[tdwg-tag] LSIDs: web based (HTTP) resolvers and web crawlers
Roger Hyam
rogerhyam at mac.com
Fri May 1 10:39:49 CEST 2009
I wish I could keep out of this debate but...
Linked data approach is an order of magnitude simpler than LSID and
very easy to layer on top of an existing LSID authority - you already
have a RDF metadata response you just need the redirect URL which can
be implemented in the Apache or IIS config or a very simple script.
It doesn't have to be only google that caches the metadata it could be
GBIF/EoL or some other party who are interested in caching metadata
from biodiversity suppliers. They could even have a submission
mechanism. So the whole architecture would go:
1) work out how to get your data into RDF (tricky bit we should be
working on as Markus points out - this could even be RDFa in a web
page - anyone for Dreamweaver templates!!)
2) set up a 303 redirect to the RDF metadata. (very easy even on an
ISP hosted domain or corporate internet - unlike messing with SRV
records)
3) tell the world about it (GBIF/EoL can then scrape it and cache it
if the license permits - and the license is in the data)
This approach is totally modular, distributed, loosely coupled and
robust. The data supplier doesn't even need to have a search/browse
function themselves they could just have a submission tool (SiteMap or
RSS feed) and allow GBIF or whoever to supply those services on top.
We handle the social side of "URLs just break" by having
recommendations for how URLs are designed. How about this one:
10.682772.info/specimen/E002719
Does that look enough like a DOI to keep people happy? I could secure
the 682772.info domain for £12.50/year (£125 secures it for the next
10 years at the least). This includes free hosting of scripts to do my
redirection etc. This is a cheeky example but I hope it illustrates
the point that a well designed string can also be a URL. I don't
include the transport protocol just as many quotes of DOIs don't
include the doi: and all those adverts on the bus stops just have
nike.com written on them not http://www.nike.com
There is plenty of room for innovation around this simple model. This
is the most important thing. No strict protocols just enough to let
people add their value. People can develop data hosting and other
tools and packages just as GBIF do today.
Now it is a long weekend for nearly everyone I guess. I must stop
thinking about identifiers!
All the best,
Roger
On 1 May 2009, at 08:41, Peter DeVries wrote:
> Hi Rod,
>
> I am in favor of couchDB based distributed solutions. I just don't
> see how LSID's can
> be justified base on their cost/benefits.
>
> The current LSID's can still be used, but if any group can easily
> make the transition to linked data it would be
> those groups that have already successfully implemented LSID's.
>
> Without the proxy, the providers can work out a caching solution
> that works well for them. The TDWG proxy has
> to cache all lsid requests, not just those for ipini. It probably
> caches less of the ipini data than ipini would.
>
> Also a lot of people use simpler crawlers that may not know how to
> correctly follow LSID proxies.
>
> My .rdf files are cached by Google
>
> Do a Google Search on:
>
> http://species.geospecies.org/specs/Ochlerotatus_triseriatus.rdf
>
> or
>
> http://species.geospecies.org/specs/Culex_pipiens.rdf
>
> The Google cache is not ideal, but it is an accessible alternative
> version. They may be open to making it work
> as a real alternative cache for linked data.
>
> - Pete
>
>
> On Fri, May 1, 2009 at 1:08 AM, Roderic Page <r.page at bio.gla.ac.uk>
> wrote:
> Dear Pete,
>
> On 1 May 2009, at 04:37, Peter DeVries wrote:
>
>> This seems to be another example of how the use of LSID's creates
>> problems and adds
>> costs for data providers.
>
> I'm not sure being hit by the Google bot is due to LSIDs as such. I
> think the problems of LSIDs lie more with the overhead of fussing
> with the DNS SRV (in theory trivial, but in practice not), the need
> for software beyond a web server, and the fact they don't resolve by
> themselves in browsers without proxies (although this hasn't
> hindered DOIs becoming widespread).
>
>
>>
>>
>> It would be much more straight forward to adopt the linked data
>> standards and have this data
>> be available in a widely supported standard.
