim, who is making noise?
- 16:39:22 [Zakim]
- ericP, listening for 12 seconds I could not identify any sounds
- 16:39:34 [Zakim]
- mscottm, listening for 10 seconds I could not identify any sounds
- 16:39:50 [Susie]
- joanne: we still have some clean up work for the paper
- 16:40:09 [Susie]
- joanne: want to work with a hospital or ctsa center
- 16:41:06 [ericP]
- q+ to talk about i2b2
- 16:41:15 [Bob]
- Susie: Been pondering collaborating w i2b2, Kohane's lab
- 16:41:43 [michel]
- q+ to talk about openmrs
- 16:41:44 [Bob]
- ...there is ontology hive inside i2b2
- 16:41:59 [Susie]
- joanne: want to make a valuable contribution
- 16:42:59 [Bob]
- Susie: We have agreed to share our extended i2b2 platform
- 16:44:02 [Bob]
- Scott: Any EHR project in IMI?
- 16:44:29 [Susie]
- JJ& is involved in the UBIOPRED and BTCure projects, and also one in oncology
- 16:44:31 [mscottm]
- I know of EHR4CR
- 16:44:40 [ericP]
- q?
- 16:45:20 [Bob]
- Scott: OPS Open Pharmacological Space
- 16:46:46 [Bob]
- Susie: Integrating omics data for clinical trials, etc, rather than for patient records per se
- 16:46:48 [ericP]
- q!
- 16:47:23 [ericP]
- Zakim, ack
- 16:47:23 [Zakim]
- I don't understand 'ack', ericP
- 16:47:24 [ericP]
- Zakim, ack me
- 16:47:24 [Zakim]
- ericP, you wanted to talk about i2b2
- 16:47:25 [Susie]
- tranSMART
- 16:47:26 [Zakim]
- I see michel on the speaker queue
- 16:48:07 [Susie]
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914663/
- 16:48:34 [mscottm]
- Zakim, ack michel
- 16:48:34 [Zakim]
- michel, you wanted to talk about openmrs
- 16:48:35 [Zakim]
- I see no one on the speaker queue
- 16:50:13 [Bob]
- Michel: We seem to be fragmenting among various task forces
- 16:50:52 [Bob]
- Eric: Where would we develop interface code? Which source do we acquire first?
- 16:50:55 [Susie]
- Michel: could we use i2b2 as a rally point?
- 16:51:56 [Susie]
- Eric: best value is in showing we can work with both i2b2 and indivo, and that they couldn't easily work together without us
- 16:53:31 [Susie]
- Scott: if we had pathology report that fits in indivo that could enable connect to other tasks
- 16:53:42 [Susie]
- Michel: absolutely what should happen
- 16:53:59 [Susie]
- Scott: anonymized data would be ideal
- 16:54:51 [Bob]
- (Chime is at Cleveland Clinic)
- 16:55:18 [Susie]
- BioRDF could be a consumer of text mined data
- 16:55:55 [Susie]
- Scott: please share other thoughts about connection points
- 16:56:33 [Bob]
- Scott: Biobanking is a great platform, tends to get wet-lab scientists excited, for search as a first step
- 16:57:18 [Bob]
- Susie: i2b2 has interest in support for biobanking, along w. omics
- 16:57:54 [Bob]
- ...Crimson hive in i2b2 is for biobanking
- 17:00:19 [mscottm]
- David Cox (Pfizer)
- 17:00:33 [Zakim]
- - +1.518.276.aadd
- 17:00:34 [Zakim]
- - +1.610.651.aacc
- 17:00:34 [Zakim]
- -??P7
- 17:00:35 [Zakim]
- - +1.617.947.aaff
- 17:00:37 [Zakim]
- -epichler
- 17:01:10 [Zakim]
- -Bob_Powers
- 17:02:30 [Zakim]
- -EricP
- 17:02:32 [Zakim]
- -mscottm
- 17:02:39 [michel]
- michel has left #HCLS
- 17:02:40 [Zakim]
- - +1.860.440.aabb
- 17:02:42 [Zakim]
- SW_HCLS()11:00AM has ended
- 17:02:48 [Zakim]
- Attendees were +1.617.947.aaaa, +1.860.440.aabb, mscottm, +1.610.651.aacc, epichler, +1.518.276.aadd, EricP, Bob_Powers, +1.617.947.aaee, +1.617.947.aaff
- 17:02:51 [mscottm]
- RRSAgent, please draft minutes
- 17:02:51 [RRSAgent]
- I have made the request to generate http://www.w3.org/2010/12/02-hcls-minutes.html mscottm
- 17:03:04 [mscottm]
- RRSAgent, please make log world-visible
- 19:00:04 [Zakim]
- Zakim has left #hcls
- 20:15:56 [mscottm]
- mscottm has joined #hcls