University of Glasgow

Roderic Page

A post by on the Plaza blog [Expanded access to images in the
Biodiversity Literature
Repository](http://plazi.org/news/beitrag/expanded-access-to-images-in-the-biodiversity-literature-repository/b86d1880198c5c7315c2d38ae3a82820/)
has prompted me to write up a little toy I created earlier this week.

The [Biodiversity Literature
Repository](https://zenodo.org/communities/biosyslit) (BLR) is a
repository of taxonomic papers hosted by Zenodo. Where possible Plazi
have extracted individual images and added those to the BLR, even if the
article itself is not open access. The justification for being able to
do this is presented here:
[DOI:10.1101/087015](http://dx.doi.org/10.1101/087015). I\'m not
entirely convinced by their argument (see [Copyright and the Use of
Images as Biodiversity
Data](http://iphylo.blogspot.com/2016/11/copyright-and-use-of-images-as.html))
but rather than rehash that argument I decide dit would be much more fun
to get a sense of what is in the BLR. I built a tool to scrape data from
Zenodo and store it in CouchDB, put a simple search engine on top (using
the search functionality in Cloudant) to search within the figure
captions, and wrote some code to use a cloud-based image server to
generate thumbnails for the images in Zenodo (some of which are quite
big). The tool is hosted at Heroku, you can try it out here:
[https://zenodo-blr-interface.herokuapp.com/](https://zenodo-blr-interface.herokuapp.com/?q=female+holotype).

![Screenshot 2017 11 10 11 03
30](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjd5ZsJttDX9vq-vZCMJEc6rOOKEwqvLLTcyAl04u4ag_cwiCMwsRS9bjkN8oDX2MUp4q5l7Ov2PjlV-WrJegkHn5mGUNmGqldm-PPiG7GzjWFcJVU_ui85wFMBKpnvIVTv2W3R/?imgmax=1600 "Screenshot 2017-11-10 11.03.30.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="370"}

This is not going to win any design awards, I\'m simply trying to get a
feel for what imagery BLR has. My initial reactions was \"wow!\".
There\'s a rich range of images, including
[phylogenies](https://zenodo-blr-interface.herokuapp.com/?q=phylogeny),
[type
specimens](https://zenodo-blr-interface.herokuapp.com/?q=holotype),
[habitats](https://zenodo-blr-interface.herokuapp.com/?q=habitat), and
more. Searching by museum codes, e.g.
[NHMUK](https://zenodo-blr-interface.herokuapp.com/?q=NHMUK) is a quick
way to discover images of specimens from various collections.

![Screenshot 2017 11 10 11 22
05](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgfzDJbNBiee4joovRxuOOB1ahKtbuBvYNd8H0cY62NSYPjqURhhHDehamPcwI86Ie-jkiYi4RlucuX2B135vtyW_DW5G5ZOUfQ02vMzy6lftP2xRg2YmuBM5KNc1y5axundmKY/?imgmax=1600 "Screenshot 2017-11-10 11.22.05.png"){style="display:block; margin-left:auto; margin-right:auto;"
border="0" width="460" height="367"}

Based on this experiment there are at least two things I think would be
fun to do.

### Adding more images

BLR already has a lot of images, but the biodiversity literature is
huge, and there\'s a wealth of imagery elsewhere, including journals not
in BLR, and of course the [Biodiversity Heritage
Library](http://biodiversitylibrary.org) (BHL). Extracting images from
articles in BHL would potentially add a vast number of additional
images.

### Machine learning

Machine learning is hot right now, and anyone using iNaturalist is
probably aware of their [use of computer
vision](https://www.inaturalist.org/pages/computer_vision_demo) to
suggest identifications for images you upload. It would be fascinating
to apply machine learning to images in the BLR. Even basic things such
as determining whether an image is a photo or a drawing, how many
specimens are included, what the specimen orientation is, what part of
the organism is being displayed, is the image a map (and of what
country) would be useful. There\'s huge scope here for doing something
interesting with these images.

The [toy I created](https://zenodo-blr-interface.herokuapp.com/) is very
basic, and merely scratches the surface of what could be done (Plazi
have also created their own tool, see
<http://github.com/punkish/zenodeo>). But spending a few minutes
browsing the images is well worthwhile, and if nothing else is a
reminder of both how diverse life is, and how active taxonomists are in
trying to discover and describe that diversity.


A post by on the Plaza blog Expanded access to images in the Biodiversity Literature Repository has prompted me to write up a little toy I created earlier this week. The Biodiversity Literature Repository (BLR) is a repository of taxonomic papers hosted by Zenodo. Where possible Plazi have extracted individual images and added those to the BLR, even if the article itself is not open access.

Postagens de Rogue Scholar

Exploring images in the Biodiversity Literature Repository