The W3C mailing lists will be limited to interest group participants.

On Jun 24, 2008, at 7:16 PM, M. Scott Marshall wrote: Membership policy - The W3C mailing lists will be limited to interest group participants. You mean public-semweb-lifesci@w3.org, for example? Jonathan

URI note

Eric informs us that the URI note will not be published as an interest group note, the reason being that the interest group has not had a chance to discuss it in its current form and will not do so before the charter closes at the end of this month. It is close to being finished, with mos

Re: URI note snapshot available

Thanks for the very detailed read! I will do my best to do justice to your comments. Just to address one of your points: The reason for emphasizing non- web naming systems and de-emphasizing URIs is to say that the real goal is clear communication, and that using URIs doesn't give you any

Re: URI note snapshot available

On Apr 28, 2008, at 11:51 AM, Mark Wilkinson wrote: "A user who places the identifier in the location bar of a web browser should get back useful information about the identified concept or object." Why? It seems an awfully steep barrier-to-entry to have *all* URI's resolve to a web pa

Re: BioRDF Telcon

Just to be clear... BioRDF is now empowered to make decisions that ordinarily would be made by the IG, right? Like whether/how to bring IG note drafts to FPWD and then from there to final version? Jonathan On Apr 26, 2008, at 11:18 AM, Susie M Stephens wrote: Here's the reminder for Mond

Re: URI note snapshot available

ead it now only if you also plan on reading a later draft, as significantly more work will be done on it over the next few days. Jonathan On Apr 20, 2008, at 5:57 AM, Jonathan Rees wrote: Some of you may have heard that the URI note has been revised since the last public draft last October

URI note snapshot available

Some of you may have heard that the URI note has been revised since the last public draft last October. This is indeed the case, and its authors are working on polishing the new version. If you would like to examine a snapshot of our work it is available here: http://www.w3.org/2001/sw/hcls/not

Re: broken links and other publication logistics for the KB and SenseLab documents

On Apr 4, 2008, at 10:51 AM, Eric Prud'hommeaux wrote: * Jonathan Rees <[EMAIL PROTECTED]> [2008-03-10 09:21-0400] On Sat, Mar 8, 2008 at 3:45 PM, Eric Prud'hommeaux <[EMAIL PROTECTED]> wrote: Alan, I believe you are the interface for these unregistered PURLS. h

Re: broken links and other publication logistics for the KB and SenseLab documents

FYI: Anyone who regularly uses the Science Commons / Neurocommons triple store should probably pay attention to our google group: http://groups.google.com/group/neurocommons-rdf/about This is where we post information about downtime, updates, and other developments. Jonathan

Re: broken links and other publication logistics for the KB and SenseLab documents

On Sat, Mar 8, 2008 at 3:45 PM, Eric Prud'hommeaux <[EMAIL PROTECTED]> wrote: > Alan, I believe you are the interface for these unregistered PURLS. > http://purl.org/commons/hcls/goa > http://purl.org/science/protein/subjects/ > http://purl.org/science/record/homologene/cluster_r54_99949 Actu

missing flipbook

I'm missing my Allen Brain Atlas flipbook, and the last I remember seeing it was when I handed it around at November's HCLS F2F in Cambridge. If you know where it is please let me know.-Jonathan

KB note

Re the "Incorporated Databases" section of http://www.w3.org/2001/sw/ hcls/notes/kb/ : 1. Many of the sources are ontologies and other loosely structured objects, not databases. The section should be "incorporated data sources" or "incorporated knowledge sources". Actually the word I lik

Re: BioRDF Telcon

Sorry, I'm taking a holiday as well (Veterans Day in US), so can't make it today.

URI note draft for review prior to F2F

Dear HCLS, Alan and I will be presenting the HCLS "URI Note" at Friday's face-to-face. As homework in preparation for this we would like for anyone attending to look over the latest draft. It is still very much a work in progress (>60 to-do items at present count) but is much more complete and

please include draft version number in comments

When commenting on a draft of the URI note, please include the version number (37 or whatever) with your comments. The URI note draft will be unstable until Monday afternoon 11/5, when I will send out a message informing HCLS of its existence. (Sure got leaked, didn't it?) If you read it

Re: comments on the uri note

Dear HCLS list - I haven't put the draft out for general review, but am planning to do so tomorrow. My reason for waiting is past experience of "draft fatigue" - most people will only read one draft of something. If you're one of those people please wait a while for the dust to settle.

Re: what would change for me?

