[Taxacom] Chameleons, GBIF, and the Red List

James Macklin james.macklin at gmail.com
Thu Aug 21 13:52:32 CDT 2014


Hi Rod,

Sorry, a little slow... I also think it is important to stress the data
quality life cycle here. What we still as yet do not do well is connect the
expert work done on these specimens or their digital derivatives (or
observations, I guess), which are not done by the source/owner, back to
them so the source/owner can clean/update the record and provide it to GBIF
and/or other aggregators. The literature is one path where there is
reference to the specimens used but as we know not everything ends up
published this way. Further, extracting the information from the literature
can be challenging even today. Lyubomir and Pensoft make this easy
(thanks!) but we are still a long way from convincing other publishers to
include the specimen data in a readily accessible form (or even mandating
its presence as evidence). Another way to get expert knowledge back to the
source is through annotation. Those of you who know me realize that my
colleagues and I have spent a fair bit of time studying this problem and
coming up with solutions (FilteredPush). I would say that in general there
are now reasonable solutions for achieving distributed annotation at
various levels of complexity but there is still a challenge/bottleneck in
pushing these annotations back to the source and into their collection
management system. The bottleneck is potentially at the source that must
process the annotations. If we automate (or even semi-auto) the annotation
process through curation workflows, something my colleagues and I are now
focusing on, we could potentially flood the "curators" of the
specimens/data. Then the question becomes how much the owners are committed
to processing potentially valuable modifications/additions and adding them
to their database. Certainly data curation and positions to support it are
in their infancy. The annotations that are not processed by the source
still have value and can inform the aggregators but have to be dealt with
in a slightly different manner. So, this returns to the issue of when GBIF
takes in a record update (or a new record), what metadata follows it to say
it has been changed (created) based on some form of expertise...

I think we also need to be careful of the use of the term "expert."  I
think it is reasonable to assume that a taxonomist is not going to be any
better at georeferencing a specimen based on the collecting event data
 (assuming
this person was not associated with the collecting event) than a
geographer, historian or even a citizen that happens to live near where the
event took place. So, in the case of the Chameleon paper, and others like
it, the issue really relates to taxonomic expertise and thus the name that
appears associated with the record and not the entire record necessarily.

Papers like the Chameleon are quick to judge the end product but do not
take into consideration what an achievement it is to simply have a GBIF
resource and the challenges the greater "we" have overcome just to get this
far! Let's stop highlighting the problem yet again and get to work on
solving it and making the GBIF resource more valuable to all ;-)

Best,  JAmes

James Macklin, Ph.D.
Research Scientist
Botany and Biodiversity Informatics
Associate Curator of the AAFC National Vascular Plant Collection (DAO)
Agriculture and Agri-Food Canada
Ottawa, Ontario, Canada


On Thu, Aug 21, 2014 at 6:20 AM, Roderic Page <Roderic.Page at glasgow.ac.uk>
wrote:

> Just to follow up on this discussion:
>
> Stephen, I think I often come across as grumpy, but your cynicism makes me
> look like a fanboy, so thank you for that ;) Can we maybe assume that
> GBIF’s primary goal isn’t to keep bureaucrats happy, that it’s genuinely
> trying to provide access to basic biodiversity information in one place
> because that seems like a worthwhile goal - leaving aside whether GBIF is
> the best way to tackle that goal.
>
> Bob, if I understand your argument correctly, it’s that access to mostly
> unveiled biodiversity data isn’t much use, and in your view that’s mostly
> what GBIF is serving up. Assuming that it would be nice to have access to
> good-quality distributional data in one place, what if GBIF provided, say,
> distributions of species that had been cleaned and had some degree of
> expert scrutiny. In other words, say a researcher publishes an
> evidence-based distribution map, what if that was stored on GBIF in a
> citable form (e.g., had a DOI), and others could download that distribution
> and make use of it?
>
> I guess this was the thinking behind the now abandoned SDR project (see
> https://code.google.com/p/gbif-sdr/wiki/PortalIntegration ), and is
> perhaps where the Map of Life http://mol.org is headed (although at the
> moment it’s simply showing you a bunch of distributions from different
> sources).
>
> Lyubo, I couldn’t agree more, having links to literature related to a
> record would be great. Many of our online biodiversity databases are devoid
> of links to the evidence for a particular assertion, but as more and more
> literature comes online we can do something to fix that. +1 for extracting
> from the literature, especially if we can automate this at scale (although
> that will give Bob nightmares).
>
> Regards
>
> Rod
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email:  Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>
> Tel:  +44 141 330 4778
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>
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