[Taxacom] Chameleons, GBIF, and the Red List

Markus Döring mdoering at gbif.org
Wed Aug 27 06:57:38 CDT 2014


Hi Stephen,

we realize at GBIF that our backbone taxonomy has various issues. Recently I have started work on ChecklistBank again and like to address many of the known problems in the coming months.
Taxonomic issues we are aware of are logged in our tracking system and can be seen here:
http://dev.gbif.org/issues/issues/?filter=12200

We are keen to know about problems that people spot in our taxonomy. Without knowing about them it is hard to fix them.
If you have time, please report them using the feedback button in our portal, preferably on the "species" page in question. 
Alternatively you can always send a short email to helpdesk at gbif.org.

This is also true for problems spotted in matching names of occurrence/specimen identifications to our backbone.

regards,
Markus


PS: Bob, I'd be curious to know where to find your "truncated" data in GBIF. Can you point me to the dataset in question as I could not find it?



--
Markus Döring
Software Developer
Global Biodiversity Information Facility (GBIF)
mdoering at gbif.org
http://www.gbif.org





On 26 Aug 2014, at 22:57, Stephen Thorpe <stephen_thorpe at yahoo.co.nz> wrote:

> The discussion here is ignoring the problem of GBIF itself getting stuff wrong, not simply repeating errors from data providers. I have already given an example (a bark louse classified as a virus, and attributed to a data provider, NZOR, which said no such thing!) How can we get these errors fixed, or even just flagged?
> 
> Stephen
> 
> --------------------------------------------
> On Wed, 27/8/14, Roderic Page <Roderic.Page at glasgow.ac.uk> wrote:
> 
> Subject: Re: [Taxacom] Chameleons, GBIF, and the Red List
> To: "Richard Pyle" <deepreef at bishopmuseum.org>
> Cc: "Chuck Miller" <Chuck.Miller at mobot.org>, "TAXACOM" <taxacom at mailman.nhm.ku.edu>, "Bob Mesibov" <mesibov at southcom.com.au>
> Received: Wednesday, 27 August, 2014, 5:59 AM
> 
> Hi Rich,
> 
> I guess we’ll have to
> disagree about this, FilteredPush isn’t what I have in
> mind (much as it may look like it).
> 
> 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
> Skype:  rdmpage
> Facebook:  http://www.facebook.com/rdmpage
> LinkedIn:  http://uk.linkedin.com/in/rdmpage
> Twitter:  http://twitter.com/rdmpage
> Blog:  http://iphylo.blogspot.com
> ORCID:  http://orcid.org/0000-0002-7101-9767
> Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> 
> 
> On 26 Aug
> 2014, at 18:29, Richard Pyle <deepreef at bishopmuseum.org<mailto:deepreef at bishopmuseum.org>>
> wrote:
> 
> No, FitleredPush is
> the *mechanism*, and it can do *EXACTLY* what you are
> proposing – but I’ll leave it to one of the people more
> directly involved with that project to elaborate.
> 
> Aloha,
> Rich
> 
> From: Roderic Page [mailto:Roderic.Page at glasgow.ac.uk]
> Sent: Tuesday, August 26, 2014 7:19 AM
> To: Richard Pyle
> Cc: Lyubomir
> Penev; Chuck Miller; TAXACOM; Bob Mesibov
> Subject: Re: [Taxacom] Chameleons, GBIF, and
> the Red List
> 
> Hi Rich,
> 
> To quote from http://wiki.filteredpush.org/wiki/
> it’s goal is
> 
> "to
> connect remote sites where annotations can be generated with
> the authoritative databases of the collections holding the
> vouchers to which those annotations apply”
> 
> This is pretty much exactly
> NOT the model I’m advocating. I regard FilteredPush as
> “sticky notes” on an authoritative database, with rules
> for processing annotations. This is not the “social
> data” model.
> 
> 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
> Skype:  rdmpage
> Facebook:  http://www.facebook.com/rdmpage
> LinkedIn:  http://uk.linkedin.com/in/rdmpage
> Twitter:  http://twitter.com/rdmpage
> Blog:  http://iphylo.blogspot.com<http://iphylo.blogspot.com/>
> ORCID:  http://orcid.org/0000-0002-7101-9767
> Citations:  http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> 
> On 26 Aug 2014, at 17:55,
> Richard Pyle <deepreef at bishopmuseum.org<mailto:deepreef at bishopmuseum.org>>
> wrote:
> 
> 
> Guys,
> 
> You do
> realize that all of this is the foundation of FilteredPush,
> right?  It was designed to allow both structured (i.e.,
> machine-actionable/automated) annotations and text-based
> (i.e., for human eyeballs) comments.
> 
> The tricky part is not the mechanism (it
> already exists).  The tricky part is the process of
> automating the structured annotations.  Should the system
> ALWAYS accept structured annotations and over-write existing
> data?  Or should it be moderated?  Or, should there be
> some sort of user model that allows people to earn some
> level of reliability, and their annotations are accepted
> without review; whereas other annotations must be
> "approved".
> 
> There
> are a million ways it can be done.  Personally, I think
> some fundamentals are:
> 1) Information should
> NEVER be obliterated.  That is, a field is never simply
> over-written with new information; the old information is
> always retrievable.
> 2) There needs to be a
> method to represent the "best" information.  For
