Re: [Fwd: Re: identifier to use]

> the non-informatics people) want to be in 2-5 years? I think we will be > > capturing most of these shortly, and I look forwards to lots of useable > > contributions. > > > > I am not weighing in on any specific side here, but do hope to see an > > outcome that

Re: [Fwd: Re: identifier to use]

Mark Wilkinson wrote: These are things that we simply cannot answer at the moment. We're lacking the "killer app" that will take the Semantic Web by storm! Indeed! But meanwhile, there are those among us whose main motivation for using Semantic Web technologies is not because we hope that o

Re: [Fwd: Re: identifier to use]

nts would never succeed... past does not imply the future! Eric -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Wilkinson Sent: Sun 8/26/2007 2:46 PM To: Hilmar Lapp; [EMAIL PROTECTED] Cc: Miller, Michael D (Rosetta); Eric Jain; Ricardo Pereira; public-semweb-lifesci; Sean Marti

RE: [Fwd: Re: identifier to use]

public-semweb-lifesci; Sean Martin > Subject: 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 gr

Re: [Fwd: Re: identifier to use]

Mark Wilkinson wrote: On Sun, 26 Aug 2007 08:40:26 -0700, Hilmar Lapp <[EMAIL PROTECTED]> wrote: If cannot do it through OMG, maybe LSID should be moved out of OMG. No matter what, there is one consensus that is LSID won't be supported as is. Consensus by whom? There are organizations th

RE: [Fwd: Re: identifier to use]

ject: 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

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

RE: [Fwd: Re: identifier to use]

lf of Mark Wilkinson Sent: Sun 8/26/2007 2:46 PM To: Hilmar Lapp; [EMAIL PROTECTED] Cc: Miller, Michael D (Rosetta); Eric Jain; Ricardo Pereira; public-semweb-lifesci; Sean Martin Subject: Re: [Fwd: Re: identifier to use] On Sun, 26 Aug 2007 08:40:26 -0700, Hilmar Lapp <[EMAIL PROTECTED]&

Re: [Fwd: Re: identifier to use]

On Sun, 26 Aug 2007 08:40:26 -0700, Hilmar Lapp <[EMAIL PROTECTED]> wrote: If cannot do it through OMG, maybe LSID should be moved out of OMG. No matter what, there is one consensus that is LSID won't be supported as is. Consensus by whom? There are organizations that support it already,

RE: [Fwd: Re: identifier to use]

G spec apply. cheers, michael > -Original Message- > From: Hilmar Lapp [mailto:[EMAIL PROTECTED] > Sent: Sunday, August 26, 2007 8:40 AM > To: [EMAIL PROTECTED] > Cc: Miller, Michael D (Rosetta); Eric Jain; Ricardo Pereira; > public-semweb-lifesci; Sean Martin > Subject: Re: [

Re: [Fwd: Re: identifier to use]

On Aug 26, 2007, at 9:08 AM, Xiaoshu Wang wrote: If cannot do it through OMG, maybe LSID should be moved out of OMG. No matter what, there is one consensus that is LSID won't be supported as is. Consensus by whom? There are organizations that support it already, such as TDWG, IPNI, uBi

Re: [Fwd: Re: identifier to use]

Miller, Michael D (Rosetta) wrote: Is there any chance that this will find it's way back into the LSID spec? great thought but... the spec is an OMG spec through the Life Sciences working group. i3c worked on it in collaboration with this group but i3c is dead and the members of the Li

Re: [Fwd: Re: identifier to use]

On Aug 25, 2007, at 1:36 PM, Eric Jain wrote: Note that the DOI spec also doesn't define http://dx.doi.org. From : The resolution spec for DOIs is the Handle spec (DOIs are technically Handles). The handbook - and the Handle Resolu

RE: [Fwd: Re: identifier to use]

August 25, 2007 11:29 AM > To: Eric Jain; Ricardo Pereira > Cc: public-semweb-lifesci; Sean Martin > Subject: RE: [Fwd: Re: identifier to use] > > > hi all, > > > Is there any chance that this will find it's way back into > > the LSID spec? > > gr

RE: [Fwd: Re: identifier to use]

it www.rosettabio.com > -Original Message- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Eric Jain > Sent: Saturday, August 25, 2007 5:38 AM > To: Ricardo Pereira > Cc: public-semweb-lifesci > Subject: Re: [Fwd: Re: identifier to use] > > > Ricardo P

Re: [Fwd: Re: identifier to use]

Hilmar Lapp wrote: That's part of the LSID resolution protocol. It's what the HTTP proxy does under the hood. I'm assuming you aren't suggesting that you can only be an LSID assigning authority if you also run a HTTP proxy? Not everything the spec talks about is required... Note that the

Re: [Fwd: Re: identifier to use]

On Aug 25, 2007, at 1:02 PM, Eric Jain wrote: Hilmar Lapp wrote: Sure. But what about it should be in the LSID spec? For the same reason the entire SOAP-based resolution stack is in the spec? That's part of the LSID resolution protocol. It's what the HTTP proxy does under the hood.