On Oct 23, 2007, at 9:58 AM, Marc-Alexandre Nolin wrote: Currently, I'm waiting for the publication of Jonathan URI recommendation to add it to the Bio2RDF system. Adding the support to the standardization effort doesn't mean to throw away the previous working system :) Marc-Alexandre I appr

Re: what would change for me? -> revised meta-requirements

OK, thanks to your stimulus I've reworked the recommendations to be more clear about what I mean by a URI Note recommendations document. I've tried to provide more motivation and examples of answers to each question. I always omit something important when I do things like this, so please

Re: what would change for me?

First let me thank you for taking a serious look at the requirements. I appreciate it. On Oct 21, 2007, at 7:44 PM, Peter Ansell wrote: Hi all, I have been using the Bio2Rdf markup system and I personally do not see what all the fuss is about but there must be something so here are my opin

Re: BioRDF Telcon

Dear BioRDF: For my agendum, I'll be talking about the latest draft: http://sw.neurocommons.org/2007/uri-note/uri-note-2007-10-21.html which y'all are encouraged to at least skim in advance of the telecon. Best Jonathan On 10/19/07, Susie M Stephens <[EMAIL PROTECTED]> wrote: > > > Here's the

Re: RFC 2616 vs. AWWW

On 10/12/07, Pat Hayes <[EMAIL PROTECTED]> wrote: > * If a network resource responds to a GET request with a 2xx > response, then that URI must be understood as referring to that > network resource. > > >Oddly, this rule doesn't tell you which network resource is > >referenced; it could be one tha

Re: RFC 2616 vs. AWWW

I think we are in agreement here, but let me blab on to make sure. On 10/12/07, Xiaoshu Wang <[EMAIL PROTECTED]> wrote: > Jonathan, > > The httpRange-14 resolution [1] is about identification (of a thing > > by/to an http server), not reference. > "httpRange-14" is an *engineer* but not a *philos

Re: RFC 2616 vs. AWWW

this year - TDWG's adoption of LSID, and inchi's adoption of info: - and the case we make (should we choose to do so) to the next 100 groups facing this decision has to be rock solid, because they have crusty technical people too. On 10/11/07, Eric Jain <[EMAIL PROTECTED]> wrot

Re: RFC 2616 vs. AWWW

As usual, I like your explanation very much. It borders on sophistry, but that doesn't bother me much, or won't until my next conversation with someone who's upset about the use of http: URIs to refer to things that aren't network resources. I've copied your email to the wiki page, reformatted a

RFC 2616 vs. AWWW

For URI fanatics only... For the purposes of my URI project I wanted to know just what IANA had to say about the use of http: URIs, so I did some poking around. I report (neutrally, I hope) on what I found here: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendati

Re: BioRDF Telcon

On 10/8/07, Susie M Stephens <[EMAIL PROTECTED]> wrote: > Hi Jonathan, > > Thanks very much for getting the draft done. :-) > > Are you primarily looking for people to send comments to you, or would you > be happy for folks to directly edit the Wiki? If you go to the top of the draft there are so

Re: BioRDF Telcon

iated. Jonathan 1. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/ URI_Best_Practices/Use_Cases On Oct 8, 2007, at 3:41 AM, Eric Jain wrote: Jonathan Rees wrote: OK, BioRDF, here's my draft, such as it is. Still quite sketchy in some places but I think it's beginning to con

Re: BioRDF Telcon

OK, BioRDF, here's my draft, such as it is. Still quite sketchy in some places but I think it's beginning to converge. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/SputnikDraft Best Jonathan

Re: BioRDF Telcon

Sorry, BioRDF, I have a URI note draft in progress which I'm happy to share, but I don't think it's worth your while yet to read it. I'll try to get something onto the wiki this weekend. -Jonathan On Oct 4, 2007, at 12:10 PM, Jonathan Rees wrote: In case it migh

Re: BioRDF Telcon

In case it might matter in some way, I'd like to point out that the 8th is part of Columbus Day weekend. http://www.opm.gov/fedhol/2007.asp Jonathan On Oct 4, 2007, at 10:47 AM, Susie M Stephens wrote: Here's the reminder for Monday's BioRDF telcon. Cheers, Susie == Conference Details =

Re: BioRDF Telcon

Dear Susie & BioRDF, I had promised a URI note draft for Oct 1. Other work has intervened and I won't be able to hit this target. I will aim to have it ready by the end of next week (i.e. 10/5). Best Jonathan

