University of Glasgow

Roderic Page

![220px The Face of a Lupine
Blue](https://lh3.googleusercontent.com/-Vbm9mlgY6sU/WFwUL5gdUyI/AAAAAAAAEVw/QRqkCxvJl4w/220px-The_Face_of_a_Lupine_Blue.jpg?imgmax=1600 "220px-The_Face_of_a_Lupine_Blue.jpg"){border="0"
width="128" height="96" style="float:right;"}Following on from [adding
DNA barcodes to
GBIF](http://iphylo.blogspot.com/2016/12/ibol-dna-barcodes-in-gbif.html)
I\'ve now uploaded a taxonomic classification of DNA barcode BINs
(Barcode Index Numbers). Each BIN is a cluster of similar DNA barcodes
that is essentially equivalent to a species. For more details see:

> Ratnasingham, S., & Hebert, P. D. N. (2013, July 8). A DNA-Based
> Registry for All Animal Species: The Barcode Index Number (BIN)
> System. (D. Fontaneto, Ed.), PLoS ONE. Public Library of Science
> (PLoS). <https://doi.org/10.1371/journal.pone.0066213>

The data I\'ve uploaded was obtained by screen scraping the BOLD web
site for each BIN in the DNA barcode dataset (BOLD\'s API doesn\'t let
me get all the information I want). In addition to the taxonomic
hierarchy associated with each BIN I\'ve also extracted any publications
mentioned on the BIN page, and subsequently tried to link those to the
corresponding DOI, if the publication has one. The code for all this is
available on GitHub <https://github.com/rdmpage/bold-bins>, which also
serves as the host for the Darwin Core Archive for this dataset.
There\'s a neat trick where you can use a .gitattributes file to tell
GitHub not store certain files in the zip file it creates for the
repository (see [Excluding files from git archive exports using
gitattributes](https://feeding.cloud.geek.nz/posts/excluding-files-from-git-archive/)
by [@fmarier](https://twitter.com/fmarier)).

Having done this, I\'ve a few thoughts.

#### Please, please use DOIs for articles

BOLD pages for BINs often include one or more papers that published the
barcodes included in that BIN. This is great, but often links to these
papers are pretty strange:

> Ever wonder why DOIs are nice? Take a look at this URL for an article
> :O This is why you want to store DOIs in databases, not links\...
> [pic.twitter.com/QzthcL8f7k](https://t.co/QzthcL8f7k)
>
> --- Roderic Page (@rdmpage) [December 20,
> 2016](https://twitter.com/rdmpage/status/811162429514256384)

If you are going to store literature in a database treat links to
articles with great care. they are often full of extraneous stuff that
depends on how the user reached that article online. DOIs greatly
simplify this process. Instead of a URL like
<http://onlinelibrary.wiley.com/store/10.1111/j.1755-0998.2009.02650.x/asset/j.1755-0998.2009.02650.x.pdf?v=1&t=hellc54c&s=e14bbc4146b66a051ad5cd1f5361ac2e16dc5831&systemMessage=Pay+Per+View+will+be+unavailable+for+upto+3+hours+from+06%3A00+EST+March+23rd+>
(I kid you not) you should use the DOI
[10.1111/j.1755-0998.2009.02650.x](http://dx.doi.org/10.1111/j.1755-0998.2009.02650.x).

Adding DOIs to these articles means GBIF will display them on the
corresponding species page, for example [*Centromerus sylvaticus*
(Blackwall, 1841)](http://www.gbif.org/species/2138546) has links to
these two papers:

> Telfer, A., deWaard, J., Young, M., Quinn, J., Perez, K., Sobel, C.,
> ... Hebert, P. (2015, August 30). Biodiversity inventories in high
> gear: DNA barcoding facilitates a rapid biotic survey of a temperate
> nature reserve. Biodiversity Data Journal. Pensoft Publishers.
> <https://doi.org/10.3897/bdj.3.e6313>

> Blagoev, G. A., deWaard, J. R., Ratnasingham, S., deWaard, S. L., Lu,
> L., Robertson, J., ... Hebert, P. D. N. (2015, July 26). Untangling
> taxonomy: a DNA barcode reference library for Canadian spiders.
> Molecular Ecology Resources. Wiley-Blackwell.
> <https://doi.org/10.1111/1755-0998.12444>

Now GBIF users can easily explore what we know about barcodes from this
species by going directly to the primary literature.