>>
>> Here is one linked data alternative:
>>
>> http://lod.ipni.org/names/783030-1 <- the entity or
>> concept ... redirects via 303 to either
>> http://lod.ipni.org/names/783030-1.html <- human readable page
>> http://lod.ipni.org/names/783030-1.rdf <- rdf data
>>
>> See
>> http://linkeddata.org/guides-and-tutorials
>>
>> Test with this service
>> http://validator.linkeddata.org/vapour
>
>
> Playing nice with linked data makes sense, but we can do this with
> appropriate proxies. For example, http://validator.linkeddata.org/vapour?vocabUri=http%3A%2F%2Fbioguid.info%2Furn%3Alsid%3Aipni.org%3Anames%3A138762-3&classUri=http%3A%2F%2F&propertyUri=http%3A%2F%2F&instanceUri=http%3A%2F%2F&defaultResponse=dontmind&userAgent=vapour.sourceforge.net
>
> (if link broken in email try http://tinyurl.com/dkl755 )
>
> Given that LSIDs are in the wild (including the scientific
> literature), we need to support them (that's the bugger with
> "persistent" identifiers, once you release them you're stuck with
> them).
>
> That said, I'm guessing that anybody starting a new data providing
> service would be well advised to use HTTP URIs with 303 redirects,
> providing that they got the memo about cool URIs (http://www.w3.org/Provider/Style/URI
> ).
>
>
>>
>> There are other ways to avoid service outages and data replication.
>> Google and others have to deal with this problem everyday.
>>
>> If you want to keep the branding on the identifier you could also
>> do something like this.
>>
>> http://lod.ipni.org/ipni-org_names_783030-1 <- the entity
>> or concept, 303 redirect to either
>> http://lod.ipni.org/ipni-org_names_783030-1.html <- human readable
>> page
>> http://lod.ipni.org/ipni-org_names_783030-1.rdf <- rdf data
>>
>> Couldn't the free and ubiquitous Google cache provide some caching
>> of these normal uri's
>
> Firstly, is there any linked data in the Google cache? If the Google
> bot is harvesting as a web browser, it will get 303 redirects to
> HTML and not the RDF. I've had a quick look for DBPedia RDF in the
> cache and haven't found any.
>
> Secondly, how would I get the cached copy? If I'm doing large-scale
> harvesting, I'll need programatic access to the cache, and that's
> not really possible (especially now that Google's SOAP API is
> deprecated).
>
> Gel jockeys don't expect to have to get GenBank sequences from
> Google's cache because GenBank keeps falling over, so why do we
> expect to have to do this? OK, our situation is different because we
> have distributed data sources, but I'd prefer something like http://www.fak3r.com/2009/04/29/resolving-lsids-wit-url-resolvers-and-couchdb
>
> Regards
>
> Rod
>
>
>
>
>>
>> - Pete
>>
>> On Mon, Apr 27, 2009 at 7:54 AM, Nicola Nicolson <n.nicolson at rbgkew.org.uk
>> > wrote:
>> Hi,
>>
>>
>> Further to my last design question re LSID HTTP proxies (thanks for
>> the responses), I wanted to raise the issue of HTTP LSID proxies
>> and crawlers, in particular the crawl delay part of the robots
>> exclusion protocol.
>>
>>
>> I'll outline a situation we had recently:
>>
>>
>> The GBIF portal and ZipCodeZoo site both inclde IPNI LSIDs in the
>> pages. These are presented in their proxied form using the TDWG
>> LSID resolver (eg http://lsid.tdwg.org/urn:lsid:ipni.org:names:783030-1)
>> . Using the TDWG resolver to access the data for an IPNI LSID does
>> not issue any kind of HTTP redirect, instead the web resolver uses
>> the LSID resolution steps to get the data and presents it in its
>> own response (ie returning a HTTP 200 OK response).
>>
>>
>> The problem happens when one of these sites that includes proxied
>> IPNI LSIDs is crawled by a search engine. The proxied links appear
>> to belong to tdwg.org, so whatever crawl delay is agreed between
>> TDWG and the crawler in question is used. The crawler has no
>> knowledge that behind the scenes the TDWG resolver is hitting
>> ipni.org. We (ipni.org) have agreed our own crawl limits with
>> Google and the other major search engines using directives in
>> robots.txt and directly agreed limits with Google (who don't use
>> the robots.txt directly).