Re: [Fwd: Re: identifier to use]

Hilmar Lapp wrote: Sure. But what about it should be in the LSID spec? For the same reason the entire SOAP-based resolution stack is in the spec?

Re: [Fwd: Re: identifier to use]

On Aug 25, 2007, at 12:44 PM, Eric Jain wrote: Hilmar Lapp wrote: This has nothing to do with the LSID spec, but with exposing content in RDF. I'm not sure what you mean? Sorry, I'm talking about the HTTP LSID proxying, this alternative resolution mechanism would be very useful even out

Re: [Fwd: Re: identifier to use]

Hilmar Lapp wrote: This has nothing to do with the LSID spec, but with exposing content in RDF. I'm not sure what you mean? Sorry, I'm talking about the HTTP LSID proxying, this alternative resolution mechanism would be very useful even outside of RDF!

Re: [Fwd: Re: identifier to use]

On Aug 25, 2007, at 8:38 AM, Eric Jain wrote: Ricardo Pereira wrote: http://wiki.tdwg.org/twiki/bin/view/GUID/ LsidHttpProxyUsageRecommendation [...] Is there any chance that this will find it's way back into the LSID spec? This has nothing to do with the LSID spec, but with exposing c

Re: [Fwd: Re: identifier to use]

Ricardo Pereira wrote: http://wiki.tdwg.org/twiki/bin/view/GUID/LsidHttpProxyUsageRecommendation Looks like a good solution for people who are using LSID (for whatever reason) and want to make their data more accessible on the Semantic Web! Together with the content negotiation mechanism de

Re: [Fwd: Re: identifier to use]

Hello all, The biodiversity informatics community, which I'm a member of, were faced with the same issues when we decided to adopt LSID. After much discussion, we extended the work from Sean Marting and others regarding LSID HTTP proxies and devised a set of recommendations to make

Re: identifier to use

Phillip Lord wrote: I want an identifier that I can do one thing with and, preferably, one thing only. Not 5. And that would be? (Drums rolling...)

Re: identifier to use

Phillip Lord wrote: No it isn't. http:// based URIs carry the assumption that they are potentially resolvable by a defined protocol. URNs do not. Yes, HTTP URIs are *potentially* resolvable. So are URNs, except that the exact mechanism, if any, is less obvious...

Re: identifier to use

Phillip Lord wrote: Actually, LSIDs are built on top of HTTP. The initial step is web service and http delivered. The second stage is multi-protocol which includes HTTP. There are other schemes up for discussion, too, but regarding LSID: If it's anyway built on top of HTTP, wouldn't it make

Re: identifier to use

> "MS" == Matthias Samwald <[EMAIL PROTECTED]> writes: MS> So you want to advertise what can be expected (or NOT expected) before MS> the web client starts the retrieval process? If we are to use http: based URIs for things which are never meant to be retrieved (like ontology concepts),

[Fwd: Re: identifier to use]

--- Begin Message --- Phillip Lord wrote: I want an identifier that I can do one thing with and, preferably, one thing only. Not 5. I am not suggesting that we put semantics into the identifiers other than those semantics that we need for using the ID. So, your analogy is wrong. What is exa

Re: identifier to use

Phil wrote: > To me it makes no sense to layer multi different protocols over a > single identifier. Imagine I get an URI like > http://uniprot.org/P4543, it could be > 1) a meaningless concept identifier in an ontology > 2) a URL which resolves to a pretty web page, via a single step > process

Re: identifier to use

> "XW" == Xiaoshu Wang <[EMAIL PROTECTED]> writes: XW> Phillip Lord wrote: >> To me it makes no sense to layer multi different protocols over a single >> identifier. Imagine I get an URI like http://uniprot.org/P4543, it could >> be >> >> 1) a meaningless concept identifier in an

Re: identifier to use

Phillip Lord wrote: To me it makes no sense to layer multi different protocols over a single identifier. Imagine I get an URI like http://uniprot.org/P4543, it could be 1) a meaningless concept identifier in an ontology 2) a URL which resolves to a pretty web page, via a single step process 3)

