IRC log of BioRDF on 2007-07-16

Timestamps are in UTC.

17:10:35 [RRSAgent]
RRSAgent has joined #BioRDF
17:10:35 [RRSAgent]
logging to http://www.w3.org/2007/07/16-BioRDF-irc
17:10:52 [ericP]
Zakim, this is BioRDF
17:10:52 [Zakim]
ok, ericP; that matches SW_HCLS(BioRDF)1:00PM
17:10:57 [ericP]
Zakim, who is here?
17:10:57 [Zakim]
On the phone I see MIT346, susie, Chimezie_Ogbuji, Don_Doherty
17:10:58 [Zakim]
On IRC I see RRSAgent, Don, chimezie, Susie, ericP, Zakim
17:11:27 [Zakim]
+??P6
17:11:54 [ericP]
Zakim, ??P6 is Khalid
17:11:54 [Zakim]
+Khalid; got it
17:12:08 [Zakim]
+??P7
17:12:23 [BillBug]
BillBug has joined #biordf
17:12:32 [jar286]
jar286 has joined #BioRDF
17:12:36 [ericP]
Zakim, ??P7 is BillBug
17:12:36 [Zakim]
+BillBug; got it
17:12:58 [Don]
FYI, the phone signal from MIT is cutting in and out.
17:13:24 [Don]
Mostly out.
17:13:26 [BillBug]
Yeah - Don's right. I'm getting every 10th word. :-(
17:13:43 [chimezie]
yes, it is getting worse
17:15:39 [Don]
Anyone from MIT on the IRC?
17:15:47 [jar286]
I am.
17:16:07 [ericP]
Zakim MIT346 holds JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna
17:16:12 [ericP]
Zakim, MIT346 holds JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna
17:16:12 [Zakim]
+JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna; got it
17:16:39 [Don]
Is anyone looking at the signal problem?
17:17:57 [ericP]
oops sorry, don.
17:18:10 [ericP]
hmm, not a problem we usually have
17:18:27 [BillBug]
Sounds like whoever - or whatever phone - is dailed in, has a signal noise squelching function running that is just way to sensitive to the breaks between words when people talk. Dialing in with another phone/or IP telephony app would probably fix it.
17:18:38 [ericP]
Zakim, who is speaking?
17:18:49 [Zakim]
ericP, listening for 10 seconds I heard sound from the following: MIT346 (28%), Don_Doherty (0%)
17:19:05 [zucker]
zucker has joined #BioRDF
17:19:05 [chimezie]
yes, plz
17:19:36 [Don]
Eric, it's not just me.
17:19:44 [Don]
Everyone is having trouble hearing.
17:19:46 [jar286]
agenda+ Review reasons for putting effort into this project
17:19:53 [Don]
Still the case.
17:20:11 [Don]
John is coming in.
17:20:25 [BillBug]
Actually, you are all coming through fine, now.
17:20:33 [Don]
Sounds good now.
17:20:54 [Don]
Thank you!
17:20:54 [alanr]
alanr has joined #biordf
17:21:01 [ericP]
Zakim, agenda?
17:21:01 [Zakim]
I see 3 items remaining on the agenda:
17:21:02 [Zakim]
1. URI note [from ericP]
17:21:03 [Zakim]
3. Demo [from ericP]
17:21:04 [Zakim]
4. Review reasons for putting effort into this project [from jar286]
17:21:06 [Bio2RDF]
Bio2RDF has joined #BioRDF
17:21:20 [ericP]
Zakim, take up agendum 4
17:21:20 [Zakim]
agendum 4. "Review reasons for putting effort into this project" taken up [from jar286]
17:21:55 [ericP]
jar286: is the interest group that same as the mailing list?
17:22:02 [ericP]
[heads nod]
17:22:07 [Zakim]
+??P9
17:22:44 [ericP]
Zakim, ??P9 is Mark_from_Quebec
17:22:44 [Zakim]
+Mark_from_Quebec; got it
17:23:05 [Bio2RDF]
My full name is Marc-Aleandre Nolin
17:23:33 [Bio2RDF]
oups.. miss an X ... Marc-AleXandre Nolin
17:23:35 [ericP]
Sudeshna: do you have a scope of Bio entities in the domain of discourse?
