[Taxacom] Chameleons, GBIF, and the Red List

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Wed Aug 27 16:15:42 CDT 2014


Hi Markus,
What appears to be missing from this feedback process is any sort of incentive to contribute one's free time to it. Why should one contribute freely to improving something which is your paid job, and do so seemingly anonymously (as far as I can tell, problems are "credited" only to "Feedback bot"). All good for you guys, who can then pretend that the problem, once fixed, never existed, but I don't really see it as a viable option, and certainly my time is better spent creating my own biodiversity data resources, not fixing yours, though occasionally I may highlight a problem in GBIF just to make a point (as in this thread).
Cheers,
Stephen

--------------------------------------------
On Wed, 27/8/14, Markus Döring <mdoering at gbif.org> wrote:

 Subject: Re: [Taxacom] Chameleons, GBIF, and the Red List
 To: "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
 Cc: "Richard Pyle" <deepreef at bishopmuseum.org>, "Roderic Page" <Roderic.Page at glasgow.ac.uk>, "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, 11:57 PM
 
 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 DöringSoftware
 Developer
 Global Biodiversity Information
 Facility (GBIF)
 mdoering at gbif.orghttp://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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