[tdwg-content] Canonical name parsing

Wed Mar 14 22:20:40 CET 2012

Hi Peter,

I think the rationale the last time this was discussed was that these rarely come with authorships, so in most cases the scientificName will be identical to what you describe for canonicalScientificName.  In cases where there is one of these names not covered by the existing canonical terms that *does* have an authorship, then in theory it should be reasonably straightforward to strip the canonical bit out of scientificName in almost all cases by trimming after the first space (monomials not having spaces within the namestring itself).

No, it's not perfect; and yes, it's less than ideal.  But the small amount of noise generated by this is VASTLY smaller than the noise that already exists in the source data.

Another limitation is for cases of infrasubspecific quadrinomials (where you have Genus species subspecies variety; or Genus species subspecies form; or Genus species variety form; or Genus species subspecies variety form; etc.)  In those cases, the convention is to only provide the terminal epithet for infraspecificEpithet, and the full-context name in scientifcName.

And, of course, there is the problem that Gregor mentioned about autonyms -- although with the parsed content, I still think it's fairly simple to reconstruct the full string algorithmically.  It can be stripped by simply finding the scientificNameAuthorship *within* scientificName (doesn't need to be at the end of scientificName) and excising it; and to concatenate it from the parsed bits, just look to see if specificEpithet=infraspecificEpithet  and check nomenclaturalCode, and place the authorship in the concatenated form appropriately.

The hybrid issue is a complex one, and isn't really helped that much by the addition of canonicalScientificName.

But I think Rod captured this one best when he asked, "Why do we let edge cases determine what we do?"

If the problem of Monomials with authorship at ranks not covered by the existing DwC terms, and/or the need to have parsed quadrinomials represents a real problem for sharing data via DwC, then I would agree with Donald that the best approach would be to refine the definition of scientificName such that it should only include authorship when the provider is unable to parse the authorship bits from the name bits.  When the provider can provided them pre-parsed, then scientificName should be effectively the same as what you proposed for canonicalScientificName, and the authorship bits should be included as scientificNameAuthorship.  Of course, that leaves the problem for the data consumer when a record has no scientificNameAuthorship, whether to interpret that as a case where no authorship information is known, vs. authorship is not parsed.

Don't get me wrong -- I understand why there would be some value in having something like canonicalScientificName (like I said, this has already been suggested and debated, so the potential need is there).  However, part of the problem is in how that thing is defined.  Paul has already indicated the issue of whether or not to include the infraspecific rank tag.  We may want some people who would like canonicalScientificNameWithRanks, and some who would like canonicalScientificNameWithoutRanks; then we might want some who want canonicalScientificNameWithInfrageneric, and some canonicalScientificNameWithoutInfrageneric; then we might want some who want canonicalScientificNameTrinomialOnly.....

The point here is that I suspect we will find that different communities have slightly different ideas about what they would want in a canonicalScientificName term definition.

Again, I haven’t looked up the dialog the last time we had this conversation in the context of DwC, but a lot of what I write above sounds familiar to me; so I think these are some of the reasons why the decision was made not to create a canonicalScientificName term.

I'm not saying it's not useful, and I'm not even saying I'm opposed to the idea.  But I am saying that there are non-obvious reasons why it could, as Donald has suggested, either simply move the same problem from one place to another, or ultimately create more noise and confusion than it attempts to solve.

Finally, I agree with Jessie that TCS confronted this issue and, in my opinion, dealt with it elegantly (that was another place this conversation happened).  But I was focusing on DwC, as that is how the original question was framed.

Aloha,
Rich

Richard L. Pyle, PhD
Database Coordinator for Natural Sciences
Associate Zoologist in Ichthyology
Dive Safety Officer
Department of Natural Sciences, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://hbs.bishopmuseum.org/staff/pylerichard.html

Note: This disclaimer formally apologizes for the disclaimer below, over which I have no control.

From: peter.desmet.cubc at gmail.com [mailto:peter.desmet.cubc at gmail.com] On Behalf Of Peter Desmet
Sent: Wednesday, March 14, 2012 8:27 AM
To: Richard Pyle
Cc: Donald Hobern (GBIF); TDWG content mailing list; dev Developers; Christian Gendreau; Tim Robertson [GBIF]; TDWG TAG mailing list
Subject: Re: [tdwg-content] Canonical name parsing

Rich,

I wished those terms were sufficient, but as mentioned in the justification for http://code.google.com/p/darwincore/issues/detail?id=150:
genus, specificEpithet, infraspecificEpithet: concatenated, this terms are identical to the canonicalScientificName for genera, species and infraspecific taxa. For higher taxa or infrageneric taxa, these terms are not sufficient. In addition, there is some ambiguity regarding the genus definition: for synonyms, is it the accepted genus or the genus that is part of the synonym name? See: http://lists.tdwg.org/pipermail/tdwg-content/2010-November/002052.html. In the former case, the genus cannot be used to concatenate a canonicalScientificName.
To give an example for a higher taxon:
scientificName: Magnoliidae Novák ex Takhtajan
taxonRank: subclass

There is no place to share the canonical name "Magnoliidae" for this taxon.

