[Tdwg-guid] Simple LSID resolver
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@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
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@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@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
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@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@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@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
Rod, Steve, and all, Are you aware that biopathways.org already provides most of the features of an HTTP GET LSID proxy you are discussing here? See: http://lsid.biopathways.org/resolver/weblinks.shtml ||http://lsid.biopathways.org/resolver/metadata/urn:lsid:indexfungorum.org:Nam... |http://lsid.biopathways.org/resolver/data/urn:lsid:indexfungorum.org:Names:2... ||http://lsid.biopathways.org/resolver/|urn:lsid:indexfungorum.org:Names:213645 |http://lsid.biopathways.org/resolver/image/|urn:lsid:indexfungorum.org:Names:213645 The first link above returns unprocessed metadata for machines to consume it. The second link provides data, and the third gives the usual human readable (html) version of the metadata call. The last one is a goodie: it renders the metadata RDF graph as an image. If you don't like the path after the resolver, that can be easily fixed by tweaking the web server configuration, but then you loose the ability to choose between metadata or data. Maybe one could have data.lsidres.org or metadata.lsidres.org, but that looks really ugly!!! I don't think that that resolver provides the getAuthorityInfo method Steve mentioned, but I'm sure it can be easily added if we think it is an important feature. Not sure if you guys noticed that functionality already existed or you are suggesting something I did not understand. In any case, I think this thread raised an important issue of setting up HTTP GET proxies for LSID. Regards, Ricardo 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@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@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
_______________________________________________ TDWG-GUID mailing list TDWG-GUID@mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid
Sorry but Mozilla Thunderbird just messed up the links from my previous message. Here are the correct links (hopefully): http://lsid.biopathways.org/resolver/metadata/urn:lsid:indexfungorum.org:Nam... http://lsid.biopathways.org/resolver/data/urn:lsid:indexfungorum.org:Names:2... http://lsid.biopathways.org/resolver/urn:lsid:indexfungorum.org:Names:213645 http://lsid.biopathways.org/resolver/image/urn:lsid:indexfungorum.org:Names:... The link to data seems to be broken. Cheers, Ricardo
participants (3)
-
Ricardo Scachetti Pereira -
Roderic Page -
Steven Perry