[Tdwg-guid] Simple LSID resolver
Roderic Page
r.page at bio.gla.ac.uk
Mon Jun 19 09:05:35 CEST 2006
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 at 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:
> >
> > 1. An LSID with authority example.org need not be handled by
> > example.org. For example, ipni.org resolves to
> > http://beta.ipni.org:9090
> >
> > 2. 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).
> >
> > 3. 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 at 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 at bio.gla.ac.uk
> >>>> web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> >>>> 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 at 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 at 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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> >>
> >>
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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 at 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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> > TDWG-GUID at 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 at 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 at mailman.nhm.ku.edu
> http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> +++++
> WARNING: This email and any attachments may be confidential and/or
> privileged. They are intended for the addressee only and are not to
> be read,
> used, copied or disseminated by anyone receiving them in error. If
> you are
> not the intended recipient, please notify the sender by return email
> and
> delete this message and any attachments.
>
> The views expressed in this email are those of the sender and do not
> necessarily reflect the official views of Landcare Research.
>
> Landcare Research
> http://www.landcareresearch.co.nz
>
> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> +++++
>
>
------------------------------------------------------------------------
----------------------------------------
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 at 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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