[Taxacom] Explicit vs implied linking

Wed Dec 1 02:03:29 CST 2010

Here is an example:
name on Wikispecies (and in fact only on Wikispecies): 
http://ptp.pensoft.eu/external_details.php?type=1&query=Esagonatopus%20floridensis

name not on Wikispecies: 
http://ptp.pensoft.eu/external_details.php?type=1&query=Esagonatopus%20perdebilis

________________________________
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: Wed, 1 December, 2010 8:42:50 PM
Subject: Explicit vs implied linking

Stephen,

There is a very practical answer to your question and I've ground-truthed it to 
some degree in my former work with uBio.   The BioOne journals used the same 
methodology to link to ITIS,  by appending a name to the end of a URL and 
casting it out as a link in case something stuck on the ITIS end.   What they 
found,  and what I used to ask people is - If you click on the dead link once - 
OK things happen.   You click the second time and you get nothing.   You gonna 
click a third time?  

Generating an explicit index of links is trivial for structured data management 
systems.    It is easier to do it the way you suggest but my experience is that 
stale links don't get used.   

DR

On Nov 30, 2010, at 11:22 PM, Stephen Thorpe wrote:

thanks David
>
>just one comment:
>
>>The method you suggest,  however, is not the best way to do this<
>
>actually I rather think it *is* the best way
>
>GBIF has rather a tendency to overcomplicate matters, but if one has good honest 
>data, then simplicity is best
>
>why would you worry if the page actually existed or not? If it doesn't exist, 
>Wikispecies will tell you that it doesn't, and you can simply press the back 
>browser button to get back to GBIF. I don't see this as a problem. On the other 
>hand, if you only add links to pages that exist, then how do you keep up with 
>new pages as they come into existence at any time? If the link is already there, 
>then it will work *as soon as* the page comes into existence, without any work 
>needed by GBIF, which is surely preferable?
>
>IMHO, GBIF should concentrate on what it can provide that nobody else can (e.g., 
>maps of distributions from unpublished museum specimens, etc.), and provide 
>links to other information that Wikispecies, for one example, might be better at 
>providing ...
>
>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: Wed, 1 December, 2010 11:03:53 AM
>Subject: Re: PS: [Taxacom] saturday morning fun
>
>
>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.
>
>
>http://code.google.com/p/gbif-dataportal/issues/detail?id=97
>
>
>DR
>
>
>
>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
>>>
>>> 
>>
>> 
>
> 