17:23:57 [ericP]
Bio2RDF, could you try "/nick Marc-Aleandre" ?
17:24:22 [Jeremy]
Agenda: 1. Review reasons for putting effort into this project
17:24:29 [ericP]
Zakim, Mark_from_Quebec is Marc-AleXandreNolin
17:24:29 [Zakim]
+Marc-AleXandreNolin; got it
17:30:03 [BillBug]
Given "Description" is in the name of RDF, it seems reasonable to use the word, so long as we are clear what associated information is included in "Description" - IDs, Definitions, relations to other resources, etc.
17:30:42 [BillBug]
Resource Description Framework (RDF)
17:31:51 [Jeremy]
1. Review reasons for putting effort into this project
17:31:53 [Jeremy]
- use same URI for same thing
17:31:54 [Jeremy]
- clarity
17:31:56 [Jeremy]
- non-punning
17:31:57 [Jeremy]
- reusing URI's for another purpose is worse than breaking link
17:31:59 [Jeremy]
- have a story about accessing
17:32:00 [Jeremy]
"description of x" =def RDF statements that describe x.
17:32:02 [Jeremy]
(definition, identification, specification, documentation...)
17:32:03 [Jeremy]
(also need to get at other statements about it.)
17:32:57 [chimezie]
aren't "description" the larger group of such 'statements', with a specific subset which provides formal definitions?
17:33:28 [chimezie]
s/"description"/"descriptions"
17:35:34 [khalid_]
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17:36:01 [khalid_]
Hi everybody
17:36:04 [chimezie]
hello
17:39:01 [Jeremy]
One example of a complicated thing that can be described with URI's is Glycolysis: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=GLYCOLYSIS&detail-level=3
17:40:00 [Jeremy]
If you click on the BioPAX format button, you get the RDF associated with it.
17:40:55 [Zakim]
+??P2
17:41:10 [BillBug]
would you please post the "glucose" link to the list?
17:41:20 [ericP]
Zakim, ??P2 is DanielRuben
17:41:20 [Zakim]
+DanielRuben; got it
17:48:38 [jar286]
agenda+ Review objectives and target audience
17:49:22 [Marc-Alexandre]
hie eric, francois belleau with marc-a
17:49:32 [Marc-Alexandre]
can you push the agenda on the irc
17:49:39 [jar286]
agenda+ Discuss process (consensus and closure)
17:49:49 [ericP]
Zakim, take up agendum 6
17:49:49 [Zakim]
agendum 6. "Discuss process (consensus and closure)" taken up [from jar286]
17:49:50 [Jeremy_Zucker]
Jeremy_Zucker has joined #BioRDF
17:49:54 [BillBug]
I agree with Chimezie's comment above - descriptions could subsume definitions as well as other things such as IDs, relations, etc..
17:51:16 [mscottm]
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17:51:52 [BillBug]
Welcome, Scott.
17:54:33 [mscottm]
Thanks Bill. Still waiting for my other half to get home from a conference to help take care of the kids but lurking here now.
17:55:30 [jar286]
agenda+ Review JAR's proposed conceptual framework: descriptions, documents, versions, access, etc. - give advice to JAR
17:56:16 [BillBug]
Ah, yes - it's evening there for you, Scott. I forgot.
17:56:22 [jar286]
editor keeps coming back to the working group with revisions
17:56:35 [jar286]
they ask for revisions, or give go ahead to publish
17:58:02 [ericP]
alanr: what would make Pfizer adopt the recommendations of this URI BP document?
17:58:49 [jar286]
meeting of hcls needs to approve publication of each draft
17:59:15 [ericP]
StevenDobson: when some implementor adopts or supports it
17:59:19 [ericP]
alanr: like who?
