IRC log of hcls on 2008-03-11

Timestamps are in UTC.

14:59:36 [RRSAgent]

RRSAgent has joined #hcls

14:59:36 [RRSAgent]

logging to http://www.w3.org/2008/03/11-hcls-irc

14:59:45 [ericP]

Zakim, this is COI

14:59:45 [Zakim]

sorry, ericP, I do not see a conference named 'COI' in progress or scheduled at this time

14:59:48 [ericP]

Zakim, this is HCLS

14:59:48 [Zakim]

ok, ericP; that matches SW_HCLS(Bio-Ont WG)11:00AM

14:59:57 [ericP]

Zakim, dial ericP-office

14:59:58 [Zakim]

ok, ericP; the call is being made

14:59:59 [Zakim]

+EricP

15:00:06 [ericP]

Zakim, who is here?

15:00:11 [Zakim]

On the phone I see +1.519.488.aaaa, EricP

15:00:19 [Zakim]

On IRC I see RRSAgent, Zakim, holger_stenzhor1, ericP

15:01:13 [ericP]

Zakim, 1.519.488.aaaa is ChristienCocos

15:01:13 [Zakim]

sorry, ericP, I do not recognize a party named '1.519.488.aaaa'

15:01:31 [ericP]

Zakim, who is here?

15:01:31 [Zakim]

On the phone I see +1.519.488.aaaa, EricP

15:01:31 [Zakim]

On IRC I see RRSAgent, Zakim, holger_stenzhor1, ericP

15:01:40 [ericP]

Zakim, +1.519.488.aaaa is ChristienCocos

15:01:40 [Zakim]

+ChristienCocos; got it

15:01:52 [Zakim]

+Jennifer

15:02:28 [Zakim]

+Rachel

15:03:08 [Zakim]

+Kerstin_Forsberg

15:03:36 [ericP]

holger_stenzhor1, are you dialing in?

15:03:45 [holger_stenzhor1]

yes

15:04:00 [Zakim]

+[IPcaller]

15:04:04 [Zakim]

+Bo

15:04:07 [Zakim]

+Jyoti

15:04:21 [ericP]

Zakim, [IPcaller] is holger_stenzhor1

15:04:21 [Zakim]

+holger_stenzhor1; got it

15:04:23 [holger_stenzhor1]

Zakim, +[IPcaller] is holger_stenzhorn

15:04:23 [Zakim]

sorry, holger_stenzhor1, I do not recognize a party named '+[IPcaller]'

15:04:33 [ericP]

Zakim, IPcaller is holger_stenzhor1

15:04:33 [Zakim]

sorry, ericP, I do not recognize a party named 'IPcaller'

15:04:42 [Jyoti]

Jyoti has joined #hcls

15:04:53 [Helen]

Helen has joined #hcls

15:05:33 [ericP]

Zakim, who is here?

15:05:33 [Zakim]

On the phone I see ChristienCocos, EricP, Jennifer, Rachel, Kerstin_Forsberg, holger_stenzhor1, Bo, Jyoti

15:05:35 [Zakim]

On IRC I see Helen, Jyoti, RRSAgent, Zakim, holger_stenzhor1, ericP

15:06:05 [holger_stenzhor1]

slides at: www.ifomis.org/acgt/coi-presentation

15:06:16 [ericP]

Zakim, please mute Jyoti

15:06:16 [Zakim]

Jyoti should now be muted

15:06:18 [Zakim]

+Helen_Chen

15:06:20 [holger_stenzhor1]

sorry -

15:06:22 [ericP]

Zakim, please unmute Jyoti

15:06:22 [Zakim]

Jyoti should no longer be muted

15:06:25 [holger_stenzhor1]

www.ifomis.org/acgt/coi-presentation.ppt

15:06:27 [ericP]

Zakim, please mute Bo

15:06:27 [Zakim]

Bo should now be muted

15:06:32 [ericP]

Zakim, please unmute Bo

15:06:32 [Zakim]

Bo should no longer be muted

15:07:56 [ericP]

ericP has changed the topic to: http://www.w3.org/mid/DBA3C02EAD0DC14BBB667C345EE2D12401E2B3CE@PHSXMB20.partners.org

15:08:01 [ericP]

http://www.w3.org/mid/DBA3C02EAD0DC14BBB667C345EE2D12401E2B3CE@PHSXMB20.partners.org

15:08:59 [ericP]

Zakim, pick a victim

15:08:59 [Zakim]

Not knowing who is chairing or who scribed recently, I propose Jyoti

15:09:00 [Jyoti]

Jyoti has left #hcls

15:09:08 [Jyoti]

Jyoti has joined #hcls

15:09:23 [Jyoti]

Hi

15:09:31 [ericP]

chair: ericP

15:09:34 [ericP]

meeting COI

15:09:40 [ericP]

meeting: COI

15:09:47 [ericP]

scribe: Jyoti

15:09:54 [ericP]

topic: ACGT ontology representation of Diabetes Patient Data

15:10:19 [ericP]

http://www.ifomis.org/acgt/coi-presentation

15:10:32 [Jyoti]

Holger: I spoke with Chris this morning and will be presenting the slides

15:10:36 [ericP]

=> http://www.ifomis.org/acgt/coi-presentation.ppt slides

15:12:08 [Jyoti]

Cris: I will give the presentation. ACGT means advanced clinical genomic trails.

