[tdwg-content] Name is species concept thinking

David Remsen (GBIF) dremsen at gbif.org
Sun Jun 13 12:55:42 CEST 2010


What you described in 1-5 was exactly the scope and function of uBio  
NameBank and ClassificationBank.   This functionality has been refined  
in our ChecklistBank index.

It serves to provide a consistent resolution service for "Taxon  
Concept Service Providers".
By linking to a populated GNUB it would also have an improved means to  
provide the protonym circumscription of the concept, as you describe  
in (5).   In addition,  we would like to support the inclusion of  
bibliographic data, specimens,  geospatial information, and general  
descriptive data.   The DwC Archive approach provides one (not  
exclusively but I would appreciate pointers to others) means to  
mobilise these data from people who have it.

In (5) you describe the protonym-based circumscription to evaluate the  
relative agreement of the identified concepts (via 'meta- 
authorities').    This provides the basis for expanding the potential  
set of names for a subsequent data retrieval from GBIF (for example)  
to include all the related nomenclatural and lexical variants for  
those names (of course checking for homonym conflicts among them).    
Again, this is consistent to what was implemented in uBio services and  
we are currently implementing in our Checklist Bank (CLB)  (I use the  
term General Concept Mapping for this process).   I'm not sure I agree  
that this provides a true concept-based system, however.  I would call  
it a concept-informed system.

In (6) it appears the output of the Taxon Concept resolution process  
is either an expanded set of name strings or an array of  
protonymIDs.   I can see this is an option in (6).  If the latter,  I  
can see how this would provide a more precise concept-informed but  
name-based retrieval method and probably the best we can expect from  
large indices like GBIF.    But I don't see how it will support a  
strict concept-based retrieval.

The real world example that forms my litmus test is the blue-headed  
vireo,  Vireo solitarius (Wilson 1810) which was originally called  
Muscicapa solitaria and has also been combined to form Vireosylvia  
solitaria and Lanivireo solitarius.   Of course there are lexical  
variants as well (Google "Lanivireo solitaria" for example).   These,  
properly structured, would be the sort of useful set of lexical/ 
nomenclatural content I would hope as a response from a  GNI/GNUB  
resolution service based on protonymID.

One current view of the taxon (concept C1) has this species occupying  
the eastern part of the US.   Another species, Vireo plumbeus Coues,  
1866, (concept C2) occupies the middle west USA, and a third species,  
Vireo cassini Xántus de Vesey, 1858 (concept C3) is on the western  

Another view lumps all three of these into a single species which,  
based on the rule of priority, has the valid name Vireo solitarius   
and results in a new concept (C4).  This concept includes C1, C2,  and  
C3.   Both concepts have the scientific name of Vireo solitarius.

We can access and represent these in a consistent fashion using our  
CLB and probably others can too in their own index models.

So, now we have a specimen of Vireo solitarius that was captured in  
Minnesota.   It might be an errant instance of C1, Vireo solitarius  
sensu stricto, that strayed a bit west of normal.   It might be (C4)  
Vireo solitarius, sensu lato.     The specimen would need that concept  
identifier tied to the record to make this explicit.    So,  let's say  
that the identifier was made using the lumped concept (C4).  Of  
course, if this doesn't make it into the record, we are stuck with the  
name alone.

Using the method (6) you described would allow a user to discover the  
different treatments of Vireo solitarius (C1 and C4) and provide some  
means to discriminate them via concept resolution.

- C4 includes C1, C2, and C3 which would include all the names above.
- C1 would only include the nomenclatural/lexical variants for Vireo  

Resolution will enable us to perform a significantly more useful and  
concept-informed search.  It will, however,  include the specimen I  
referenced above in BOTH cases because "Vireo solitarius" or it's  
protonymID will be a search term in both cases.

