Friday, June 04, 2021

Thoughts on BHL, ALA, GBIF, and Plazi

If you compare the impact that BHL and Plazi have on GBIF, then it's clear that BHL is almost invisible. Plazi has successfully in carved out a niche where they generate tens of thousands of datasets from text mining the taxonomic literature, whereas BHL is a participant in name only. It's not as if BHL lacks geographic data. I recently added back a map display in BioStor where each dot is a pair of latitude and longitude coordinates mentioned in an article derived from BHL's scans.

This data has the potential to fill in gaps in our knowledge of species distributions. For example, the Atlas of Living Australia (ALA) shows the following map for the cladoceran (water flea) Simocephalus:

Compare this to the localities mentioned in just one paper on this genus:

Franklin, D. C., Michael, B., & Mace, M. (2005). New location records for some butterflies of the Top End and Kimberley regions. Northern Territory Naturalist, 18, 1–7. Retrieved from https://biostor.org/reference/254167

There are records in this paper for species that currently have no records at all in ALA (e.g., Simocephalus serrulatus):

As it stands BioStor simply extracts localities, it doesn't extract the full "material citation" from the text (that is, the specimen code, date collected, locality, etc. for each occurrence). If it did, it would then be in a position to contribute a large amount of data to ALA and GBIF (and elsewhere). Not only that, if it followed the Plazi model this contribution would be measurable (for example, in terms of numbers of records added, and numbers of data citations). Plazi makes some of its parsing tools available as web services (e.g., http://tb.plazi.org/GgWS/wss/test and https://github.com/gsautter/goldengate-webservices), so in principle we could parse BHL content and extract data in a form usable by ALA and GBIF.

Notes on Plazi web service

The endpoint is http://tb.plazi.org/GgWS/wss/invokeFunction and it accepts POST requests, e.g. data=Namibia%3A%2058%20km%20W%20of%20Kamanjab%20Rest%20Camp%20on%20road%20to%20Grootberg%20Pass%20%2819%C2%B038%2757%22S%2C%2014%C2%B024%2733%22E%29&functionName=GeoCoordinateTaggerNormalizing.webService&dataUrl=&dataFormat=TXT and returns XML.