[Tdwg-guid] Simple LSID resolver
Roger Hyam
roger at tdwg.org
Thu Jun 15 16:15:11 CEST 2006
Great stuff Rod.
Roger
Roderic Page wrote:
> 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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>>>
>> -----------------------------------------------------------------------
>> -
>> ----------------------------------------
>> 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
>
>
--
-------------------------------------
Roger Hyam
Technical Architect
Taxonomic Databases Working Group
-------------------------------------
http://www.tdwg.org
roger at tdwg.org
+44 1578 722782
-------------------------------------
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