[Taxacom] Chameleons, GBIF, and the Red List

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Tue Aug 26 15:57:04 CDT 2014


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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