Wednesday, January 24, 2018

Guest post: The Not problem

Bob mesibovThe following is a guest post by Bob Mesibov.

Nico Franz and Beckett Sterner created a stir last year with a preprint in bioRxiv about expert validation (or the lack of it) in the "backbone" classifications used by aggregators. The final version of the paper was published this month in the OUP journal Database (doi:10.1093/database/bax100).

To see what effect "backbone" taxonomies are having on aggregated occurrence records, I've recently been auditing datasets from GBIF and the Atlas of Living Australia. The results are remarkable, and I'll be submitting a write-up of the audits for formal publication shortly. Here I'd like to share the fascinating case of the genus Not Chan, 2016.

I found this genus in GBIF. A Darwin Core record uploaded by the New Zealand Arthropod Collection (NZAC02015964) had the string "not identified on slide" in the scientificName field, and no other taxonomic information.

GBIF processed this record and matched it to the genus Not Chan, 2016, which is noted as "doubtful" and "incertae sedis".

There are 949 other records of this genus around the world, carefully mapped by GBIF. The occurrences come from NZAC and nine other datasets. The full scientific names and their numbers of GBIF records are:

2Not argostemma
14not Buellia
1not found, check spelling
1Not given (see specimen note) bucculenta
1Not given (see specimen note) ortoni
1Not given (see specimen note) ptychophora
1Not given (see specimen note) subpalliata
1not identified on slide
1not indentified
1Not known not known
1Not known sp.
1not Lecania
4Not listed
873Not naturalised in SA sp.
18Not payena
5not Punctelia
18not used
6Not used capricornia Pleijel & Rouse, 2000

GBIF cites this article on barnacles as the source of the genus, although the name should really be Not Chan et al., 2016. A careful reading of this article left me baffled, since the authors nowhere use "not" as a scientific name.

Next I checked the Catalogue of Life. Did CoL list this genus, and did CoL attribute it to Chan? No, but "Not assigned" appears 479 times among the names of suprageneric taxa, and the December 2018 CoL checklist includes the infraspecies "Not diogenes rectmanus Lanchester,1902" as a synonym.

The Encyclopedia of Life also has "Not" pages, but these have in turn been aggregated on the "EOL pages that don't represent real taxa" page, and under the listing for the "Not assigned36" page someone has written:

This page contains a bunch of nodes from the EOL staff Scratchpad. NB someone should go in and clean up that classification.

"Someone should go in and clean up that classification" is also the GBIF approach to its "backbone" taxonomy, although they think of that as "we would like the biodiversity informatics community and expert taxonomists to point out where we've messed up". Franz and Sterner (2018) have also called for collaboration, but in the direction of allowing for multiple taxonomic schemes and differing identications in aggregated biodiversity data. Technically, that would be tricky. Maybe the challenge of setting up taxonomic concept graphs will attract brilliant developers to GBIF and other aggregators.

Meanwhile, Not Chan, 2016 will endure and aggregated biodiversity records will retain their vast assortment of invalid data items, character encoding failures, incorrect formatting, duplications and truncated data items. In a post last November on the GitHub CoL+ pages I wrote:

Being old and cynical, I can speculate that in the time spent arguing the "politics" of aggregation in recent years, a competent digital librarian or data scientist would have fixed all the CoL issues and would be halfway through GBIF's. But neither of those aggregators employ digital librarians or data scientists, and I'm guessing that CoL+ won't employ one, either.