A more precise concept based system would utilise a required taxon  
concept identifier in the specimen record to discriminate different  
uses of the SAME NAME.  In other words,  if you did a search of Vireo  
solitarius and the concept resolver indicated the different concepts  
above and you chose the sensu stricto (split) version,  you would get  
the C1 labelled records but the C4 labelled records would be excluded  
or at least come with a warning (may not be what you are looking  
for).  This of course requires our specimen records to have a concept  
identifier.   Or,  the concept definition itself will include  
additional annotations to enable us to make inferences


Publication date of the concept - If the split didn't happen until  
1980 and the specimen is from 1960 then we could infer C4.
Distribution information for the concept - if we disregard errant  
specimens then we might infer a 1985 Minnesota specimen is a C2 in  
spite of the different name.

In sum,  we are on track for achieving this and I believe our data  
mobilisation strategy will support getting these sort of data  
published.   When Markus returns from paternity leave I would hope we  
could include his thoughts on how we might expose these as RDF via our  
indices to support all aspects of this discussion.


On Jun 13, 2010, at 2:37 AM, Richard Pyle wrote:

> Tim: Coffee time.
> Dave:
> Here's how I imagine this would work under GNA, integrated with GBIF:
> 1. Person submits text-string "Puma concolor" to a GNA-aware mapping
> service.
> 2. Service fires text string off to GNI, and sees how many lexical  
> buckets
> are involved, and how many protonyms are represented in those buckets.
> 3. If problems of Homonymy/Homography exist (i.e., if more than one
> legitimate Protonym for a species-group name "concolor" has ever been
> combined with a genus-group name "Puma"), then the service replies  
> with a
> page that says "Do you mean the big cat, or do you mean the protozoa?"
> (pretending, for a moment, that the name "Puma concolor" has also been
> applied to a protozoa).  Perhaps the service can also review the usage
> history of the two names, and algorithmically determine that they most
> likely meant the big cat -- but at least alert the user that a  
> potential
> case of homonymy/homography exists.
> 4. If step 2 yielded no apaprent homonymy/Homography, or if the user
> selected one from among more than one Homonyms/Homographs, then the  
> service
> takes the selected ProtonymID and throws it at a GNUB-aware taxon  
> concept
> resolver.
> 5. The GNUB-aware Taxon Concept resolver looks at how many Taxon  
> Concept
> Service Providers (e.g., ITIS, EOL, WoRMS, etc.) have made some sort  
> of
> concept-definition assertion about the Protonym. In most cases, this
> could/should be as simple as "Concept Service [X] says that for  
> Protonym
> [IDp], follow taxon name usage-instance [IDtnu]". Given [IDtnu],  
> GNUB will
> tell us which Genus combination to use, which orthographic spelling  
> to use,
> which taxon rank to use, and which set of Protonyms should be  
> regarded as
> subjective synonyms of the taxon concept represented by [IDtnu].  If  
> the
> different taxon concept providers (I call them "Meta Authorities")  
> all agree
> (i.e., each taxon concept provider yields the same set of  
> ProtonymIDs), then
> no user interaction is required on this step. If there are different
> interpretations of what the current treatment of "Puma concolor [big  
> cat]"
> should be, then the user is presented with the different options (and
> perhaps a bit of information on what the different active concepts  
> are, in
> terms of distribution and/or classification).
> 6. The resultant set of Protonym IDs from step 5 (the original  
> ProtonymID
> from step 2/3, plus the exploded set of Protonyms for subjective/ 
> hetrotypic
> synonyms from step 5), are then thrown at GBIF (which would be GNA- 
> Aware,
> and thus know how to translate all the ProtonymIDs into a larger set  
> of
> text-string names and/or GBIF may have already cashed this by  
> converting
> text-string names from occurrence providers into ProtonymIDs via GNI).
> 7. The user is then presented with a distributional map from GBIF  
> occurrence
> records, based on the selected Protonym of the original submitted
> text-string name, cast in the context of the set of heterotypic  
> synonyms
> established in Step 5.