17:59:44 [ericP]
VijayBuluse: ACCELYRS
17:59:54 [Jeremy_Zucker]
Jeremy_Zucker has joined #BioRDF
18:02:18 [jar286]
group recommends that editor maintain an issues list
18:07:48 [ericP]
Zakim, MIT346 hods ericN
18:07:48 [Zakim]
I don't understand 'MIT346 hods ericN', ericP
18:07:52 [BillBug]
Definitions + examples is the ONLY way to avoid confusion, as the examples help to constrain the meaning of the collection of words you call a definition, although in OWA the definition can still be easily misinterpretted. At least a good collection of non-overlapping examples can HELP to avoid misinterpretation of a definition by itself.
18:07:59 [ericP]
Zakim, MIT346 has ericN
18:07:59 [Zakim]
+ericN; got it
18:08:26 [ericP]
Zakim, who is here?
18:08:26 [Zakim]
On the phone I see MIT346, susie, Chimezie_Ogbuji, Don_Doherty, Khalid, BillBug, Marc-AleXandreNolin, DanielRuben
18:08:28 [Zakim]
MIT346 has ericN
18:08:29 [Zakim]
On IRC I see Jeremy, mscottm, khalid_, Marc-Alexandre, alanr, jar286, BillBug, RRSAgent, Don, chimezie, Susie, ericP, Zakim
18:09:25 [BillBug]
To follow on Alan's comment on OBI - it's really in OBI and the Basic Formal Ontology (BFO), as that foundation needs to support those classes we define in OBI.
18:09:27 [ericP]
Zakim, MIT346 holds JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna, EricNeuman
18:09:27 [Zakim]
+JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna, EricNeuman; got it
18:10:44 [BillBug]
I'd be careful of using version as given in LSID, as this is probably THE most problematic aspect of the LSID spec - and the one that is interpreted in a rather divergent way by those who've actually implemented an "LSID"-based respository.
18:15:26 [jar286]
ok
18:24:25 [jar286]
EN: Clear policy expression is VERY IMPORTANT. (for versioning, etc)
18:24:41 [jar286]
AR: OBO has a reasonable process for ontology evolution.
18:25:29 [jar286]
Eric N says HCLS is likely to be extended to end of year.
18:26:03 [Zakim]
-Chimezie_Ogbuji
18:27:58 [BillBug]
Guidelines/requirements for published versioning/update policy are critical. I can see how one could create guidelines for such policies, where we at least say you must specify what you MEAN by 'version', 'variant', 'dynamic content', 'stable content', and 'unchanging document' (as you've outlined them, JAR). Recommendation would include specifying a range for the temporal boundaries for...
18:27:59 [BillBug]
...each of these properites.
18:28:55 [BillBug]
We'd have to provide some examples - hopefully a range of examples for each property.
18:29:21 [ericP]
ACTION: EricN to see if terms from URI Recommendations Document adequately support [a strawman] version and revision ontology, i.e. can you express policies
18:32:58 [BillBug]
LSID has partly suffered by being so highly constrained in terms of its versioning policy. I could see 'version' as defined by LSID as being an ideal to work toward. In practice, people who have implemented LSIDs have implemented version differently. It would help in any URI policy HCLS IG publishes to explicity declare we recognize at this point in time - given how much the technology...
18:32:59 [BillBug]
...and the requirements are still in flux - there is a need to constrain the RANGE of what is acceptable for 'version' - give clear examples of versions - and provide short pros & cons on each example given the consensus HCLS IG understanding of how we would like to compute on these resources.
18:33:28 [ericP]
ACTION: ericP to determin HCLS charter close
18:42:32 [BillBug]
Jonathan - one practice that MIGHT help to make your definitions more clear - and make it easier for people to come to consensus on them - would be to use DC Metadata Elements in the body of the definitions. A lot of work went into the creation of DC, and we MIGHT be able to gain a further level of clarity and agreement by leaning on CD Metadata element definitions and examples. This is...
18:42:34 [BillBug]
...just a suggestion. If you think going out to DC metadata only complicates and further obscures the defs, then skip it.
18:58:56 [BillBug]
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19:00:21 [BillBug]
remember - if you are thinking of the publishing world, when they think of persistent references, they think of DOI - which I don't think we have the time to sort through before HCLS IG runs out.
19:02:08 [BillBug]
Is anyone reading the IRC?
