Re: [BioRDF] All about the LSID URI/URN

On Jul 31, 2006, at 11:05, Alan Ruttenberg wrote: On Jul 25, 2006, at 12:55 PM, Phillip Lord wrote: But if the file you are referencing is, say 5Tb, then it doesn't work in a browser at all. With LSID's on the other hand, you may get back a choice of methods to access the data, including

Re: [BioRDF] All about the LSID URI/URN

Thanks, Carole.Bon Voyage!For the uninitiated, here is a PPT presentation Ben gave on the Boca Enterprise-ready RDF Server at the SWTech meeting held in Edinburgh in June: http://www.nesc.ac.uk/action/esi/contribution.cfm?Title=683 (Day 1, Session 2, presentation 1)I'd also recommend Daniele's pres

Re: [BioRDF] All about the LSID URI/URN

Bill we do, and when Boca comes on line we will play with that too Sean ;-) Daniele can field further questions - I am really really on holiday now, honest! Carole Hi All, I was following up on Carole's presentation regarding the myGRID use of LSIDs [1

Re: [BioRDF] All about the LSID URI/URN

Hi All,I was following up on Carole's presentation regarding the myGRID use of LSIDs [1].  I wanted to confirm whether they were using the IBM code base [2][3].  This post from 2 years back by Chris Roe [4] does confirm that and gives a little more detail from earlier in the myGRID chronology which

Re: [BioRDF] All about the LSID URI/URN

If we go with Sean's suggestion of an HTTP gateway, you can have one line of code that looks like: InputStream lsidData = new URL("http://lsid.info/urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank:32345422").openStream(); Ben Szekely IBM Software Engineer Advanced Internet Technology, Camb

Re: [BioRDF] All about the LSID URI/URN

Benjamin H Szekely wrote: The LSID Java Toolkit supports both SOAP and HTTP. The HTTP version is very simple and does not use Axis. I believe work is being done outside of development team to implement a more lightweight, HTTP-only version of the LSID Java stack. As far as I am concerne

Re: [BioRDF] All about the LSID URI/URN

Benjamin H Szekely wrote: The LSID Java Toolkit supports both SOAP and HTTP. The HTTP version is very simple and does not use Axis. I believe work is being done outside of development team to implement a more lightweight, HTTP-only version of the LSID Java stack. As far as I am concerne

Re: [BioRDF] All about the LSID URI/URN

The LSID Java Toolkit supports both SOAP and HTTP.   The HTTP version is very simple and does not use Axis.  I believe work is being done outside of development team to implement a more lightweight, HTTP-only version of the LSID Java stack.   - Ben   [EMAIL PROTECTED] wrote on 07/31/2006 11:36:58

Re: [BioRDF] All about the LSID URI/URN

Carole Goble wrote: However, we have problems with the implementation, specifically the use of SOAP within the resolution system, because: 1. its not needed conceptually 2. its costly 3. its overkill which affects performance 4. the main implementation is Axis based - not suitable for phones, p

Re: [BioRDF] All about the LSID URI/URN

Alan Ruttenberg writes: > Could this specific issue be handled in the http protocol? Could > there be a new response code that in effect says: "Status > 999: The information resource you have requested is too #&%^ > big and the provider has decided that you need to use one of the > fo

Re: Re: [BioRDF] All about the LSID URI/URN

The recent discussion about URIs has made me change my perspective on the whole issue. It seems that it is getting much more complicated than it needs to be. Here is my new suggestion: 1.) Every agent/user on the Semantic Web connects to one or more RDF query endpoints. The HTTP addresses of t

Re: [BioRDF] All about the LSID URI/URN

Tim well said -- I concur entirely Carole I think Susie is performing a valuable service which we all respect and which may help to advance the discussion. HOWEVER... ... I STRONGLY RECOMMEND that no-one consider the Bio-RDF call Monday as anything else than a very preliminary discussion

