[Tdwg-guid] Simple LSID resolver
Kevin Richards
RichardsK at landcareresearch.co.nz
Mon Jun 19 00:54:45 CEST 2006
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
>
>
>
> _______________________________________________
> 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
_______________________________________________
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
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