> example, a single specimen/occurrence may have multiple
> competing taxonomic determinations.  All determinations
> should be visible, but it's helpful to the non-expert
> user if one of them can be represented as the
> "correct" (per someone) determination.
> 3) Over-reliance on non-automated,
> human-mitigated processes = DEATH.  This is because
> everyone is already too busy.
> 
> Including me.
> 
> Aloha,
> Rich
> 
> 
> 
> 
> -----Original Message-----
> From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu]
> On Behalf
> Of Roderic Page
> Sent: Monday, August 25, 2014 11:49 PM
> To: Lyubomir Penev
> Cc: Chuck
> Miller; TAXACOM; Bob Mesibov
> Subject: Re:
> [Taxacom] Chameleons, GBIF, and the Red List
> 
> Hi Lyubo,
> 
> Yes, you could have structured annotations and
> free text for comments. But
> what I’d like
> to avoid is the idea that simply putting a comment system
> onto a
> database is the answer. It’s easy
> to do that (I use Disqus on my blog, and on
> BioStor and BioNames, for example), but that
> doesn’t get us terribly far
> (useful as
> people’s comments are).
> 
> If we focus on the structured annotations, and
> the idea that multiple
> authorities can write
> about the same thing, then this leads inevitably to the
> idea of having a single, global annotation
> store that holds data about all kinds
> of
> things that we care about.
> 
> This was what I was trying to articulate in
> http://iphylo.blogspot.co.uk/2014/03/rethinking-annotating-biodiversity-
> data.html  It can be done in a way that makes
> almost no demands on data
> providers at all,
> and if it’s done cleverly it will (as a side effect)
> provide a
> potentially powerful database we
> can use to ask some of the bigger
> questions
> about biodiversity data.
> 
> 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<mailto:Roderic.Page at glasgow.ac.uk%3cmailto:Roderic.Page at glasgow.ac.uk>>
> Tel:  +44 141 330 4778
> Skype:  rdmpage
> Facebook:  http://www.facebook.com/rdmpage
> LinkedIn:  http://uk.linkedin.com/in/rdmpage
> Twitter:  http://twitter.com/rdmpage
> Blog:  http://iphylo.blogspot.com<http://iphylo.blogspot.com/>
> ORCID:  http://orcid.org/0000-0002-7101-9767
> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> 
> 
> On 26 Aug
> 2014, at 08:56, Lyubomir Penev
> <lyubo.penev at gmail.com<mailto:lyubo.penev at gmail.com<mailto:lyubo.penev at gmail.com%3cmailto:lyubo.penev at gmail.com>>>
> wrote:
> 
> Rod,
> 
> Your proposal is indeed
> elegant, but what about using two separate general
> types of annotations, e.g.: (1)
> Corrections/Additions and (2) Comments
> ("sticky notes")?
> 
> The Type 1 (Annotations=Corrections/Additions)
> can go straight to
> improve/amend the data
> (after approval or not is a different story), for
> example adding geocoordinates for a well-known
> locality or adding a
> collector's name
> missing on label data but known from other source, etc.
> 
> Annotations Type 2
> (Annotations=Comments) could be associated with the
> original data or with Type 1 Annotations, e.g.,
> "velvet worms cannot live in
> the ocean,
> correct geocoordinates for this locality", or
> "this locality might be
> wrongly
> spelled", etc.
> 
> No need
> to explain that Type 2 annotations could be based on a
> rich
> controlled vocabulary of statements,
> besides the free text option, which will
> allow machine processing of a part of the
> process, including automated
> verification of
> the original data in some particular cases. For example,
> annotation of the kind  "Now in different
> genus"  could automatically query a
> trusted taxonomy source (CoL, GNUB, etc,) and
> display all possible versions
> and validity
> status of that name and its combinations.
> 
> Regards,
> Lyubomir
> 
> 
> 
> 
> On Mon, Aug
> 25, 2014 at 11:32 PM, Chuck Miller
> <Chuck.Miller at mobot.org<mailto:Chuck.Miller at mobot.org<mailto:Chuck.Miller at mobot.org%3cmailto:Chuck.Miller at mobot.org>>>
> wrote:
> Rod,
> I see what you
> are thinking.
> 
> I'm
> thinking too much about the alternate views that seem to
> always come
> up in comments about taxonomic
> data, even right here on Taxacom.  So, an
> annotation thread could be something like:
> "Now in different genus"
> "No way, respectfully what century are you
> from?. It's not even a species."
> "Maybe they meant Africa."
> "Yeh, in Namibia it was split and revised
> to Y, I think."
> "The phylogeny for
> Y is totally different. It's now in Z. Does no one read
> my
> work? Taxonomic tyranny!"
> "Consider this DOI that refers to new
> collections and it seems to contradict all
> y'all."
> 
> What does "social" annotation turn
> into?  Lots of useful information but if it
> starts being contradictory or overlapping, can
> it be databased and which
> contradiction is
> the primary?  Hopefully, annotation of localities could
> be
> straightforward as in your example.
> 
> Chuck
> 
> 
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> 
> 
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> 
> Celebrating 27 years of
> Taxacom in 2014.
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