Re: [BioRDF] All about the LSID URI/URN

All Of course Susie is doing a fabulous job! And I have already told her this. Gracious! calm down, my point was that this had been reported to me as a key "make or break" meeting on LSIDs and I just wanted to point out that many people who are interested cannot come today. It was no crit

Re: [BioRDF] All about the LSID URI/URN

On Jul 25, 2006, at 12:55 PM, Phillip Lord wrote: But if the file you are referencing is, say 5Tb, then it doesn't work in a browser at all. With LSID's on the other hand, you may get back a choice of methods to access the data, including one which can cope with 5Tb of data. Could this specif

Re: [BioRDF] All about the LSID URI/URN

Hi All, I second Tim's suggestions. This is a really community effort to move this important SW component forward. Best, -Kei Tim Clark wrote: Hi All, I think Susie is performing a valuable service which we all respect and which may help to advance the discussion. HOWEVER... ... I S

Re: [BioRDF] All about the LSID URI/URN

Hi All, I think Susie is performing a valuable service which we all respect and which may help to advance the discussion.  HOWEVER..  I STRONGLY RECOMMEND that no-one consider the Bio-RDF call Monday as anything else than a very preliminary discussion FOR INITIAL EDUCATIONAL PURPOSES ONLY, whic

Re: [BioRDF] All about the LSID URI/URN

Hi All,I would also give a strong DITTO to the leadership Susie is providing on this extremely important issue.  Getting clarification on the pros & cons is essential to catalyzing broader adoption of SWTech.I would also add I'm extremely grateful to ALL the experts who've been presenting clear arg

Re: [BioRDF] All about the LSID URI/URN

> (who very much appreciates Susie's efforts to > coordinate) Ditto on that! jb Quoting Alan Ruttenberg <[EMAIL PROTECTED]>: > > Susie shouldn't take any blame for this - The meeting is > one in a > series, is well announced, and would certainly have been > rescheduled > if, like, anyon

Re: [BioRDF] All about the LSID URI/URN

Susie shouldn't take any blame for this - The meeting is one in a series, is well announced, and would certainly have been rescheduled if, like, anyone with an interest had bothered to request it with adequate advance notice. There's nothing particularly special about this meeting. If other

Re: [BioRDF] All about the LSID URI/URN

Sean We will be joining you on Monday for the telecon. As you know, our projects use LSIDs heavily. And we find it invaluable. Our practical experiences are, in a nutshell Conceptually we like 1. decoupled naming from physical location (essential) 2. versioning (very useful) 3. separate data

Re: [BioRDF] All about the LSID URI/URN

Hello Dan, > Thanks for continuing to explain the requirements. I haven't seen > LSID requirements that can't be met with http/DNS yet, but that > doesn't mean they're not there. > > Yes, it's easy to see how starting fresh simplified some things. > But I am not convinced that starting fresh is t

Re: [BioRDF] All about the LSID URI/URN

On Fri, 2006-07-07 at 12:42 -0400, Sean Martin wrote: > > As background, it might help to know that one of the earliest > requirements of the I3C's LSID group was that bio/pharma companies be > able to copy large chunks of public databases internally so as to be > able to access them repeatedly i

Re: [BioRDF] All about the LSID URI/URN

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sean Martin writes: > Apologies if at any point I appear to be shifting the goal posts on you, > but the LSID scheme seems to have been developed in response to a > significant list of requirements gathered from a large number of stake > holders

Re: [BioRDF] All about the LSID URI/URN

Hello Henry, Apologies if at any point I appear to be shifting the goal posts on you, but the LSID scheme seems to have been developed in response to a significant list of requirements gathered from a large number of stake holders  across the Life Science industry, so there is a fair amount of thi

Re: [BioRDF] All about the LSID URI/URN

Phil Well said! As a practical user of LSIDs for all our infrastructure we are interested in building bioinformatics platforms that work. We are preparing carefully developed argument about why we use LSIDs and why they have been proven invaluable. And what we would like to see done better