Re: NCBI Resource Locator

I can't find any discussion of NCBI URLs from May 2006 (the 5/9/06 messages from you seem to be about something a bit more glorious) but the topic was raised at the 5/18/06 teleconference, which I didn't attend: http://www.w3.org/mid/[EMAIL PROTECTED] Olivier offered to help out, but th

NCBI Resource Locator

"The NCBI Resource Locator provides stable, uniform addressing for NCBI content, making it easy to link to individual records. Some NCBI resources also provide services (like search) through these URLs." http://view.ncbi.nlm.nih.gov/ Looks like a gift. Makes a lie of my assertion that ther

Re: BioRDF Telcon

I've written my status report on the page named in your agenda, which in longhand is: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/ 2007-09-10_Conference_Call/UriNoteStatus Jonathan On Sep 7, 2007, at 9:53 AM, Susie M Stephens wrote: Here's the reminder for Monday's BioRDF call

Re: [Fwd: Re: identifier to use]

Thanks for your comments, Eric. On Aug 26, 2007, at 3:51 PM, Eric Neumann wrote: In an attempt to modulate the tone a bit, it's clear that with such a large and complex group of people and communities, many who had not been part of earlier OMG/I3C discussions are not aware of all the detail

feasibility; purl.org/commons

the recommendations note. If they need to be relocated or redesigned, that's fine too. Better to do that now than after they're widely deployed. Jonathan On Aug 25, 2007, at 8:09 AM, Eric Jain wrote: Jonathan Rees wrote: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Me

Re: BioRDF Telcon

I won't be able to attend on Monday, but have written up my current status. See http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/ 2007-08-27_Conference_Call/UriNoteStatus Jonathan On Aug 24, 2007, at 12:50 PM, Susie M Stephens wrote: Hi Folks, Here's the reminder for Monday's Bio

Re: Does follow-your-nose apply in the enterprise? was: RDF for molecules, using InChI

On Aug 22, 2007, at 7:03 PM, Bijan Parsia wrote: Following Matthias's suggestion, I started adding them to this page: (At the bottom under issues.) Would you prefer they migrated to the recommendations page (which is where, IIRC, Alan s

Re: Does follow-your-nose apply in the enterprise? was: RDF for molecules, using InChI

Sure - to list alternatives with costs and benefits is just what I've proposed to do in order to civilize these debates, and as a waypoint toward drafting the fabled 'recommendations' report. I'm sorry I've been inactive on the list but other matters have been pressing. I have been trying t

URN namespace ids

On Aug 21, 2007, at 12:11 PM, Eric Jain wrote: That's not accidental reuse as cold happen with e.g. urn:bm:ipi:12 where someone who has never heard of Banff might end up with the same identifier for something completely unrelated (e.g. hotels in the Bahamas). There is a registry of URN n

Re: BioRDF Informal F2F

Here are my notes on Monday's meeting. [Bracketed] phrases are my after-the-fact clarifications and don't necessarily reflect anything that happened at the meeting. This should go into the wiki, but I'm too busy to do the formatting right now, and I will probably forget later. If someone else d

Re: IDs + 5; everybody - 10

;[EMAIL PROTECTED]> wrote: My apologies. I wasn't sure, which is why I asked. I just found your idea of reproducing LSIDs advantages (and implicitly DOI) in http a little worrying. I may have misread your email. Phi >>>>> "JR" == Jonathan Rees <[EMAIL PROTEC

Re: IDs + 5; everybody - 10

ROTECTED]> wrote: >>>>> "JR" == Jonathan Rees <[EMAIL PROTECTED]> writes: JR> It may look like unnecessary replication, but it's not really, since JR> we're already committed to the http: space and all the issues that LSID JR> addressed are i

Re: IDs + 5; everybody - 10

Let me try to review what's going on here, since Mark W and others have reasonably asked why we're putting so much effort into the URI question. The W3C HCLS SIG was created according to a charter [1] that specifes that the "The Interest Group will provide guideline[s] on how best to identify HC

Re: URL +1, LSID -1

On 7/13/07, Xiaoshu Wang <[EMAIL PROTECTED]> wrote: Interestingly, when RDF was first developed some 8-9 year ago, it was intended for the framework of metadata. "The solution proposed here is to use /metadata/ to describe the data contained on the Web." (From the introduction of the 1999 reco

Re: BioRDF Informal F2F

The editor proposes the following agenda: 1. Review reasons for putting effort into this project 2. Review objectives and target audience 3. Discuss process (consensus and closure) 4. JAR's proposals, see http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/Dra