#### Dark taxa

In an earlier post I discussed [dark
taxa](http://iphylo.blogspot.com/2011/04/dark-taxa-genbank-in-post-taxonomic.html),
which are taxa that lack formal scientific names. BOLD is full of these,
so many of the taxa I\'ve added to GBIF don\'t have Linnean names.
Instead I\'ve used a combination of higher taxon name and the BIN
itself.

#### Composite taxa

Having said that BINs are essentially the same as species, this need not
imply that there\'s a one-to-one match between BINs and currently
recognised species (indeed, this is of the things that makes barcoding
so interesting, it\'s ability to discover hidden variation without taxa
currently considered to be a single species). This means that some BINs
will have the same name (significant variation within a species), and
some BINs will have multiple names (more than one species name assigned
to the same BIN). For example,
[BOLD:AAA2525](http://bins.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAA2525)
is a cluster of DNA barcodes with the following names attached:

- *Icaricia lupini*
- *Icaricia acmon*
- *Icaricia neurona*
- *Plebejus lupini*
- *Aricia* sp. RV-2009
- *Aricia acmon*
- *Plebejus acmon*
- *Plebejus elvira*
- *Icaricia lupini texanus*
- *Icaricia lupini monticola*
- *Icaricia lupini chlorina*
- *Icaricia lupini lupini*
- *Icaricia lupini alpicola*

This cluster of names includes subspecies, synonyms (e.g. ). Looking at
the phylogeny for this BIN (PDF-only) some of these names are
intermingled suggesting that some specimens might be misidentified,
apparently *Icaricia lupini* and *I. acmon* are very similar:

> Coutsis, J. G. (2011). The male genitalia of N American Icaricia
> lupini and I. acmon; how they differ from each other and how they
> compare to those of the other two members of the group, I. neurona and
> I. shasta (Lepidoptera: Lycaenidae, Polyommatiti). Phegea, 39(4),
> 144-151. Retrieved from <http://biostor.org/reference/160269>

#### Summary

This is a first attempt to integrate DNA barcode taxonomy into GBIF, so
there are going to be some issues to explore. GBIF currently assumes
taxa can be easily mapped to a Linnean hierarchy. While this is
ultimately likely to be true for animal COI barcodes, getting there is
going to be messy while we have numerous dark taxa and/or BINs which
don\'t match the current identifications of the voucher specimens.

Perhaps it\'s worth asking whether attempt to fit the results of DNA
barcoding into a classical taxonomy is the best way forward. In doing so
we loose much of what makes barcodoing so powerful, namely a
specimen-level phylogenetic tree. Maybe what we should be really
thinking about is ways to explore barcoding data natively. See [Notes on
next steps for the million DNA barcodes
map](http://iphylo.blogspot.com/2016/05/notes-on-next-steps-for-million-dna.html)
for some thoughts on how to do that.

Image from Wikimedia Commons [The Face of a Lupine
Blue](https://en.wikipedia.org/wiki/File:The_Face_of_a_Lupine_Blue.jpg)
by [Ingrid Taylar](http://flickr.com/photos/49503118795@N01).


Following on from adding DNA barcodes to GBIF I've now uploaded a taxonomic classification of DNA barcode BINs (Barcode Index Numbers). Each BIN is a cluster of similar DNA barcodes that is essentially equivalent to a species.

Messaggi di Rogue Scholar

DNA barcoding taxonomy now in GBIF