[Taxacom] iSpecies

Thompson, Alexander M godfoder at acis.ufl.edu
Tue Jan 26 20:56:37 CST 2016

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

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!

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

 - 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
 belong together. As Rod is pointing
 out, iSpecies is basically a
 demonstrator of
 the fact that you can take an input species name, throw
 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
 content of its own (although arguably a
 list of taxonomic names and their
 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
 the iSpecies environment, but my
 feeling is that this is outside the scope
 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.) which is ultimately how you end up with the likes of
 however with substantially (read lots!)
 more investment in both IT
 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
 to produce a product, or some
 interesting value- adding, that is currently
 *not* available elsewhere with a few mouse

 Regards - Tony

 Tony Rees, New South Wales,

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

 > Such
 annotation, though requiring appropriate moderation, has
 > 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
 > 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
 > > of "garbage in, garbage
 out" is by allowing free and unrestricted (but
 > > moderated in case of spam)
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