Peter

On Wed, Mar 14, 2012 at 14:13, Richard Pyle <deepreef at bishopmuseum.org> wrote:

I guess the parts that confuse me are:

1) What providers are able to produce a canonicalScientificName as per Peter’s definition, but are unable to provide the pre-parsed elements of genus | subgenus | specificEpithet | infraspecificEpithet?

2) What consumers could make use of a canonicalScientificName as per Peter’s definition, but are unable to make (even better) use of the pre-parsed elements of genus | subgenus | specificEpithet | infraspecificEpithet?

Aloha,
Rich

From: tdwg-content-bounces at lists.tdwg.org [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Peter Desmet
Sent: Wednesday, March 14, 2012 7:03 AM
To: Donald Hobern (GBIF)
Cc: TDWG content mailing list; Christian Gendreau; Tim Robertson [GBIF]; TDWG TAG mailing list; dev Developers
Subject: Re: [tdwg-content] Canonical name parsing

Hi Donald,

scientificName, with its current definition [1] is a great term and should be continued to used as such. As with most Darwin Core terms, it offers flexibility, so its not an impediment for publishing data. In the GBIF context, this term is considered mandatory: records without it are ignored during indexing (I believe). All of this can stay.

canonicalScientificName would be an additional term with a clear rule (see my proposed definition [2]). This is the case for other Darwin Core terms as well, such as
decimalLatitude [3], minimalElevationInMeters [4] or countryCode [5]. They serve as an ready-to-use addition/alternative to verbatimLatitude [6], verbatimElevation [7] and country [8] respectively. These terms don't stop anyone from publishing data, but data publishers who can provide this kind of information have the choice to do so. It would be the same for canonicalScientificName.

And yes, an aggregator like GBIF can play an important role in providing consistent data to its users and figuring out what they really need, but not all data is consumed that way. In addition, I hope a user would be able to download cleaned data from the GBIF portal as Darwin Core. Wouldn't it be nice that the parsed canonicalScientificName created by GBIF can be provided in its proper term? There are users out there who want this!

Regards,

Peter

[1] http://rs.tdwg.org/dwc/terms/index.htm#scientificName
[2] http://code.google.com/p/darwincore/issues/detail?id=150
[3] http://rs.tdwg.org/dwc/terms/index.htm#decimalLatitude
[4] http://rs.tdwg.org/dwc/terms/index.htm#minimumElevationInMeters
[5] http://rs.tdwg.org/dwc/terms/index.htm#countryCode
[6] http://rs.tdwg.org/dwc/terms/index.htm#verbatimLatitude
[7] http://rs.tdwg.org/dwc/terms/index.htm#verbatimElevation
[8] http://rs.tdwg.org/dwc/terms/index.htm#country

