[Taxacom] iSpecies

[Thompson, Alexander M]

Whoops, i guess I failed at reading back through the message history properly. :(

iDigBio tries to do that for biodiversity data:

http://api.idigbio.org/v2/view/records/23a41d15-6ab4-4b04-87a2-c92ab39858a2 (current version)
http://api.idigbio.org/v2/view/records/23a41d15-6ab4-4b04-87a2-c92ab39858a2?version=0 (first version in iDigBio)

To do this, we had to focus on a hyperspecific prescription for our primary data type though. iDigBio's core type is not "specimen" or "occurrence" but the "record". We fully expected to have both multiple records for the same specimen present in the database, and records that were difficult to map back to a physical specimen (aggregated from symbiota portals records missing a collection assigned GUID). Both of these problems are getting less sever over time, as we work to get authoritative datasets online directly from the source with GUIDs assigned, and to remove overlapping datasets from other aggregators, but the record concept is still very important to us. Even deleted records don't vanish from iDigBio, although they do become impractically hard to track down if you don't know the GUID of the record - iDigBio staff with access to the database can do it, they just vanish from the indexes.

It is for this reason that we think we have a pretty good foundation on which to build an annotation system, we can capture full provenance and state information for what the annotation references with just the record UUID and version number (or etag to get even more specific).

- Alex

Aside: This also means we're capable of generating a complete data snapshot at an arbitrary point in our history should the need arise at some point in the future. 
________________________________________
From: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
Sent: Tuesday, January 26, 2016 10:12 PM
To: taxacom; Thompson, Alexander M
Subject: Re: [Taxacom] iSpecies

>Lyubo's potential annotation that sparked this discussion, "this is an Australian species which is introduced in N.Z., and the only records currently displayed on the map are mine from around Auckland", is inherently temporal in nature<

Actually, that was my potential annotation, not Lyubo's! Forgive me while I just annotate that error! :)

Possibly the answer is to look at just about the only thing that Wikimedia gets right: Each Wikimedia article has a complete edit history from which you can display any previous version and know exactly who (username and/or IP) edited what when. So, something along these lines could be done for biodiversity related websites, whereby each version of a page would be a historical document (possibly even assigned a doi?) That way, a no longer relevant annotation would just be a part of a no longer current version of the page, but could be retrieved if desired.

Stephen


--------------------------------------------
On Wed, 27/1/16, Thompson, Alexander M <godfoder at acis.ufl.edu> wrote:

 Subject: Re: [Taxacom] iSpecies
 To: "taxacom" <taxacom at mailman.nhm.ku.edu>, "Stephen Thorpe" <stephen_thorpe at yahoo.co.nz>
 Received: Wednesday, 27 January, 2016, 3:56 PM

 That's not quite what
 I meant, although not entirely wrong either.

 I think that iSpecies
 shouldn't bother with annotations on _the thing that it
 currently presents_ primarily because the concept of what
 its referencing is somewhat inherently nebulous. What is the
 point of collecting an annotation that is based on the
 ephemeral concept of a collection of query results at a
 given time. My assumption is that an annotation is something
 more permanent than a blog comment, but less permanent than
 a physical object or authoritative database record. A
 "good" annotations denotes some kind of desired
 transition on, or at very least clarification in the state
 of, a more permanent object. I'll admit that that's
 a limited proscription of the concept, and might betray the
 aggregator centered nature of my thoughts.

 Annotations on more ephemeral
 things, like the current collection of GBIF query results
 for a specific taxonKey, lose their value very rapidly.
 Lyubo's potential annotation that sparked this
 discussion, "this is an Australian species which is
 introduced in N.Z., and the only records currently displayed
 on the map are mine from around Auckland", is
 inherently temporal in nature. This could of course be
 remedied. You could save the generated map as an image,or
 generate a download file from GBIF to get a DOI. Then you
 could create the annotation on that more permanent object,
 but doing so would require a much more complex
 infrastructure than iSpecies currently implements.

 iSpecies could also handle
 annotations not for the species page itself but for the
 underlying resources by passing the content through to the
 other services that do have well defined concepts. If Google
 Scholar gained the capability to support annotations on
 texts, then iSpecies could be a good place to generate them,
 especially if the Google Scholar annotations were queryable
 in some form that could recursively enhance iSpecies. An
 example would be capturing the some of the content in the
 other current taxacom megathread as annotations on the
 papers in question, allowing queries for whatever name
 eventually ends up as synonym for the species to show
 results for the paper with the accepted name, and vice
 versa.

 - Alex

 ________________________________________
 From:
 Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
 Sent: Tuesday, January 26, 2016 8:11 PM
 To: taxacom; Thompson, Alexander M
 Subject: Re: [Taxacom] iSpecies

 Alex,
 You seem
 to be saying that iSpecies should not bother with
 annotations because other aggregators would have difficulty
 dealing with the annotations? Is that correct? Seems a bit
 naff!
 Stephen

 --------------------------------------------
 On Wed, 27/1/16, Thompson, Alexander M <godfoder at acis.ufl.edu>
 wrote:

  Subject: Re:
 [Taxacom] iSpecies
  To: "taxacom"
 <taxacom at mailman.nhm.ku.edu>
  Received: Wednesday, 27 January, 2016, 1:11
 PM

  I agree with Tony
 here.
  On two different fronts.