> The bad news is that this sounds incredibly complicated.  The good  
> news is
> that it's actually not.  Especially not from the user's perspective.
> In the WORST case scenario, the user needs to provide three pieces of
> information:
> 1. The text-string name submitted in Step 1.
> 2. A decision in the case of Homonyms/Homographs, what critter/weed/ 
> microbe
> they're after.
> 3. A decision about which Meta Authority to follow for the taxon  
> concept.
> This, again, is the WORST case scenario.  A much more likely scenario
> involves fewere steps for the end user.
> Consider:
> Step 2 only applies in the 10%(ish) cases of text-string names  
> involved in
> some sort of Homonymy/Homography problem.  So in 90%(ish) of cases,  
> step 2
> won't come into play.
> Step 3 only applies in cases where the Meta-Authorities disagree on  
> the
> current usage of a name (e.g., ITIS is a lumper, WoRMS is a  
> splitter).  Even
> in cases where there is disagreement, the user could simply be  
> presnted with
> two (or more) maps, showing each of the current interpretations/ 
> statuses of
> the selected critter/weed.  For example, the user might get a page  
> that says
> "If you follow the ITIS interpretation of this species, the map  
> looks like
> this. If you follow the WoRMS interpretation of the name, the map  
> looks like
> that."
> And, indeed, Step 1 wouldn't exist in the majority of cases, because I
> suspect most people will get to the Map service by clicking on a  
> link from
> some web page article or database system.  In most cases, this link  
> would
> also bypass Step 2 as well.
> In other words, if we can continue to develop GNA the way we're  
> already
> developing it, we should be able to get the the point (Soon!) where  
> a user
> clicks a link on a web page, and immediately gets a single map  
> distribution
> using the taxon concpet adopted by the overwhelming majority of
> Meta-Authorities, or (at worst) gets more than one map based on more- 
> than
> one contemporary/contentious views of what the species concept  
> should be
> (with links to more information, if the user wants the details).
> So, if we keep building GNA, we should have exactly the service that  
> Pete
> says he'd like to have (i.e., a single map with the full  
> distribution of the
> species, regardless of what text-string name is used to lable the  
> georef'd
> occurrence data-points).
> Simple, really....
> :-)
> Rich
>> -----Original Message-----
>> From: David Remsen (GBIF) [mailto:dremsen at gbif.org]
>> Sent: Saturday, June 12, 2010 10:50 AM
>> To: Peter DeVries
>> Cc: David Remsen (GBIF); Richard Pyle;
>> tdwg-content at lists.tdwg.org; Kevin Richards; Jerry Cooper
>> Subject: Re: [tdwg-content] Name is species concept thinking
>> Pete -
>> This statement has been sticking with me since I read it.   It might
>> be me but I don't see any relationship between that statement
>> and how
>> this relates to taxon concepts.   In a concept-based system
>> you could
>> easily have two different maps for Puma concolor.    Whether Felis
>> concolor is included is not relevant because nomenclatural
>> synonyms have no bearing on the circumscription.  They are
>> both names for the same type.
>> There may be two different concepts (circumscriptions) published for
>> Aedes triseriatus.   It could be quite legit for a different
>> (objective synonym only) name like Oclerotatus triseriatus to
>> refer to
>> that same concept.  So in that sense,   there is a rationale for
>> different scientific names to be able to reference the same
>> concept to
>> meet that requirement of the example you cite.   But in
>> zoology these
>> examples aren't even considered different names and the rule
>> of priority would prevent truly different (heterotypic names)
>> from referring to the same type so the use cases for
>> different scientific names being able to refer to a single
>> concept ID are quite limited.
>> Mapping objective (homotypic) synonymy provides the basis for
>> providing a single map for those examples you cite but it's
>> not using true concept-based principles.
>> Best,
>> David
>>> Frankly I think it would be an improvement if we could get maps etc
>>> that combine Aedes triseriatus / Ochlerotatus triseriatus
>> into one map
>>> and Felis concolor and Puma concolor into a different
>> single map. :-)
>>> Respectfully,
>>> - Pete

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