Re: [BioRDF] All about the LSID URI/URN

> "HST" == Henry S Thompson <[EMAIL PROTECTED]> writes: HST> Sean Martin writes: HST> So, register one of lsids.org, lsids.net, lsids.name or HST> lsids.info, and use e.g. http://lsids.or/xxx instead of HST> URN:LSID:xxx. Bingo -- no new tools required, works in all HST> modern br

Re: [BioRDF] All about the LSID URI/URN

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Sean Martin writes: >> Well, either your scheme is intended to be dereferenceble, or it >> isn't. >> >> If it is, then instances are likely/virtually certain to contain some >> kind of named starting point, which needs to be looked up and >> reso

Re: [BioRDF] All about the LSID URI/URN

> Well, either your scheme is intended to be dereferenceble, or it > isn't. > >  If it is, then instances are likely/virtually certain to contain some >  kind of named starting point, which needs to be looked up and >  resolved to an IP address start the dereferencing process.  Domain >  names an

Re: [BioRDF] All about the LSID URI/URN

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 [HST comments in additional to Dan's] Dan Connolly writes: > http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jun/0210.html > >> The root of the problem is that the URL >> contains in it more than just a name. It also contains the netw

Re: [BioRDF] All about the LSID URI/URN

Hello Alan, The short answer is that only some parts of what the LSID scheme does could be done using the means you suggest. The reason for this is that what you outline is more or less part of the LSID resolution process under the covers. However in the end it would not meet a number the original

RE: [BioRDF] All about the LSID URI/URN

Hello Xiaoshu, [EMAIL PROTECTED] wrote on 07/07/2006 11:32:58 AM: > > In short, the myth of URN vs. URL is in our perception but not in actuality. > W3C's recommendation to use URI, as opposed to use URN and URL, to refer all > http, ftp, lsid, mailto, etc., is a good first step. As an identifi

Re: [BioRDF] All about the LSID URI/URN

Excellent recommendation, Chimezie.I've looked far and wide for some clarity on this issue beyond the specs & standard committee discussion, and I was really greatly relieved when I finally came across this article.  I really owe a great debt to the IBM DeveloperWorks site for all the many valuable

Re: [BioRDF] All about the LSID URI/URN

Sean, couldn't what LSID achieves be done, for instance, by having a convention that if someone dereferences, for example, http://bla.com/path/to/document/foo.lsid it is understood to obey a protocol, namely to return a snippet of rdf that says, here's a handle to my metadata, here's a han

RE: [BioRDF] All about the LSID URI/URN

BTW, with regards to the whole LSID/URI/URN/URL conversation, I thought it would be worthwhile to point out this article (by Dan Connolly no less - so I'm glad he's weighing in on this conversation) on URIs/URLs/URNs which was instrumental for me in getting to the bottom of the confusion (and

Re: [BioRDF] All about the LSID URI/URN

As background, it might help to know that one of the earliest requirements of the I3C's LSID group was that bio/pharma companies be able to copy large chunks of public databases internally so as to be able to access them repeatedly in private. They also wanted to be certain of exactly what version

RE: [BioRDF] All about the LSID URI/URN

tance http://www.purl.org/, or other similar services. Xiaoshu > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of > Dan Connolly > Sent: Friday, July 07, 2006 8:58 AM > To: public-semweb-lifesci@w3.org > Cc: Henry S. Thompson

Re: [BioRDF] All about the LSID URI/URN

Adding to the identifier discussion - here are my notes summarizing discussions at/after the initial Semantic Web for Life Science workshop (primarily between myself, Sean Martin, and Eric Miller). Some of the points have come up in other posts and I haven't tried to go through and update this,

Re: [BioRDF] All about the LSID URI/URN

http://lists.w3.org/Archives/Public/public-semweb-lifesci/2006Jun/0210.html > The root of the problem is that the URL > contains in it more than just a name. It also contains the network > location where the only copy of the named object can be found (this is the > hostname or ip address) Wh