[Taxacom] PS: saturday morning fun

David Remsen (GBIF) dremsen at gbif.org
Tue Nov 30 16:03:53 CST 2010

Perhaps because it's more complex than you think.   I know exactly how  
to do it.   I did say we don't have programmer capacity to add that  
functionality now.   In fact,  we have a linking mechanism in place  
via the Global Names Index for just this sort of thing.   The method  
you suggest,  however, is not the best way to do this.   Rather than  
concatenate any taxon name to the template you provided,  it would be  
better to generate an explicit link of only those pages which actually  
exist and provide them as an index to globalnames.org

This provides a systematic way to link multiple collections of links,   
it uses a simple international data standard as the format for the  
index, and it works.    That feature is on a feature request list as  
is, now,  your recommendation.



On Nov 30, 2010, at 9:35 PM, Stephen Thorpe wrote:

> David,
> I am utterly astonished that you currently lack the technical  
> capacity to have a link on each of your taxon pages to http://species.wikimedia.org/wiki/NAME_OF_TAXON
> it is even odder that BHL also seem to lack such a capacity
> by contrast, my *friends* ZooKeys seem to have managed to do it just  
> fine on their taxon profiles facility ...
> Stephen
> From: David Remsen (GBIF) <dremsen at gbif.org>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Cc: David Remsen (GBIF) <dremsen at gbif.org>; taxacom at mailman.nhm.ku.edu
> Sent: Tue, 30 November, 2010 9:13:46 PM
> Subject: Re: PS: [Taxacom] saturday morning fun
> Actually I think linking to wikispecies and other select databases  
> (such as species pages currently offered by GBIF national Nodes) is  
> a great idea.   In fact,  it would be done if we had the technical  
> capacity to actively refactor the data portal as it's on a feature  
> request list.    I hope we will be able to add this as you suggest.
> As to the purity of my motives,  I really don't know what that is  
> all about.
> On Nov 29, 2010, at 10:58 PM, Stephen Thorpe wrote:
>> PS: you see the bit where I become suspicious and start doubting  
>> your apparently pure motives is this: it would be very technically  
>> easy and fully consistent with your stated aims and motivations to  
>> simply put on each of your taxon pages a link to the corresponding  
>> Wikispecies page (for example, for Mimus,http://species.wikimedia.org/wiki/Mimus 
>> , and note that all Wikispecies pages have this simple URL structurehttp://species.wikimedia.org/wiki/NAME_OF_TAXON) 
>> , perhaps saying something like "here you may find useful data on  
>> this taxon, though being open edit, we cannot vouch for its  
>> accuracy". But this would require (1) genuinely pure motives on  
>> your part; and (2) a grasp of the difference between theory and  
>> reality (i.e., in theory Wikispecies is unreliable and a pointless  
>> waste of your time, but in *reality* ...)
>> From: David Remsen (GBIF) <dremsen at gbif.org>
>> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
>> Cc: David Remsen (GBIF) <dremsen at gbif.org>;  
>> taxacom at mailman.nhm.ku.edu
>> Sent: Tue, 30 November, 2010 10:30:05 AM
>> Subject: Re: [Taxacom] saturday morning fun
>> Stephen,
>> Thanks for the summary.  I'd be interested to hear what various  
>> Catalogue of Life providers think of all this.  I know some  
>> taxonomic sectors,  like the Lepidoptera,  derived from LepIndex  
>> NHM-London,  have not been thoroughly reviewed, falling into your  
>> 'raw' category.
>> You hit the nail on the head when you say it provides you with a  
>> starting point.   We use it as a starting point too.   We could  
>> forego this and simply leave the raw data as it is but it seemed an  
>> improvement to go with it.  We are trying to expand the capacity to  
>> access other, perhaps more comprehensive or refined sources,   
>> should they be offered or available.   At the moment, that starting  
>> place is the one of the few places we can go.  Of course, flaking  
>> together disparate sets of even high quality data introduces  
>> additional complications but I'd be happy to take them on.
>> I'm sure we (at least I) have not fully grasped all the  
>> ramifications of this.  Ive tried to relay some of the complexities  
>> and a rationale behind what we are faced with and do.   I failed to  
>> mention the constraints we are under to improve the issues raised  
>> this weekend.  Until very recently we have had 2.5 programmers  
>> working on the entirety of our infrastructure with nearly no  
>> resources for the portal to fix these problems.   This will change  
>> in 2011.
>> Best,
>> David
>> On Nov 29, 2010, at 9:47 PM, Stephen Thorpe wrote:
>>> You mention some key issues here. Let me focus on just one of them  
>>> for the moment, namely COL and its suitability as a data provider  
>>> for GBIF. I suspect that GBIF have basically just thought  
>>> something like "well, COL is an aggregation of trusted specialist  
>>> databases in a form that GBIF can use" - but the reality is *way*  
>>> more complex. For me, when starting to compile a Wikispecies page,  
>>> I will often use COL as a *starting point only*, actually little  
>>> more than a convenient way of getting big lists of taxa formatted  
>>> and put on Wikispecies pages for further scrutiny. Sometimes, the  
>>> COL data is so obviously worse than useless, that I don't use it  
>>> at all, not *even* as a starting point. The data providers from  
>>> COL vary widely in nature. Some of them are near complete for  
>>> their group, others are highly fragmentary. Some are *very* raw,  
>>> others are quite well polished. Sometimes, there are problems in  
>>> the way that COL interprets the data from sources, so all sorts of  
>>> synonyms get interpreted as valid, etc. Another issue, which I  
>>> don't fully understand yet, and I could perhaps be mistaken (???),  
>>> is that even in COL 2010, much of the data seems to have been  
>>> harvested in 2008 ... I would have thought that COL 2010 would  
>>> have harvested its data in 2010. If not, then COL is running a  
>>> couple of years behind its own data providers, who will typically  
>>> not be completely up-to-date either. So, in summary, I would say  
>>> that COL is nothing more than a convenient *starting point* for  
>>> building solid biodiversity data, and it requires a fair amount of  
>>> careful and informed interpretation, not to mention a great deal  
>>> of manual work to improve on it. I'm not sure that GBIF has fully  
>>> grasped this? For example, in COL, the family Scarabaeidae is  
>>> actually what would almost universally be called the subfamily  
>>> Scarabaeinae of the family Scarabaeidae, and this is not at all  
>>> obvious. So, COL is actually quite good if you want data on  
>>> Scarabaeinae, but completely lacking in any data whatsoever on the  
>>> *huge* scarabaeid subfamilies Melolothinae and Rutelinae.
>>> Cheers,
>>> Stephen

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