Re: identifier to use

> "DS" == "Booth, David (HP Software <- Boston)" <[EMAIL PROTECTED]>> > writes: >> From: Phillip Lord [ . . . ] I don't understand the desire to implement >> everything using HTTP. Why call lots of things, which are actually >> several protocols by a name which suggests that they a

Re: identifier to use

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Phillip Lord wrote: >> I don't understand the desire to implement everything using HTTP. EJ> Likewise, I don't understand the desire to implement everything using EJ> anything but HTTP :-) If there is an existing system that is EJ

RE: identifier to use

> From: Phillip Lord > [ . . . ] > I don't understand the desire to implement everything using > HTTP. Why call lots of things, which are actually several > protocols by a name which suggests that they are all one. How > to distinguish between an HTTP URI which allows you to do > location independ

Re: identifier to use

Phillip Lord wrote: I don't understand the desire to implement everything using HTTP. Likewise, I don't understand the desire to implement everything using anything but HTTP :-) If there is an existing system that is (incredibly) widely adopted and that can be built upon, surely that's the w

Re: identifier to use

Bijan Parsia wrote: [...] the turning of the screw is slower [...] Well that's great comfort :-)

Re: identifier to use

Hilmar Lapp wrote: Yeah, because they are URLs. But don't almost all of the databases you have listed there use identifiers (accession numbers, etc) for identifying their objects? I wish :-) Some databases are just a bunch of static web pages, and many like to use something nice like gene n

Re: identifier to use

On Aug 23, 2007, at 11:18 AM, Eric Jain wrote: Almost no database, data center, or publisher uses HTTP URIs for identifying their digital objects, and stable HTTP URIs at present aren't adopted or the common denominator for identifying digital objects in the life science domain either.

Re: identifier to use

Hilmar Lapp wrote: I'm not sure what you mean by "closed archive." If the UniProt consortium decided to set up an archive for all their data, that's what I mean by "closed". Obviously much easier than getting the entire life sciences community to agree on implementing one scheme :-) Almos

Re: identifier to use

> "BP" == Bijan Parsia <[EMAIL PROTECTED]> writes: BP> On 23 Aug 2007, at 14:12, Phillip Lord wrote: >> >> If you loose a trademark BP> Trademark *suit*. I.e., you are infringing on someone else's trademark. >> and have to stop using identifiers with a "uniprot" in them, then any

Re: identifier to use

On 23 Aug 2007, at 14:12, Phillip Lord wrote: "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: [snip] EJ> Note that any other name-based registration system could run into EJ> trouble, too: Let's say UniProt lost a trademark suite and was forced to EJ> change its name to something else,

Re: identifier to use

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Do you mean fail over at run time, so when an identifier can't be EJ> resolved, the resolver retries with a backup service? Hilmar described the mechanism in his last email. Again, perhaps I am wrong. EJ> In general, my feeling is t

Re: identifier to use

On Aug 23, 2007, at 9:58 AM, Eric Jain wrote: Digital archives will use opaque identifier systems that aren't HTTP URIs whether the W3C likes it or not - they look at time horizons beyond our lifetimes, when HTTP may not even exist anymore. The need for GUIDs existed before HTTP URIs and

Re: identifier to use

Hilmar Lapp wrote: Digital archives will use opaque identifier systems that aren't HTTP URIs whether the W3C likes it or not - they look at time horizons beyond our lifetimes, when HTTP may not even exist anymore. The need for GUIDs existed before HTTP URIs and will continue to exist afterward

Re: identifier to use

Hilmar Lapp wrote: That said, I'm thinking that maybe that doesn't need to have any bearing on how resources are identified on the semantic web. This is the point. Many identifiers, like ISBN, SSN, Passport Number, license plate doesn't have any bearing on the web. So, it doesn't have to use

Re: identifier to use

Hilmar Lapp wrote: You don't mind that the others on the list are as lazy? There are entire papers about this topic in information science journals, and I'm not sure we want to repeat these here (read: I'm lazy and don't want to repeat these here ...). If I was familiar with one of these sys

Re: identifier to use

On Aug 23, 2007, at 8:19 AM, Eric Jain wrote: As far as I can see, LSIDs are basically location independent. The only whole I can see is if someone else buys uniprot.org, sets up an LSID resolution service and then returns crap. purls have the same issue I think. Yes, I guess that's a pr

Re: identifier to use

Phillip Lord wrote: As I understand it, there is a fail over mechanism. If uniprot.org falls over, the first resolution step can be performed by an LSID server not at uniprot.org. I can't remember exactly how this works, as I haven't read the spec for ages. As far as I can see, LSIDs are basi

Re: identifier to use

On Aug 23, 2007, at 8:21 AM, Eric Jain wrote: Phillip Lord wrote: Eric, trying putting "digital preservation" into google. There many projects out there working in this area. I know, but I'm not very familiar with any of these projects, and, being lazy, hoped that someone who follows th

Re: identifier to use

Phillip Lord wrote: Eric, trying putting "digital preservation" into google. There many projects out there working in this area. I know, but I'm not very familiar with any of these projects, and, being lazy, hoped that someone who follows this list might be and could comment.