19:02:10 [BillBug]
Can it be projected on the board so remote folks can add something to the discussion?
19:03:30 [Marc-Alexandre]
Im reading it, but Im not in the MIT 346 room
19:04:02 [mscottm]
I'm reading too..
19:05:49 [BillBug]
One question on Jonathan's OK URI - he mentions 'stable' -"...but the URI's intended meaning must remain consistent." Constant and consistent mean something different. For LSID's, meaning AND content must remain constant. I'd think for an OK URI, we should at least say the meaning remains constant (even if not EVERY bit in the content is stable).
19:06:34 [Marc-Alexandre]
having a set of rules that anyone can simply apply when building their URI is what Bio2RDF is telling from the Banff Conference
19:06:51 [BillBug]
Sorry - I meant to say even if EVERY bit in the content is NOT stable.
19:09:12 [BillBug]
Marc - did you mean at the Banff Conference, the Bio2RDF group stated they were committed to establishing a set of rules anyone can simply apply when building their URIs?
19:10:59 [Marc-Alexandre]
yes, we said, that Purl or HCLS have a set of rules about how to build URI (like, all lowercase, namespaces followed by a semi-colon then the id then a dot then the version, etc)
19:11:39 [Marc-Alexandre]
ok... it's not all the rules... but somes rules that can be uses
19:12:23 [BillBug]
That would be wonderful, Marc. To date, mostly what we've been doing on the HCLS IG list is to debate the issue, which is partly why Jonathan is so anxious for us to reach some consensus and publish it.
19:12:36 [BillBug]
In the end, whatever "ontology" we use for defining URI-related policies should try to re-use DC metadata where ever practical, and stay compatible with the SKOS effort that Daniel Rubin and Alan Ruttenberg are contributing to.
19:12:43 [Marc-Alexandre]
I've elaborate a bit more here http://bio2rdf.org/JSPWiki/Wiki.jsp?page=Bio2RDFURIProposal
19:14:09 [Marc-Alexandre]
I'm not speaking on the phone because i've already a bad enough time to just follow a face 2 face conversation on the phone and english is not my native language, but i'm listening
19:15:16 [BillBug]
Good idea. It can be very tough to follow the back-n-forth in the conversations, when you can't see the people - especially when its not your first language.
19:15:49 [Marc-Alexandre]
indeed
19:16:05 [Marc-Alexandre]
It would have been easier to be in person
19:18:37 [ericP]
Zakim, who is here?
19:18:37 [Zakim]
On the phone I see MIT346, susie, Don_Doherty, Khalid, BillBug, Marc-AleXandreNolin, DanielRuben
19:18:39 [Zakim]
MIT346 has JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna, EricNeuman
19:18:41 [Zakim]
On IRC I see BillBug, Jeremy, mscottm, khalid_, Marc-Alexandre, jar286, RRSAgent, Don, chimezie, Susie, ericP, Zakim
19:19:12 [alanr]
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19:19:15 [alanr]
Call for questions/comments to be had by the end of the call...
19:22:36 [eneumann]
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19:25:14 [ericP]
agenda+ how to re-publish LSID data as OK URIs [Khalid]
19:27:12 [ericP]
BillBug: are our identifiers intended to provide persistent identifiers for database records?
19:27:29 [alanr]
marc are you there?
19:28:23 [ericP]
Marc-AleXandreNolin: doing well in current direction. need a simple set of rules for URIs
19:29:00 [BillBug]
Sorry - I had a question and a statement:
19:29:01 [BillBug]
statement: OK URIs are intended to provide persistent identifiers for database records.
19:29:03 [BillBug]
question: Are we convinced the definition of OK URIs will be able to accommodate the different requirements between retrieving static "documents" and retrieving resources that only ever exist at the other end of an algorithmically and dynamically generated URL?
19:29:36 [ericP]
DanielRuben: want NCBO ontologies to be synergistic with what we produce
19:29:42 [Marc-Alexandre]
and publish these rules on community managed pages like Purl
19:30:34 [BillBug]
What I read in the current document (http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/DraftTalk#preview) re: public database records seems way to loose to provide this guarantee - at least if the desire is for long-term stability for these derived URIs.
