[Tdwg-guid] Simple LSID resolver [ Scanned for viruses ]
Roderic Page
r.page at bio.gla.ac.uk
Mon Jun 19 10:02:13 CEST 2006
Dear Paul,
On 19 Jun 2006, at 08:12, Paul Kirk wrote:
> lsid.ipni.org doesn't ping either ... ;-)
That's OK because IPNI's LSIDs resolve to beta.ipni.org:9090
>
> first I've heard of a requirement for a 'subdomain'
> lsid.indexfungorum.org ... do I need to set one up?
Yes, but only because that's what the SRV record for indexfungorum.org
LSIDs points to. You don't need to set up a subdomain as part of the
standard, but that's how IndexFungorum has been set up (apparently).
Regards
Rod
>
> Paul
>
> -----Original Message-----
> From: tdwg-guid-bounces at mailman.nhm.ku.edu
> [mailto:tdwg-guid-bounces at mailman.nhm.ku.edu]On Behalf Of Roderic Page
> Sent: 19 June 2006 08:06
> To: Kevin Richards
> Cc: tdwg-guid at mailman.nhm.ku.edu
> Subject: Re: [Tdwg-guid] Simple LSID resolver [ Scanned for viruses ]
>
>
> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
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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
>>>>
>>>>
>>>>
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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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>> ----------------------------------------------------------------------
>> -
>> -
>> ----------------------------------------
>> 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
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>> +
>> +++++
>> 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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------------------------------------------------------------------------
----------------------------------------
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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