15:12:40 [ericP]

Zakim, ChristienCocos is really CristianCocos

15:12:40 [Zakim]

+CristianCocos; got it

15:15:27 [Jyoti]

ACGT is an OWL-DL ontology. Formally defined relations and other restrictions.

15:16:41 [Jyoti]

ACGT leverages BFO (Basic Formal Ontology) as the top-level ontology

15:19:44 [ericP]

Chris: adding an OWL anatomy ontology

15:20:05 [Jyoti]

As of Oct 2007, there were a total of 1109 classes (primitive: 1028, defined: 81)

15:20:24 [Jyoti]

Cris: there were a total of 121 restrictions

15:25:23 [ericP]

Cris: constraints extension includes identifying disjoint classes

15:25:28 [Jyoti]

Cris: important upcoming work is to start adding FMA (anatomy) classes

15:27:08 [ericP]

Helen: will you be able to do classifications with your reasoner after adding FMA?

15:27:54 [ericP]

Cris: old slides; we have given up on this because FMA doesn't lend itself well to OWL

15:28:02 [ericP]

Helen: try Galen

15:28:21 [ericP]

Cris: Alan Rector suggested we set our sights on something more modest

15:28:33 [Jyoti]

Cris: we spoke with Alan Rector and he suggested something less complex

15:34:19 [Jyoti]

Cris: "Patient" is a role in ACGT and Jennifer agrees with that characterization

15:38:17 [Jyoti]

ericP: difference between a role and a object?

15:38:45 [Jyoti]

Cris: role is a dependent continuant and object is an independent continuant.

15:39:36 [Jyoti]

Cris: dependent continuant depends on something else for its own existence. E.g., quality of an "item" depends on the "item" for its own existence.

15:40:10 [Jyoti]

Cris: role is a dependent continuant because certain entities can play different roles, and so it can attach to independent continuant at different times

15:47:15 [Zakim]

-CristianCocos

15:47:53 [ericP]

[slide 26]

15:49:07 [Jyoti]

Holger: ACGT contains concepts for clinical trials and genomic research

15:52:12 [Jyoti]

Holger: concepts/relationships encoded in the ontology are represented in Trial of Principle (TOP Trial) forms

15:55:19 [ericP]

Topic: Discussion on Logistics for loading and using Patient Data

15:55:22 [Jyoti]

ericP: we will discuss the last agenda item

15:55:56 [Jyoti]

ericP: we will NOT discuss the last agenda item :-)

15:56:12 [ericP]

Topic: Mappings if any between ACGT ontology and CDISC/HL7

15:57:00 [ericP]

holger_stenzhor1: was hoping Christian could address this

15:57:02 [Jyoti]

Holger: Cris will probably be able to explain the mapping issue much better. ACGT does not directly encode the mappings directly.

15:57:24 [Jyoti]

Holger: ACGT partners (from Greece?) will be addressing the mapping issue

15:58:20 [ericP]

Action: Holger to invite Chris to discuss Mappings if any between ACGT ontology and CDISC/HL7 or to provide a narrative himself

15:58:58 [Jyoti]

Helen: is ACGT.owl is the latest file?

15:59:03 [holger_stenzhor1]

www.ifomis.org/acgt/1.0

15:59:04 [Jyoti]

Holger: yup its latest

15:59:23 [ericP]

=> http://www.ifomis.org/acgt/1.0 ACGT ontology

16:01:04 [ericP]

Topic: overall mapping plan

16:07:15 [Jyoti]

Helen: we should think how the inclusion/exclusion criteria is not buried under the SPARQL query

16:07:31 [Jyoti]

Helen: these criteria are part of the trials protocol itself

16:08:09 [Jyoti]

ericP: not sure if there are other ways of encoding the inclusion/exclusion apart from it being a part of the query

16:09:20 [Zakim]

-Kerstin_Forsberg

16:09:45 [ericP]

RRSAgent, please draft minutes

16:09:45 [RRSAgent]

I have made the request to generate http://www.w3.org/2008/03/11-hcls-minutes.html ericP

16:09:48 [Zakim]

-Jennifer

16:09:52 [Zakim]

-Bo

16:09:56 [Zakim]

-holger_stenzhor1

16:10:02 [Jyoti]

Jyoti has left #hcls

16:10:06 [Zakim]

-Jyoti

16:18:26 [Zakim]

-Rachel

16:19:33 [Zakim]

-EricP

16:19:35 [Zakim]

-Helen_Chen

16:19:35 [Zakim]

SW_HCLS(Bio-Ont WG)11:00AM has ended

16:19:36 [Zakim]

Attendees were EricP, Jennifer, Rachel, Kerstin_Forsberg, Bo, Jyoti, holger_stenzhor1, Helen_Chen, CristianCocos

16:32:43 [holger_stenzhorn]

holger_stenzhorn has joined #hcls

16:34:20 [holger_stenzhor1]

holger_stenzhor1 has joined #hcls

17:31:06 [Zakim]

Zakim has left #hcls

18:24:00 [ericP]

RRSAgent, please draft minutes

18:24:00 [RRSAgent]

I have made the request to generate http://www.w3.org/2008/03/11-hcls-minutes.html ericP

18:24:08 [ericP]

RRSAgent, please make log world-visible