[tdwg-tag] LSIDs: web based (HTTP) resolvers and web crawlers

Fri May 1 09:41:20 CEST 2009

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 addscosts 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
> ------------------------------------------------------------
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>
>
> ---------------------------------------------------------
> 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
------------------------------------------------------------
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