On Wed, Mar 14, 2012 at 11:19, Donald Hobern (GBIF) <dhobern at gbif.org> wrote:
>
> Hi Peter.
>
> I certainly agree that aggregators only represent one use case here but, having seen a lot of the mess of real-world data, I don't believe that simply adding a new term will fix this problem for the users you describe.  To get the results you want, we would need a sufficiently large majority of data sets to follow the rules perfectly that we could ignore those that were non-conformant.  This would mean we should mandate that every data set must use the new element (with or without the existing scientificName element) and that they must present scientific names in the expected way (or else have their data considered non-compliant). Until now, the philosophy on publishing Darwin Core data has been to make it as easy as possible for data providers to expose their data, even at the expense of greater complexity for consumers.  I suspect that we would have a lot less data available for use now if we had taken a more stringent approach.
>
> In some ways, this proposal reminds me of the structures in ABCD which seek to offer users verbatim and more normalised ways to represent several types of information.  This actually makes consuming all the possible forms of such data very complex, since a record may contain all variant forms or just any one of them.  If multiple forms are available, which one should be considered the primary version?
>
> I suspect that things may also get complicated as soon as you discuss botanical subspecies, varieties, subvarieties, forms and subforms.  There are recommended ways to abbreviate the rank markers in these cases but some variation can be expected.
>
> Of course aggregators should be providing more robust services for accessing exactly what you want in a consistent, predictable way and I would suggest that the best place to attack the problem is to define exactly what a typical user needs to see and then for GBIF and similar projects to work on delivering predictable data downloads and web services that clean out all of these nomenclatural inconsistencies - and perhaps also add value in other ways such as augmenting the data with associated environmental values (as the Atlas of Living Australia does).  This would allow us all to work together on developing a consistent and predictable algorithm for handling interpretation of name strings, including synonymy, misspellings, virus names and everything else that makes this such a difficult problem.
>
> Best wishes,
>
> Donald
>
> ----------------------------------------------------------------------
> Donald Hobern - GBIF Director - dhobern at gbif.org
> Global Biodiversity Information Facility http://www.gbif.org/
> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
> Tel: +45 3532 1471  Mob: +45 2875 1471  Fax: +45 2875 1480
> ----------------------------------------------------------------------
>
>
> -----Original Message-----
> From: peter.desmet.cubc at gmail.com [mailto:peter.desmet.cubc at gmail.com] On Behalf Of Peter Desmet
> Sent: Wednesday, March 14, 2012 3:41 PM
> To: Tim Robertson [GBIF]
> Cc: Donald Hobern (GBIF); dev Developers; TDWG content mailing list; TDWG TAG mailing list; Christian Gendreau
> Subject: Re: Canonical name parsing
>
> Hi Tim,
>
> I agree, aggregators like GBIF and Canadensys will have to deal with clean and dirty data in each field anyway: they need code libraries to deal with this and it is good that these are being developed. But, that doesn't help someone who wants to use data from a Darwin Core Archive with his data in Excel or a Roderic Page who wants to get things done for a prototype.
> Having to use Java libraries or even the Name Parser [1] (though both
> great) is a barrier to data use. Darwin Core (Archives) is not only used for machine to machine interaction, humans use it too, and I think we should allow easy hacking (I mean this in the good sense), especially for something as important as the scientific name.
> In addition, as a data publisher (e.g. for our VASCAN checklist) I
> *do* have the information to provide a clean and simple to use canonicalScientificName, but I just can't share it via the otherwise excellent biodiversity sharing standard Darwin Core. I think that's a pity.
>
> Peter
>
> [1] http://tools.gbif.org/nameparser/
> [2] http://data.canadensys.net/vascan
>
> PS: Yes, Canadensys will use the GBIF interpretation libraries. Since we develop in Java as well, using those libraries is as easy as the proverbial "one line of code". We're looking forward in testing them and providing patches to enhance them. Open source FTW! :-)
>
>
> On Wed, Mar 14, 2012 at 07:32, Tim Robertson [GBIF] <trobertson at gbif.org> wrote:
> > Hi Peter,
> >
> > I'm replying off the TDWG list, since it is a bit of a tangent to your discussion.  If you feel it is relevant, please CC the list again.
> >
> > At GBIF as you know, we have to interpret all kinds of quality of content.  I tend to agree with Donald that this would not really help in consumption, as in my experience we will have to deal with both clean and dirty data in each field *anyway* when this is used at network scale.  I would rather see us evolve the interpretation libraries to handle all the corner cases, which we need to develop anyway.  We already do a pretty decent job at extracting canonicals.  This is further enhanced when you couple the extracted canonical with a fuzzy match against the "authoritative names" we can now index thanks to the availability of checklists in DwC-A format.
> >
> > I know you are a Java shop.  Are you using the GBIF interpretation libraries [1] at the moment?  If not, is there a reason why you don't?
> > They are used in all GBIF projects (portal, checklistbank etc), and the more we enhance them, the better it is for everyone.  We have a significant test coverage [2,3] and there have been quite some man months (years?) spent already in their development and with some real regular expression experts (most notably Markus D. and Dave M.).  All our work is Maven-ized, versioned and available in our Maven repository [4].
> >
> > I hope these are interesting to you.  We would welcome any patches to enhance them, or assistance in identifying the corner cases and capturing those as unit tests.
> >
> > Hope this helps,
> > Tim
> >
> > [1]
> > http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src
> > /main/java/org/gbif/ecat/parser/NameParser.java
> > [2]
> > http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src
> > /test/java/org/gbif/ecat/parser/NameParserTest.java
> > [3]
> > http://code.google.com/p/gbif-ecat/source/browse/trunk/ecat-common/src
> > /#src%2Ftest%2Fresources [4]
> > http://repository.gbif.org/index.html#nexus-search;quick~ecat-common
> >
>
>
>
> --
> Peter Desmet
> Biodiversity Informatics Manager
> Canadensys - www.canadensys.net
>
> Université de Montréal Biodiversity Centre
> 4101 rue Sherbrooke est
> Montreal, QC, H1X2B2
> Canada
>
> Phone: 514-343-6111 #82354
> Fax: 514-343-2288
> Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
> Skype: anderhalv
> Public profile: http://www.linkedin.com/in/peterdesmet
>
>
> _______________________________________________
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--
Peter Desmet
Biodiversity Informatics Manager
Canadensys - www.canadensys.net

Université de Montréal Biodiversity Centre
4101 rue Sherbrooke est
Montreal, QC, H1X2B2
Canada

Phone: 514-343-6111 #82354
Fax: 514-343-2288
Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
Skype: anderhalv
Public profile: http://www.linkedin.com/in/peterdesmet

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-- 
Peter Desmet
Biodiversity Informatics Manager
Canadensys - www.canadensys.net

Université de Montréal Biodiversity Centre
4101 rue Sherbrooke est
Montreal, QC, H1X2B2
Canada

Phone: 514-343-6111 #82354
Fax: 514-343-2288
Email: peter.desmet at umontreal.ca / peter.desmet.cubc at gmail.com
Skype: anderhalv
Public profile: http://www.linkedin.com/in/peterdesmet