Re: [Tdwg-guid] Simple LSID resolver
Ricardo notes that I've duplicated what Biopathways.org already provides (albeit with the use longer URLs). However, there are a couple of reasons for persisting in this. Firstly, I like short URLs. Secondly, I find having another implementation (and one that I can play with) to be useful.
For example, Biopathways.org caches the metadata, so the links given by Ricardo work. I don't cache the metadata, and hence discover that the IndexFungorum LSID authority seems broken. The LSID resolves to host lsid.indexfungorum.org:8080, but if I ping lsid.indexfungorum.org I get nothing back, and my LSID resolver eventually fails with HTTP 504.
What I think would be nice is to return metadata with a XSLT style sheet, so that the browser displays nice HTML, but view-source displays XML (which is also what a script would get), so that it supports both people and machines. For an example of this, see the handle demo for a paper on ants (http://hdl.handle.net/2254/20791) and view the source.
Lastly, I need a LSID client for my ant stuff, so developing the resolver helps me debug this code.
Regards
Rod
On 18 Jun 2006, at 23:54, Kevin Richards wrote:
Ok, I think I see where you are coming from now. You want a URL that you can prepend to ANY LSID to resolve the metadata for it, without having to go through any of the standard resolution steps. In theory the correct way to do this is as I suggested - resolve the authority name to get the urls to use, eg resolve urn:lsid:example.org:... to get the metadata and data url addresses (I wasnt assuming just using port 80 at the domain name specified in the LSID). But if you dont want to use any resolution (ie you must be doing somehting like a search and replace of all LSIDs in a document?) then you will need a static url that will resolve any LSID, as you have suggested. In this case I think it is a great idea, and will be interested to see some use cases/examples in action for where you need to do this, and normal resolution cannot be used. Kevin
Roderic Page r.page@bio.gla.ac.uk 15/06/2006 11:20 p.m. >>>
OK, I've grabbed lsidres.org, so to resolve a LSID straight to metadata, stick http://lsidres.org in front of the LSID, e.g.:
urn:lsid:lsid.zoology.gla.ac.uk:predicates:objectiveSynonym
becomes
http://lsidres.org/urn:lsid:lsid.zoology.gla.ac.uk:predicates: objectiveSynonym
and
urn:lsid:ubio.org:namebank:2735664
becomes
http://lsidres.org/urn:lsid:ubio.org:namebank:2735664
So now, it's as easy as DOIs...
Regards
Rod
On 15 Jun 2006, at 11:56, Roderic Page wrote:
Dear Kevin,
The reasons against doing what you suggest (which I agree works in
most
cases) are:
- An LSID with authority example.org need not be handled by
example.org. For example, ipni.org resolves to http://beta.ipni.org:9090
- You're assuming that we're all going to use port 80, whereas some
may serve metadata and data over a different port (e.g., IPNI use 9090).
- I feel having a standard prefix before the LSID that remains the
same makes it easier for people to remember (i.e., we don't have to think, "gee, so what bit of the LSID to I extract, and what was that mumbo jumbo I stick on the end?"). Probably we should make it even simpler by grabbing a short domain name to make it even easier. Remember, DOIs make it simple - just tack the DOI onto the end of http://dx.doi.org, and it's resolved.
Regards
Rod
On 15 Jun 2006, at 10:32, Kevin Richards wrote:
The theory is that most lsid resolvers/authorities will implement
the
http get protocol for resolving lsids. This means that:
http://example.org/authority/?lsid=urn:lsid.... will return the wsdl equivalent to the getAvailableServices SOAP call
http://example.org/authority/data/?lsid=urn:lsid... will return the data for that lsid
http://example.org/authority/metadata/?lsid=urn:lsid... will return the metadata for that lsid
so why not just use these urls if you want to use urls?
Kevin
Roderic Page r.page@bio.gla.ac.uk 06/15/06 10:13 AM >>>
Dear Steve,
It's written in PHP, and is basically a cleaner version of the LSID test. I developed it on my iBook running Apache and PHP 4.3.10, and deployed it on Fedora Core 4 with PHP 5. I've not tested it on Windows,
the issue would be whether the Net:DNS module I use to do the resolution also works on Windows (who in their right mind uses
Windows
as a server ;-)
Yep, the error reporting is bad, but I could work on this. It tries
to
trap some errors and report them in XML, but I put it together when
I
should have been listening to the talks at GUID2, so it's a bit
rough
and ready.
Having a HTTP GET service sounds like a good idea, if it helps
people
play with this stuff. Maybe it could be as simple as a convention
that
if the "LSID" lacks a namespace and id (i.e., is just the authority) the service returns metadata about the authority. For data, perhaps the
prefix "data" could be inserted before the LSID, rather like a lot
of
static URLs have the format of the data embedded in them, such as http://www.connotea.org/rss/recent/user/rdmpage?q=Formicidae (an RSS feed).
Not elegant, but simple.
Regards
Rod
On 14 Jun 2006, at 17:07, Steven Perry wrote:
Hi Rod,
This is pretty cool. What language is it in? What kind of server does it require (application server, apache, etc.)? When I tried to put in an LSID that I knew didn't exist, I got an
XML
parsing error. No worries, since this is an early prototype, but I was wondering if you're planning on trapping these kinds of errors and
returning an HTTP status code like 204 (NO_CONTENT), 404
(NOT_FOUND),
or 410 (GONE), or if you had something else in mind.
I've also been thinking about an HTTP-GET based LSID resolution gateway that might be exposed as a service. It could support
several
additional functions besides (the default) getMetadata():
getAuthorityInfo :: given an LSID, return information (in RDF)
about
the authority extracted from the authority metadata getData:: might work a bit differently from the spec in that it always
sends through HTTP and it tries to set the correct mime type.
However getMetadata is the critical function and these others may not,
upon more reflection, make much sense.
Given that we want to be able to integrate with existing semantic
web
apps and tools that can't currently understand the LSID resolution process, I think we'll come to depend upon these kinds of services. They also provide convenience to developers who are working with languages that don't yet have a resolution client API. It might be nice to work out how such a service ought to behave and present it
to
TAG.
-Steve
Roderic Page wrote:
It was good to see everybody who made it to sunny Edinburgh over
the
weekend.
I've put together a very simple LSID resolver that returns RDF metadata for a LSID. I wanted something very simple, so all you
do
is stick your LSID on the end of http://lsid.zoology.gla.ac.uk/, e.g.
http://lsid.zoology.gla.ac.uk/urn:lsid:ubio.org:namebank:2735664
http://lsid.zoology.gla.ac.uk/urn:lsid:lsid.zoology.gla.ac.uk: predicate:isBasionymOf
It's far from bullet proof, and not as pretty as other resolvers. However, it means you see the RDF straight away, and if you
wanted
to
aggregate the RDF for a LSID you could use this to do the resolution
for you.
Regards
Rod
Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom
Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
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Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom
Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names:
http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com
TDWG-GUID mailing list TDWG-GUID@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
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Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom
Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names:
http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com
TDWG-GUID mailing list TDWG-GUID@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom
Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com
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The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research.
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------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom
Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page@bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html iChat: aim://rodpage1962 reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html
Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com
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