Re: identifier to use

Phillip Lord wrote: As I understand it, there is a fail over mechanism. If uniprot.org falls over, the first resolution step can be performed by an LSID server not at uniprot.org. I can't remember exactly how this works, as I haven't read the spec for ages. Do you mean fail over at run time,

Re: identifier to use

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: >> These archives will all need to use opaque identifiers to track >> relationships, provenance, versions, and other metadata. EJ> The only digital archive project I'm vaguely familiar with is the EJ> Internet Archive project, and that

Re: identifier to use

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> Phillip Lord wrote: >> Actually, LSIDs are domain specific, or rather they were designed to >> support the needs of the Life Sciences; this is not to say that different >> domains do not have the same needs. EJ> You're right, that

Re: identifier to use

Hilmar Lapp wrote: In the LSID resolver spec resolution doesn't depend on the authority domain name. Neither does the HTTP URI scheme: You can set up common HTTP proxy software to reroute HTTP requests (if you don't want to do application-level rewriting). I don't quite see how that's less e

Re: identifier to use

Hilmar Lapp wrote: I just don't understand the relevance the current usage stats of DOIs in UniProt queries should have for how and in which ways they may be used in the Semantic Web in 3 years from now. I understood that the apparent success of the DOI system was being used as an argument t

Re: identifier to use

On Aug 22, 2007, at 9:57 AM, Eric Jain wrote: Note: While most publishers seem to have adopted the DOI system, I don't see many people using it (e.g. in queries) on our site. But if someone who works for a publisher is lurking, they might have better usage stats! I'm don't want to come

RE: identifier to use

> From: Hilmar Lapp > [ . . . ] > In the LSID resolver spec resolution doesn't depend on the authority > domain name. Just so you're aware, the *exact* same thing can be achieved with HTTP URIs, as described here: http://dbooth.org/2006/urn2http/ For example, given the URI > http://entrez.exam

Re: identifier to use

On Aug 22, 2007, at 1:37 PM, Eric Jain wrote: If I have an LSID like urn:lsid:uniprot.org:uniprot:P12345 and uniprot.org disappears (assuming there was even a resolver running there in the first place), how is that URI going to be more useful than a simple HTTP URL In the LSID resolver

Re: identifier to use

Phillip Lord wrote: Actually, LSIDs are domain specific, or rather they were designed to support the needs of the Life Sciences; this is not to say that different domains do not have the same needs. You're right, that's a better way to put it! Look at DOIs and LSIDs. They are different, th

Re: identifier to use

> "EJ" == Eric Jain <[EMAIL PROTECTED]> writes: EJ> I guess that could happen... Do you have some examples of EJ> domain-specific standards that became de-facto standards, supported by EJ> generic tools etc? The web leaps to mind. Remember that? >> As for being limited to a domain

Re: identifier to use

Hilmar Lapp wrote: Right. That was one of the problems that was faced when the I3C consortium started (namely multiple identifier systems with idiosyncratic translation rules to convert to a resolvable URL), and which it tries to address by unifying the identifier and resolution schemes. Gr

Re: identifier to use

Hilmar, It seems to me that domain-specific resolution systems are rather a fact and we deal with them all the time. This is what we try to avoid. The reasoning should not be: Oh, we should use it because it is already there. The reasoning should be: would it be better if we do it in another

Re: identifier to use

Hi - I'm new to this whole discussion, and I'm relatively naive so please forgive me if what I'll say sounds terribly stupid. I also apologize in advance if I seem to be reiterating points that have long been settled - again I've just started to watch this forum recently. On Aug 21, 200

Re: identifier to use

On Aug 21, 2007, at 1:39 PM, Eric Jain wrote: Hilmar Lapp wrote: It seems to me that domain-specific resolution systems are rather a fact and we deal with them all the time. We try to deal with it, but it's a pain, even though the number of different systems I need to deal with is limited

Re: identifier to use

Hilmar Lapp wrote: It seems to me that domain-specific resolution systems are rather a fact and we deal with them all the time. We try to deal with it, but it's a pain, even though the number of different systems I need to deal with is limited compared to someone who is developing applicatio