June 2006 - tdwg-tag - lists.tdwg.org

Re: [Tdwg-guid] Simple LSID resolver
by Kevin Richards 18 Jun '06

18 Jun '06

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(a)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(a)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(a)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(a)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(a)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(a)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 >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> + >> +++++ >> >> >> >> > ----------------------------------------------------------------------- > - > ---------------------------------------- > 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(a)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(a)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(a)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(a)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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Re: [Tdwg-guid] Throttling searches
by Chuck Miller 15 Jun '06

15 Jun '06

Sally, I don't think it's a problem. GBIF/DIGIR currently enables providers to limit the size of query responses. It's not impolite to impose limits on a public query interface. Without a limit, your provider service could become overloaded and inaccessible to everyone. So making tradeoffs like this should be understandable and acceptable to all. The fallback for the query user would be to contact the provider directly and make a special request. Making the provider contact information more visible might help in enabling a fallback for this tradeoff. Chuck -----Original Message----- From: Sally Hinchcliffe [mailto:S.Hinchcliffe@kew.org] Sent: Thursday, June 15, 2006 6:08 AM To: tdwg-guid(a)mailman.nhm.ku.edu Subject: [Tdwg-guid] Throttling searches Hi all another question that has come up here. As discussed at the meeting, we're thinking of providing a complete download of all IPNI LSIDs plus a label (name and author, probably) which will be available as an annually produced download Most people will play nice and just resolve one or two LSIDs as required, but by providing a complete list, we're making it very easy for someone to write a crawler that hits every LSID in turn and basically brings our server to its knees Anybody know of a good way of enforcing more polite behaviour? We can make the download only available under a data supply agreement that includes a clause limiting hit rates, or we could limit by IP address (but this would ultimately block out services like Rod's simple resolver). I beleive Google's spell checker uses a key which has to be passed in as part of the query - obviously we can't do that with LSIDs Any thoughts? Anyone think this is a problem? Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid

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[Tdwg-guid] Simple LSID resolver
by Roderic Page 15 Jun '06

15 Jun '06

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(a)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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Re: [Tdwg-guid] Simple LSID resolver
by Roderic Page 15 Jun '06

15 Jun '06

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(a)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(a)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(a)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(a)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(a)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 > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > +++++ > > > > ------------------------------------------------------------------------ ---------------------------------------- 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(a)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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Re: [Tdwg-guid] Simple LSID resolver
by Kevin Richards 15 Jun '06

15 Jun '06

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(a)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(a)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(a)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(a)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(a)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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[Tdwg-guid] Throttling searches
by Sally Hinchcliffe 15 Jun '06

15 Jun '06

Hi all another question that has come up here. As discussed at the meeting, we're thinking of providing a complete download of all IPNI LSIDs plus a label (name and author, probably) which will be available as an annually produced download Most people will play nice and just resolve one or two LSIDs as required, but by providing a complete list, we're making it very easy for someone to write a crawler that hits every LSID in turn and basically brings our server to its knees Anybody know of a good way of enforcing more polite behaviour? We can make the download only available under a data supply agreement that includes a clause limiting hit rates, or we could limit by IP address (but this would ultimately block out services like Rod's simple resolver). I beleive Google's spell checker uses a key which has to be passed in as part of the query - obviously we can't do that with LSIDs Any thoughts? Anyone think this is a problem? Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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Re: [Tdwg-guid] Some questions re metadata tags [ Scanned for viruses ]
by Paul Kirk 15 Jun '06

15 Jun '06

there is more than one reason why a record might be 'suppressed' - should this be indicated? IF currently supresses three types of record: 1. orthographic variants (one to many) 2. deprecated records (either absolute duplicates or keyboarding/OCR/other 'duplicates') 3. unpublished names (e.g. from 'herbarium' specimens or BRCs (a.k.a. culture collection) all these have a 'isReplacedBy' pointer ... Paul -----Original Message----- From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu]On Behalf Of Sally Hinchcliffe Sent: 15 June 2006 11:43 To: tdwg-guid(a)mailman.nhm.ku.edu Subject: [Tdwg-guid] Some questions re metadata tags [ Scanned for viruses ] Hi all Having gone through my notes from GUIDs 2 I realise we need a couple of tags in the IPNI metadata - any suggestions for what would be a good standard term to use? We need something to tag version, and something to indicate that a record has been suppressed (rather than just reporting 'not found') We will use Darwin Core's 'isReplacedBy' for records that have been suppressed in favour of another record Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk _______________________________________________ TDWG-GUID mailing list TDWG-GUID(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid

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[Tdwg-guid] Some questions re metadata tags
by Sally Hinchcliffe 15 Jun '06