19:31:07 [ericP]
... need mapping layer covering entities described by multiple ontologies
19:33:10 [ericP]
Sudeshna: keep track of who's using OK URIs in what ontologies and datasets
19:33:49 [Marc-Alexandre]
Has an example, the set of rules to write URI's on the Bio2RDF system is written there http://bio2rdf.org/JSPWiki/Wiki.jsp?page=URISyntax . I don't say that should be the set of rules that HLCS adopt, it is just the rules we used here.
19:34:44 [ericP]
alanr: jar's doc discusses validating a comittee to establish and bless OK URIs
19:35:02 [ericP]
Jeremy: there are cool URIs that are not OK URIs?
19:36:12 [ericP]
alanr: yes. we don't know how to use conneg in OK URIs and Cool URIs doc grounded on Tag findings that jar and alanr can't grock
19:36:38 [ericP]
s/grock/grok/
19:37:12 [alanr]
jonathan.rees@gmail.com
19:39:05 [ericP]
Steven: interested in how you get a description of a resource given it's identifier
19:39:53 [BillBug]
For resource type, can't we use/extend the DC Types:
19:39:54 [BillBug]
http://dublincore.org/documents/dcmi-type-vocabulary/
19:41:11 [Marc-Alexandre]
isn't rdf:type supposed to be used for the type or I'm missing something
19:41:29 [ericP]
Paolo: am particularly interested in version and variance
19:43:03 [ericP]
... want a common vocabulary for axes of version and variant
19:43:38 [BillBug]
From http://www.w3.org/TR/rdf-schema/#ch_type
19:43:39 [BillBug]
"rdf:type is an instance of rdf:Property that is used to state that a resource is an instance of a class.
19:43:41 [BillBug]
A triple of the form:
19:43:42 [BillBug]
R rdf:type C
19:43:44 [BillBug]
states that C is an instance of rdfs:Class and R is an instance of C.
19:43:45 [BillBug]
The rdfs:domain of rdf:type is rdfs:Resource. The rdfs:range of rdf:type is rdfs:Class."
19:43:47 [BillBug]
This is too unconstrained for the purpose of type that Jonathan was talking about.
19:43:54 [ericP]
ericN: would like some framework for identifying contracts of term evolution
19:44:23 [Marc-Alexandre]
ok, I see
19:46:05 [Zakim]
-DanielRuben
19:46:06 [Zakim]
-BillBug
19:46:07 [Zakim]
-Khalid
19:46:08 [Zakim]
-MIT346
19:46:09 [Zakim]
-Marc-AleXandreNolin
19:46:10 [Zakim]
-Don_Doherty
19:46:19 [Zakim]
-susie
19:46:20 [Zakim]
SW_HCLS(BioRDF)1:00PM has ended
19:46:22 [Zakim]
Attendees were susie, Chimezie_Ogbuji, Don_Doherty, Khalid, BillBug, JonathanR, AlanR, JeremyZucker, VijayBuluse, StevenDobson, ericP, ElizabethWu, PaoloCiccarese, Sudeshna,
19:46:24 [Zakim]
... Marc-AleXandreNolin, DanielRuben, ericN, EricNeuman
19:46:30 [ericP]
RRSAgent, please draft minutes
19:46:30 [RRSAgent]
I have made the request to generate http://www.w3.org/2007/07/16-BioRDF-minutes.html ericP
19:46:43 [ericP]
RRSAgent, make log world-visible
19:47:21 [BillBug]
If dc:type were a subclass of rdf:type, then it would be equivalent, but I think DC and RDF are somewhat orthogonal on this issue. The RDF version of DC terms defines dc:type as:
19:47:23 [BillBug]
rdfs:isDefinedBy http://purl.org/dc/elements/1.1/
19:47:24 [BillBug]
rdfs:label (en-US) : Type
19:47:26 [BillBug]
rdfs:comment (en-US) : The nature or genre of the resource.
19:47:27 [BillBug]
bye
19:48:06 [Marc-Alexandre]
bye
20:55:56 [jar286]
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21:05:47 [Jeremy_Zucker]
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