Re: URL +1, LSID -1

I must have misspoken. What I meant is this. Suppose I have an LSID (used as a URI sensu semantic web) that I got from email or a scientific publication, and I want to know more about the resource that it denotes. That is, I want some metadata for the resource, at the very least. My understandin

Re: URL +1, LSID -1

When I asked for a HOWTO I meant something a bit more general and protocol oriented. Surely you're not advising that a new semweb application should link against Firefox, or that it should have a particular LSID resolver address wired in. As Mark W has pointed out, a single point of failure and c

Re: URL +1, LSID -1

A half-baked idea just occurred to me... if we take SPARQL endpoint as analogous to LSID resolver, then merging metadata from multiple sources just means consulting several endpoints. This requires almost no programming, and could be hidden behind a simple API if desired. The difficulty of findi

Re: URL +1, LSID -1

On 7/11/07, Mark Wilkinson <[EMAIL PROTECTED]> wrote: On Tue, 10 Jul 2007 23:34:10 -0700, Alan Ruttenberg <[EMAIL PROTECTED]> wrote: > The cost of using an http identifier, and providing a 303 and a pointer > to more information, instead of using an LSID, seems a small cost to > satisfy this c

Re: URL +1, LSID -1

On 7/10/07, Michel_Dumontier <[EMAIL PROTECTED]> wrote: Unfortunately, this again demonstrates the problem in which the identifier for a biological entity - say mitochondrial Aspartate aminotransferase resolves to a nicely formatted HTML page. What if I have a semantic web application in which

Rod Page: Rethinking LSIDs versus HTTP URI

Recommended reading for those who care about which GUIDs to choose: http://iphylo.blogspot.com/2007/06/rethinking-lsids-versus-http-uri.html While I don't agree with everything said here, it exemplifies the kind of attitude and analysis I'd like to see more of. Jonathan

Re: URL +1, LSID -1

On 7/10/07, Alan Ruttenberg <[EMAIL PROTECTED]> wrote: > URIs are cheap, we suggest creating as many distinctive URIs as is > meaningful. You want one and only one URI for each thing you might want to name. It sounds like this is true - there is a URI for the record, one for the RDF form, on

Re: BioRDF Telcon

Here are some comments on http://bio2rdf.org/JSPWiki/Wiki.jsp?page=BanffManifesto : Rule #1 - normalized and dereferencable. What we need is to agree on a single URI for each resource, so that we have the best chance possible of getting matches when joining one data source with another. Which U

Re: BioRDF Telcon

Here's my report, for perusal before or during the telecon Action items from 6/25 Did Alan or Susie contact LSID stakeholders? Did Eric N add anything about navigation to RequirementsTalks ? Did Scott Marshall review the requirements page(s) and add his comments to RequirementsTalks ? Oth

Re: BioRDF Telcon

Susie asked me to put together a list of potentially contentious issues. Here are few that I thought of. - Purpose. The recommendations document is in effect a plea for others to publish RDF according to certain "recommendations", and an agreement to work with what each of us publishes assum

Re: BioRDF Telcon

ople more about it (I wasn't at the > follow-up meeting). > > Best, > > -Kei > > Jonathan Rees wrote: > > > > > > On 6/11/07, *Eric Neumann* <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>> wrote: > > > > > > +1 ! > &g

Re: Last Year's URI Discussion

Thanks Susie - I've added these links to http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations On 6/18/07, Susie M Stephens <[EMAIL PROTECTED]> wrote: These links point to the majority of last year's URI discussion. http://lists.w3.org/Archives/Public/public

Re: BioRDF Telcon

Yes, by all means. Edit http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations/RequirementsTalk . On 6/20/07, Eric Jain <[EMAIL PROTECTED]> wrote: Jonathan Rees wrote: > I really think we should put together a set of requirements and > desiderata

Re: BioRDF Telcon

I think I can be more blunt... I was put off by your saying that you "wanted to give a base of discussion with this text" since we (HCLS) already have a base of discussion, consisting of the wiki pages and email threads that have been developing since spring of 2006. But this doesn't matter. I a

Re: BioRDF Telcon

iprot. With dbpedia http://dbpedia.org rdfizing Wikipedia, this could be very useful. Sorry for the long reply, but you ask for comments :) Marc-Alexandre 2007/6/19, Jonathan Rees <[EMAIL PROTECTED]>: > I hate to see the number of wikis used for this purpose multiply. >