15 Jun '06

Hi all Having gone through my notes from GUIDs 2 I realise we need a couple of tags in the IPNI metadata - any suggestions for what would be a good standard term to use? We need something to tag version, and something to indicate that a record has been suppressed (rather than just reporting 'not found') We will use Darwin Core's 'isReplacedBy' for records that have been suppressed in favour of another record Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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[Tdwg-guid] IPNI LSID server will not be available for a couple of weeks
by Sally Hinchcliffe 13 Jun '06

13 Jun '06

Hi all - a bit of advanced notice Due to electrical work, one of our IPNI servers will be unavailable for a couple of weeks starting from the 24th June. As our beta site (including the LSID server) runs on this machine, that will mean that the LSID server will not be available during this time. Sally *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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Re: [Tdwg-guid] Ant demo [SEC=UNCLASSIFIED]
by Levy, David 12 Jun '06

12 Jun '06

Hi Rob, I've been working with Google maps for about 2 months now and have an workable demo going too. I'm currently talking with my project manager about changing the way the site works, but thought you might enjoy having a look at it. Some notable bits of functionality you may be interested in: - Implemented my own "Tile Server" to show points on the map; this was to get around the issue of showing many points with Google's GMarker and the page pretty much stopping moving; I found result sets as low as a few hundred caused performance issues, but the Tile server keeps on working with millions of points - Implemented bounding box functionality for searches (still has some bugs though) The URL is over here - but is currently in testing mode and is up and down like a yo-yo http://203.36.88.39:8080/AbifSpecimenSearch/gui/main.html As mentioned, the interface should be having an overhaul over the next few weeks, but the essential mapping functionality will remain. Implementing my own tile server was really worthwhile and probably one of the only ways to show so many points on the map - the other realistic option is to hook into a WMS (which I still may do to get some extra features on the map). Currently, the map displays all known specimens (400K) and then reduces this when a search filter is applied. Again, the usability of this is a bit backwards so will probably make it so the results aren't display until a search filter is created. I guess I was just happy to show my project manager that I could render all the points we had: ) I'll try find some time to write up a blog on the tile server functionality, there were three main areas which I had to get over to do it and are happy to pass on the knowledge: 1.) Creating a tile layer in Google Maps (pretty easy, but getting it to refresh when the data changes is suprisingly difficult) 2.) Using the mathematics of Mercator projection to adjust my points latitudes on to the grids - this was mainly backwards engineering Google's FromPixelToLatLng methods + also understanding the way points get put into tiles 3.) Finding a nice Java graphics library to do the rendering (ended up with the standard Java 2D API) Each one of the steps above presented a little bit of a challenge, but was doable after some thought. If there is sufficient interest I'll write up those 3 challenges above in a blog format. Cheers, David Levy ABIF Portal Developer -----Original Message----- From: Lawrence, Robyn Sent: Tuesday, 13 June 2006 8:38 AM To: Levy, David Subject: FW: [Tdwg-guid] Ant demo [SEC=UNCLASSIFIED] Hi David, Here is a system that some-one has done on ants using Google Maps. I found matches on the following Genus. Gnamptogenys They do the sort of maps you do, I thought you might be interested. May be you could also discuss with him the API problem. Robyn -----Original Message----- From: tdwg-guid-bounces(a)mailman.nhm.ku.edu [mailto:tdwg-guid-bounces@mailman.nhm.ku.edu] On Behalf Of Roderic Page Sent: Friday, 9 June 2006 11:52 PM To: tdwg-guid(a)mailman.nhm.ku.edu Cc: Simon Rycroft; Vince Smith; Donat Agosti Subject: [Tdwg-guid] Ant demo I've set up a half-functioning demo of the ant triple store here: http://linnaeus.zoology.gla.ac.uk/~rpage/ants/ It is not complete, and there's a problem with Google's Map API, but it's a start. I'll be demoing it at the workshop, but thought it would be useful to have a version other people could see. Hopefully after the demo it will make more sense... To get started, the search box accepts text (such as the name of an ant), or a GUID. Try, for example, Atta Proceratium Dracula doi:10.1016/j.ympev.2004.06.017 urn:lsid:ncbi.nlm.nih.gov.lsid.zoology.gla.ac.uk:gi:34398464 I've updated the relevant page on the TDWG-GUID wiki (http://wiki.gbif.org/guidwiki/wikka.php? wakka=LSIDBasedIntegrationAntsDemo), but more useful background is on my blog: http://semant.blogspot.com/. 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: 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(a)mailman.nhm.ku.edu http://mailman.nhm.ku.edu/mailman/listinfo/tdwg-guid If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments.

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