08.11.2017 13:16

Expanded access to images in the Biodiversity Literature Repository

Zenodeo interface and displayed images of Ocellus, search for Plusiinae

The Biodiversity Literature Repository at Zenodo is holding now over 160,000 figures originally included in scientific publications and is daily updated. Each image is open access. It has a link to the original source – also included in the image metadata – and to related items, such as the taxonomic treatment that cites the image.

Originally, Zenodo has been created as a repository for the deposition of single documents, research data, files, but with an option to automate the upload (and download) automatically using its API.

With the expansion of our text and data mining activities at Plazi we started to upload not only the articles, but the images extracted in the process of text and data mining taxonomic literature. Similarly, Pensoft uploaded all the images contained in their publications. Not only can the upload of images of a single article become quickly complex and time consuming when including all the links, but it is impossible batch processed articles.

A feature that yet had to be implemented is to access, find and compare images. Currently only one image at a time can be viewed. 

The above example is made possible by a new API developed by Plazi member Puneet Kishor and available at github.com/punkish/zenodeo. A working example may be seen at zenodeo.punkish.org/examples and an advanced version at ocellus.punkish.org. This is a first step from BLR and ultimately Zenodo to provide access to multiple images following a simple search. An alternative access has recently been provided by Rod Page. 

Even though the example is not intended as a proper user interface, it shows immediately the power of having multiple images available at one glance, or to visualize a search in BLR.  In fact, it is a by product of an effort to document the Zenodo API, that will be used to create a dedicated image search user interface at BLR. With that in mind, remember that it might take a moment to see the images if you enter a search term that not has been used before.

The API behind this little example is available at github.com/punkish/zenodeo and is intended to foster more use of the images included in the rapidly growing Biodiversity Literature Repository. It hopefully also stimulates further developments of the API and BLR as such. For further inquiries contact plazi.