  One, as a holder of data,
 iDigBio is very
  interested in collecting
 these types of annotations for the
  data
 that we serve. So I would hope that any efforts to
  build an annotation system into something like
 iSpecies
  would include provisions for the
 ability to pass those
  annotations down to
 all information providers capable of

 receiving them (as iDigBio plans to do).

  Two, in terms of the general annotation
  ecosystem, I think its very important that
 annotation
  systems are very clear about A)
 what exactly the annotations
  applies too,
 and B) who is ultimately responsible for the
  annotation. For A, without a nearly
 universally recognized
  and applied
 identifier system (such as DOIs for papers) this
  virtual requires that the service archive
 copies of the
  annotated resource. Even then
 it is possible for annotations
  on archived
 content to effectively vanish if the system is
  not very careful
  to manage
 churn. For B, I
  firmly believe this
 requires the nomination of a
  organization
 to be the default holder of annotation records.
  This organization needs to be responsible for
 ensuring that
  "action" is taken
 on all annotations, even if the
  only viable
 action is to simply display them alongside the
  annotated content when it is queried. Other
 organizations
  could step up to the plate
 and take more comprehensive
  actions on
 annotations (such as a collection modifying its
  authoritative database), but in order to build
 trust in the
  system every accepted
 annotation needs a guaranteed minimum
  level
 of service.

  I think
  that iSpecies as currently envisioned fails on
 these fronts,
  so annotations would not
 really be an appropriate feature.
  That
 said, I think it's a neat little tool that has a
  lot of potential, and could definitely evolve
 to the point
  (either by building features
 internally, or by continuing to
  incorporate
 finer grained data from additional sources)

 where annotation features would be both useful and
  appropriate.


 - Alex
  iDigBio Infrastructure Lead


 ________________________________________

 From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu>
  on behalf of Tony Rees <tonyrees49 at gmail.com>
  Sent: Tuesday, January 26, 2016 6:29 PM
  To: David Campbell; taxacom

 Subject: Re: [Taxacom] iSpecies

  I don't think

 "annotation" and an on-the-fly aggregator such
 as
  iSpecies
  belong
 together. As Rod is pointing
  out, iSpecies
 is basically a
  demonstrator of
  the fact that you can take an input species
 name, throw
  it
  at a select
 number of (hopefully
  comprehensive)
 taxonomic resources, and do

 "something" with whatever comes back,
  on-the-fly. The system is just a
  piece of
  code (large or
 small) to do that job, and does not hold

 any
  content of its own (although arguably
 a
  list of taxonomic names and their
  synonyms
  might be helpful,
 for query expansion, also homonyms, for

 disaggregation...). So any annotations would
  need to reside in the external
  data sources
  that the
 "aggregator" queries.

  Of course a step away from this model is to
  start to hold actual content

 locally for
  query, then annotations *could*
 be attached as desired
  within
  the iSpecies environment, but my
  feeling is that this is outside the scope
  of
  Rod's present
 "demonstrator" system. There is
  a
 conceptual progression
  from a basic
 system
  as shown to something with a lot
 more behind it
  (databases, locally hosted
 content,
  annotations, lists and systems of
 taxa,
  etc.
  etc.) which is
 ultimately how you end up with the likes of

 EOL,
  however with substantially (read
 lots!)
  more investment in both IT
  infrastructure,
  editorial
 input, and community engagement.

  Personally (no disrespect to

 Rod) if I wanted EOL content I would go to

 EOL, GBIF content I would go to GBIF,

 literature I would go to Google
  Scholar
 and
  BHL at this time, but Rod is trying to
 show that
  "some" of the
  required human mouse
  clicks
 can be automated at least (though that is

 hardly a new message, thanks in part to his

 original iSpecies of 2006 or
  so). I
 think
  the value will be to see what else he
 can do with the
  system
  to
 produce a product, or some
  interesting
 value- adding, that is currently
  *not*
 available elsewhere with a few mouse

 clicks.

  Regards - Tony

  Tony Rees, New South
 Wales,
  Australia
  https://about.me/TonyRees

  On 27 January 2016 at
 09:25,
  David Campbell <pleuronaia at gmail.com>
  wrote:

  >
 Such
  annotation, though requiring
 appropriate moderation, has
  particular
  > advantages of being easy and
  convenient for the people competent to make
  > corrections.  They're likely to
 be
  working on their own projects and not
  >
  have time or funding to
 tackle a thorough review of a
  dataset.
 But they
  > are likely to
  search for information and, in the process,
 spot
  > misinformation.  A quick way to
 flag
  problems, provide supplemental
 info,
  >
  etc., and the
 researcher is likely to contribute.  If it

 takes 10 minutes
  > of searching
 through
  multiple links just to find a
 possible way to submit a
  > correction,
 then there will be a lot fewer
  edits
 submitted.  This applies
  > for
  many contexts - BHL could improve indexing if
 readers could
  flag
  >
 unrecognized scientific names and
  false
 positives, for example.
  >
  >
  >

 >
  On Tue, Jan 26, 2016 at 3:26 PM,
 Stephen Thorpe <
  > stephen_thorpe at yahoo.co.nz>
  > wrote:
  >
  > > Rod,
  > >
  > > The only way that this sort of
 thing
  is ever going to get beyond the
  >
  stage

 > > of "garbage in, garbage

 out" is by allowing free and unrestricted (but
  > > moderated in case of spam)
  annotation....
  >
  >

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