>>
>>
>> On a couple of occasions in the past we have had to deny access to
>> the TDWG LSID resolver as it has been responsible for far more
>> traffic than we can support (up to 10 times the crawl limits we
>> have agreed with search engine bots) - this due to the pages on the
>> GBIF portal and / or zipcodezoo being crawled by a search engine,
>> which in turn triggers a high volume of requests from TDWG to IPNI.
>> The crawler itself has no knowledge that it is in effect accessing
>> data held at ipni.org rather than tdwg.org as the HTTP response is
>> HTTP 200.
>>
>>
>> One of Rod's emails recently mentioned that we need a resolver to
>> act like a tinyurl or bit.ly. I have pasted below the HTTP headers
>> for an HTTP request to the TDWG LSID resolver, and to tinyurl /
>> bit.ly. To the end user it looks as though tdwg.org is the true
>> location of the LSID resource, whereas with the tinyurl and bitly
>> both just redirect traffic.
>>
>>
>> I'm just posting this for discussion really - if we are to mandate
>> use of a web based HTTP resolver/proxies, it should really issue
>> 30* redirects so that established crawl delays between producer and
>> consumer will be used. The alternative would be for the HTTP
>> resolver to read and process the directives in robots.txt, but this
>> would be difficult to implement as it is not in itself a crawler,
>> just a gateway.
>>
>>
>> I'm sure that if proxied forms of LSIDs become more prevalent this
>> problem will become more widespread, so now - with the on-going
>> attempt to define what services a GUID resolver should provide -
>> might be a good time to plan how to fix this.
>>
>>
>> cheers,
>> Nicky
>>
>>
>> [nn00kg at kvstage01 ~]$ curl -I http://lsid.tdwg.org/urn:lsid:ipni.org:names:783030-1
>> HTTP/1.1 200 OK
>> Via: 1.1 KISA01
>> Connection: close
>> Proxy-Connection: close
>> Date: Mon, 27 Apr 2009 11:41:55 GMT
>> Content-Type: application/xml
>> Server: Apache/2.2.3 (CentOS)
>>
>>
>> [nn00kg at kvstage01 ~]$ curl -I http://tinyurl.com/czkquy
>> HTTP/1.1 301 Moved Permanently
>> Via: 1.1 KISA01
>> Connection: close
>> Proxy-Connection: close
>> Date: Mon, 27 Apr 2009 12:16:38 GMT
>> Location: http://www.ipni.org/ipni/plantNameByVersion.do?id=783030-1&version=1.4&output_format=lsid-metadata&show_history=true
>> Content-type: text/html
>> Server: TinyURL/1.6
>> X-Powered-By: PHP/5.2.9
>>
>>
>> [nn00kg at kvstage01 ~]$ curl -I http://bit.ly/KO1Ko
>> HTTP/1.1 301 Moved Permanently
>> Via: 1.1 KISA01
>> Connection: Keep-Alive
>> Proxy-Connection: Keep-Alive
>> Content-Length: 287
>> Date: Mon, 27 Apr 2009 12:19:48 GMT
>> Location: http://www.ipni.org/ipni/plantNameByVersion.do?id=783030-1&version=1.4&output_format=lsid-metadata&show_history=true
>> Content-Type: text/html;charset=utf-8
>> Server: nginx/0.7.42
>> Allow: GET, HEAD, POST
>>
>>
>>
>>
>> - Nicola Nicolson
>> - Science Applications Development,
>> - Royal Botanic Gardens, Kew,
>> - Richmond, Surrey, TW9 3AB, UK
>> - email: n.nicolson at rbgkew.org.uk
>> - phone: 020-8332-5766
>>
>>
>> _______________________________________________
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>>
>>
>>
>>
>> --
>> ---------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> ------------------------------------------------------------
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> DEEB, FBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>
>
>
>
>
>
>
>
> --
> ---------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> ------------------------------------------------------------
> _______________________________________________
> tdwg-tag mailing list
> tdwg-tag at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
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