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Great stuff Rod.<br>
<br>
Roger<br>
<br>
<br>
<br>
Roderic Page wrote:
<blockquote cite="midf77549980fa9b2faca0be9cdc4dca10f@bio.gla.ac.uk"
type="cite">
<pre wrap="">OK, I've grabbed lsidres.org, so to resolve a LSID straight to
metadata, stick <a class="moz-txt-link-freetext" href="http://lsidres.org">http://lsidres.org</a> in front of the LSID, e.g.:
urn:lsid:lsid.zoology.gla.ac.uk:predicates:objectiveSynonym
becomes
<a class="moz-txt-link-freetext" href="http://lsidres.org/urn:lsid:lsid.zoology.gla.ac.uk:predicates:">http://lsidres.org/urn:lsid:lsid.zoology.gla.ac.uk:predicates:</a>
objectiveSynonym
and
urn:lsid:ubio.org:namebank:2735664
becomes
<a class="moz-txt-link-freetext" href="http://lsidres.org/urn:lsid:ubio.org:namebank:2735664">http://lsidres.org/urn:lsid:ubio.org:namebank:2735664</a>
So now, it's as easy as DOIs...
Regards
Rod
On 15 Jun 2006, at 11:56, Roderic Page wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
<a class="moz-txt-link-freetext" href="http://beta.ipni.org:9090">http://beta.ipni.org:9090</a>
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
<a class="moz-txt-link-freetext" href="http://dx.doi.org">http://dx.doi.org</a>, and it's resolved.
Regards
Rod
On 15 Jun 2006, at 10:32, Kevin Richards wrote:
</pre>
<blockquote type="cite">
<pre wrap="">The theory is that most lsid resolvers/authorities will implement the
http get protocol for resolving lsids.
This means that:
<a class="moz-txt-link-freetext" href="http://example.org/authority/?lsid=urn:lsid">http://example.org/authority/?lsid=urn:lsid</a>.... will return the wsdl
equivalent to the getAvailableServices SOAP call
<a class="moz-txt-link-freetext" href="http://example.org/authority/data/?lsid=urn:lsid">http://example.org/authority/data/?lsid=urn:lsid</a>... will return the
data
for that lsid
<a class="moz-txt-link-freetext" href="http://example.org/authority/metadata/?lsid=urn:lsid">http://example.org/authority/metadata/?lsid=urn:lsid</a>... will return
the
metadata for that lsid
so why not just use these urls if you want to use urls?
Kevin
</pre>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Roderic Page <a class="moz-txt-link-rfc2396E" href="mailto:r.page@bio.gla.ac.uk"><r.page@bio.gla.ac.uk></a> 06/15/06 10:13 AM >>>
</pre>
</blockquote>
</blockquote>
</blockquote>
<pre wrap="">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
<a class="moz-txt-link-freetext" href="http://www.connotea.org/rss/recent/user/rdmpage?q=Formicidae">http://www.connotea.org/rss/recent/user/rdmpage?q=Formicidae</a> (an RSS
feed).
Not elegant, but simple.
Regards
Rod
On 14 Jun 2006, at 17:07, Steven Perry wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">returning an HTTP status code like 204 (NO_CONTENT), 404 (NOT_FOUND),
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">sends through HTTP and it tries to set the correct mime type.
However getMetadata is the critical function and these others may
not,
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">upon more reflection, make much sense.
Given that we want to be able to integrate with existing semantic web
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<blockquote type="cite">
<pre wrap="">TAG.
-Steve
Roderic Page wrote:
</pre>
<blockquote type="cite">
<pre wrap="">It was good to see everybody who made it to sunny Edinburgh over the
</pre>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">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 <a class="moz-txt-link-freetext" href="http://lsid.zoology.gla.ac.uk/">http://lsid.zoology.gla.ac.uk/</a>,
e.g.
<a class="moz-txt-link-freetext" href="http://lsid.zoology.gla.ac.uk/urn:lsid:ubio.org:namebank:2735664">http://lsid.zoology.gla.ac.uk/urn:lsid:ubio.org:namebank:2735664</a>
<a class="moz-txt-link-freetext" href="http://lsid.zoology.gla.ac.uk/urn:lsid:lsid.zoology.gla.ac.uk:">http://lsid.zoology.gla.ac.uk/urn:lsid:lsid.zoology.gla.ac.uk:</a>
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
</pre>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap=""> aggregate the RDF for a LSID you could use this to do the
resolution
</pre>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap=""> for you.
Regards
Rod
</pre>
</blockquote>
</blockquote>
<pre wrap="">----------------------------------------------------------------------
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">-- ----------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a>
web: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a>
reprints: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/pubs.html">http://taxonomy.zoology.gla.ac.uk/rod/pubs.html</a>
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Search for taxon names:
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</blockquote>
</blockquote>
<pre wrap=""><a class="moz-txt-link-freetext" href="http://darwin.zoology.gla.ac.uk/~rpage/portal/">http://darwin.zoology.gla.ac.uk/~rpage/portal/</a>
</pre>
<blockquote type="cite">
<blockquote type="cite">
<pre wrap="">Find out what we know about a species: <a class="moz-txt-link-freetext" href="http://ispecies.org">http://ispecies.org</a>
Rod's rants on phyloinformatics: <a class="moz-txt-link-freetext" href="http://iphylo.blogspot.com">http://iphylo.blogspot.com</a>
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</blockquote>
<pre wrap="">
</pre>
</blockquote>
<pre wrap="">----------------------------------------------------------------------
-
-
----------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a>
web: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a>
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Find out what we know about a species: <a class="moz-txt-link-freetext" href="http://ispecies.org">http://ispecies.org</a>
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<pre wrap="">-----------------------------------------------------------------------
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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: <a class="moz-txt-link-abbreviated" href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a>
web: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a>
iChat: aim://rodpage1962
reprints: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/pubs.html">http://taxonomy.zoology.gla.ac.uk/rod/pubs.html</a>
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Find out what we know about a species: <a class="moz-txt-link-freetext" href="http://ispecies.org">http://ispecies.org</a>
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</blockquote>
<pre wrap=""><!---->------------------------------------------------------------------------
----------------------------------------
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: <a class="moz-txt-link-abbreviated" href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a>
web: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a>
iChat: aim://rodpage1962
reprints: <a class="moz-txt-link-freetext" href="http://taxonomy.zoology.gla.ac.uk/rod/pubs.html">http://taxonomy.zoology.gla.ac.uk/rod/pubs.html</a>
Subscribe to Systematic Biology through the Society of Systematic
Biologists Website: <a class="moz-txt-link-freetext" href="http://systematicbiology.org">http://systematicbiology.org</a>
Search for taxon names: <a class="moz-txt-link-freetext" href="http://darwin.zoology.gla.ac.uk/~rpage/portal/">http://darwin.zoology.gla.ac.uk/~rpage/portal/</a>
Find out what we know about a species: <a class="moz-txt-link-freetext" href="http://ispecies.org">http://ispecies.org</a>
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<br>
<br>
<pre class="moz-signature" cols="72">--
-------------------------------------
Roger Hyam
Technical Architect
Taxonomic Databases Working Group
-------------------------------------
<a class="moz-txt-link-freetext" href="http://www.tdwg.org">http://www.tdwg.org</a>
<a class="moz-txt-link-abbreviated" href="mailto:roger@tdwg.org">roger@tdwg.org</a>
+44 1578 722782
-------------------------------------
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