University of Glasgow

Roderic Page

**TL;DR;** The Plant List is now in GBIF
<http://doi.org/10.15468/btkum2>.

Readers of this blog may recall that I\'ve had a somewhat jaundiced view
of [The Plant List](http://www.theplantlist.org). The first version was
release with a Creative Commons Attribution-NonCommercial-NoDerivs (CC
BY-NC-ND) license which allowed copying so long as didn\'t create a
derived work ([The Plant List: nice data, shame it\'s not
open](http://iphylo.blogspot.com/2010/12/plant-list-nice-data-shame-it-not-open.html)).
This is frankly about the silliest possible license for a data set as,
from my perspective, the whole reason for releasing data is so that it
can be combined and enhanced with other data.

The second release (version 1.1) dropped an explicit CC license in
favour of almost the reverse position (!). You can\'t copy the list \"as
is\" without permission, but you can make derivative works \"without
prior written permission from us\" (see [Terms of Use for The Plant
List](http://www.theplantlist.org/1.1/terms/)). Progress, of a sort.

So, for the last week I\'ve been working on getting a version of The
Plant List into GBIF, and I\'ve finally managed to achieve this.
There\'s isn\'t a single place you can grab the whole plant list, so you
have to scrape the web site for CSV files, then glue them together. I
would could argue that converting the data into the Darwin Core Archive
is a derived work, but in case this seems not derivative enough (of
course, nobody seems ready to define just what \"derived\" actually
means) I started to augment the list of names by adding bibliographic
identifiers. I\'ve long argued (see e.g. [Surfacing the deep data of
taxonomy](http://dx.doi.org/10.3897/zookeys.550.9293)) that a
fundamental limitation of existing taxonomic database is that they
don\'t explicitly link to the primary literature. This is why I built
[BioNames](http://bionames.org), and why I\'ve been working to link the
\"micro citations\" in [IPNI](http://www.ipni.org) to identifiers such
as DOIs, JSTOR likes, BioStor URLs and BHL page links (see [project on
github](https://github.com/rdmpage/ipni-names)). So, I\'ve added about
120,000 DOIs and JSTOR links to names in the plant list. This is a
subset of the links I\'ve found for IPNI, but for this first release
I\'ve tried to keep things simple. I\'ve also made the link between
Plant List name and DOI/JSTOR via the IPNI identifier for a name, and
the Plant List has ommitted quite a few IPNI ids for reasons which
aren\'t clear.

The Plant List version I\'ve created is available in GBIF
(<http://doi.org/10.15468/btkum2> and
<http://www.gbif.org/dataset/d9a4eedb-e985-4456-ad46-3df8472e00e8>).
Having another list of plant names will be a useful addition to the
checklists that GBIF already has, even if the Plant List is already
somewhat out of date.

#### DOIs

One feature of enhanced Plant List in GBIF is that for a subset of names
(currently about 10%) there are direct links to the original publication
of that name. For example, the record for [*Haniffia
albiflora*](http://www.theplantlist.org/tpl1.1/record/kew-247962) in the
Plant List has a fairly cryptic bibliographic citation *Nordic J. Bot.
20: 287 2000* and no link to that publication. In the version I\'ve
uploaded to GBIF the name [*Haniffia
albiflora*](http://www.gbif.org/species/118470013) looks like this:
![Haniffia](https://lh3.googleusercontent.com/-53RPfncCGZs/VuxsNBOoHBI/AAAAAAAAEJM/Kq1HPJ1IHmU/Haniffia.png?imgmax=1600 "Haniffia.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="165"} Note the full citation. But more
importantly, the **Publisher record** link is the DOI
<http://doi.org/10.1111/j.1756-1051.2000.tb00745.x> so clicking on it
takes you to the original description of this species:
![Doi4](https://lh3.googleusercontent.com/-WdOdiPDiMIo/VuxsOK_GhUI/AAAAAAAAEJQ/2SICqYo9izM/doi4.png?imgmax=1600 "doi4.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="232"} There is a lot of plant taxonomic
literature available in JSTOR, sadly most of it (along with specimen
images) behind a paywall (see [Why are botanists locking away their data
in JSTOR Plant
Science?](http://iphylo.blogspot.com/2013/02/why-are-botanists-locking-away-their.html)).
Some of the links from GBIF take you to JSTOR:
![Doi3](https://lh3.googleusercontent.com/-eNxnm-4v484/VuxsPFN3v-I/AAAAAAAAEJU/DNTTxTALKFw/doi3.png?imgmax=1600 "doi3.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="235"} The DOI landscape is evolving, and
there are now multiple DOI registration agencies minting DOIs for
scientific papers. CrossRef provides easily the best services for
discovery and metadata harvesting, other agencies often have no
equivalent, which makes it hard to discover DOIs for those papers hard.
I\'ve spent some time getting this information for Chinese and Taiwanese
articles, e.g. <http://dx.doi.org/10.6165/tai.1985.30.5>:
![Doi1](https://lh3.googleusercontent.com/-vEnzeeftmK4/VuxsQA2egkI/AAAAAAAAEJY/p0G_VrdaiLI/doi1.png?imgmax=1600 "doi1.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="391"} and
<http://dx.doi.org/10.3969/j.issn.2095-0845.2005.04.002>:
![Doi2](https://lh3.googleusercontent.com/-mvw7ivTX-ec/VuxsRPqM4eI/AAAAAAAAEJc/sVtBGd0RxEI/doi2.png?imgmax=1600 "doi2.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="392"} to give two example of articles
that are now linked to from the corresponding species page in GBIF.

**It\'s all about the links** To reiterate, I believe that one of the
key challenges facing biodiversity informatics is cross linking between
disparate types of data and source of information. At the moment most of
our data resides in disconnected silos. The links I\'m adding to plant
names are a small step, but they can lead to all sorts of possibilities.
For example, users of GBIF can click on a link and see the original
paper. If, for example, GBIF doesn\'t have a map for the species
discussed in that paper, it\'s likely that the paper may have some
information (e.g., the type locality). If users click on the links, then
that is going to drive more traffic to the original literature, thus
increasing its visibility. Furthermore, now that we have a taxon
identifier (from GBIF) linked to a bibliographic identifier, we can go
in the opposite direction. Earlier I proposed a Javascript bookmarklet
as a way to augment the information on a web page (see [Rethinking
annotating biodiversity
data](http://iphylo.blogspot.com/2014/03/rethinking-annotating-biodiversity-data.html)).
We could have a popup on a article web page that can tell the user about
the taxa mentioned in that paper. If GBIF has a ma for those taxa, we
can immediately place that paper in a geospatial context (e.g., Africa).
This is barely scratching the surface of what is possible once we start
breaking out of silos and share deeply linked data.


<strong>
 TL;DR;
</strong>
The Plant List is now in GBIF http://doi.org/10.15468/btkum2. Readers of this blog may recall that I've had a somewhat jaundiced view of The Plant List.

Messaggi di Rogue Scholar

The Plant List, GBIF, and the primary literature