Re: BioRDF Telcon

after the HCLS demo that Eric and > others might be able to tell people more about it (I wasn't at the > follow-up meeting). > > Best, > > -Kei > > Jonathan Rees wrote: > > > > > > On 6/11/07, *Eric Neumann* <[EMAIL PROTECTED] > > <mailto

[BioRDF] Process for developing the URI Practices document

Per our discussion at yesterday's BioRDF teleconference, I've written down my ideas on how to proceed on the task of producing a document giving recommendations for choice and use of URI's. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Work_Plan I also created a couple

Re: BioRDF Telcon

On 6/11/07, Eric Neumann <[EMAIL PROTECTED]> wrote: +1 ! I've also added a reference to the Banff discussion on URI's. I plan to put this also on the agenda for the next HCLSIG TC (June 21). -Eric Thanks, but for the benefit of those of us who weren't at this dicussion in Banff, could you

Re: BioRDF Telcon

I've prepared a status report on the "URI Best Practices" task and placed it here: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Status_2007-06-08 Some of this bears on my agendum for today's meeting, so if you get a chance please look it over before the meeting. Jonath

Re: BioRDF Telcon

When's the next BioRDF telecon? Are there minutes for the one on 6/4? On 6/1/07, Susie M Stephens <[EMAIL PROTECTED]> wrote: Here's a reminder for Monday's BioRDF telcon. Cheers, Susie == Conference Details == * Date of Call: Monday June 4, 2007 * Time of Call: 11:00am Eastern Time * Dia

Re: Adding addition resources to the accruing in the NeuroCommons

Thanks for the suggestions. We'll be looking at these once we dig out from under all the things that we had put off until after Banff. Of course, if someone else would like to tackle them first, that would be great. It would be especially interesting to have good examples of queries that one wou

Neurocommons text mining alpha release

ld be most welcome. Best Jonathan Rees (speaking also for Alan Ruttenberg) Neurocommons project Science Commons

Re: HCLSIG TC FEB 8, 2007

As promised last time I've posted more verbiage about URI best practices. It's linked from this page: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommendations Discussion is already taking place in the "URI Resolution" thread on this list, so please comment there, no

Re: [BioRDF] URI Resolution

I've posted a newer version that may make some things clearer, and undoubtedly will make other things less clear. Thanks to everyone for raising questions - every confusion surfaced helps to improve the end result. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/URI_Best_Practices/Recommen

Re: RE: [BioRDF] URI Resolution

Doing HTTP operations on an information resource, while abstractly similar to answering SPARQL queries relating to it (in either case you are learning something), seems to have a different feel given present technology. The protocol used is HTTP and the stuff you get has types (e.g. image, PDF) t

Re: [BioRDF] URI Resolution

This leads me to think that the main relation we are looking for is one between an information resource (which may have multiple URI's) and a *string* that is a URL that will help us to get its representation. Maybe this is obvious. The www notion of 'resource' includes things that have differen

Re: [BioRDF] URI Resolution

Sorry, I should have changed the subject line. Please reply to this message, not the previous one, so that the thread gets properly threaded. On 2/1/07, Jonathan Rees <[EMAIL PROTECTED]> wrote: As promised, here's a draft of a document about what we've been calling the "UR

Re: [BioRDF] Meeting Minutes

As promised, here's a draft of a document about what we've been calling the "URI resolution" problem, building on Alan's presentation at the Amsterdam F2F. It's obviously not finished but comments are welcome. http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Documents?action=AttachFile&do=get&targ

Re: Shared google calendar?

I have updated the calendar with information on meetings of which I'm aware. Please report problems to me. THIS CALENDAR IS NOT AN OFFICIAL COMMUNICATIONS MEDIUM OF HCLSIG OR ANY OF ITS SUBGROUPS. USE AT YOUR OWN RISK. Jonathan On 5/18/06, Alan Ruttenberg <[EMAIL PROTECTED]> wrote: As an expe

Re: Shared google calendar?

I think the calendar still shows the phone conference as being weekly, not every other week. Believing it, I expected a call yesterday. Also there doesn't seem to be anything in the wiki about how to use or change the calendar. - Jonathan On 5/18/06, Alan Ruttenberg <[EMAIL PROTECTED]> wrote:

Introduction: Jonathan Rees

I've been lurking on this list for over a year, so it's probably time for me to post my self-introduction. I work for Science Commons on the NeuroCommons (http://neurocommons.org/), a pilot project to develop and promote some of the ideas behind Science Commons (http://sciencecommons.org/). The N