This document discusses challenges with accessing and processing biodiversity literature and describes efforts to make literature from Biodiversity Heritage Library (BHL) more accessible and machine-readable. BioStor extracts text and figures from over 200,000 BHL articles and makes them searchable online. Efforts are underway to link BHL content to databases and Wikidata to connect literature to species and other entities. The goal is to extract more articles from BHL, enable geographic searches of content, break articles into smaller pieces, and embed literature within a biodiversity knowledge graph.

1. BioStor Next
(AKA: Text-mining BHL: towards new interfaces to the biodiversity
literature)
@rdmpage
https://iphylo.blogspot.com

2. Biodiversity literature challenges
•Discovery (is it online?)
•Accessibility (can I read it?)
•Machine-friendly (can I process it?)
•Knowledge-friendly (is it linked?)

3. BHL makes stuff available… but where are the articles?

4. BHL Item 261937 before BioStor...

5. … and after BioStor

6. An article from BHL Item 261937 on BioStor
200K+ articles from BHL, running since 2009 (new version last week), https://biostor.org

7. • Extract figures from PDF
• Upload to Zenodo, each with a DOI
• Searchable at ocellus.punkish.org
• Can we do this for BHL?
Beyond the PDF…
(see plazi.ch)

8. Fig 1 Distribution of
Begonia sumbawaensis
Girm. (triangles), B.
brangbosangensis Girm.
(circles) and B.
jaranpusangensis Girm.
(square).
Fig. 2 Begonia
sumbawaensis Girm. A.
Habit. B. Female flower.
C. Style. D. Male flower.
E. Stamen. F. Fruit in
cross section. G. Fruit. H.
Stipule. I. Seed. J. Bract.
Drawn by A.
Kusumawati.
Fig. 3 Begonia
brangbosangensis Girm.
A. Habit. B. Male flower.
C. Stamen. D. Female
flower. E. Style. F.
Stipule. G. Seed. H. Fruit
in cross section. I. Fruit.
J. Ovary. Drawn by A.
Kusumawati.
Fig. 4 Begonia
jaranpusangensis Girm.
A. Habit. B. Male flower.
C. Male flower tepal. D.
Stamen. E. Female
flower. F. Female flower
tepal. G. Fruit. H. Style.
Drawn by A. Kusumawati
& Wahyudi.
Three new species of Begonia (Begoniaceae) from Sumbawa Island, Indonesia
(extracted from “born digital” PDF doi:10.3850/s2382581216000041)
Born digital is “easy” 

9. Three new species of Begonia (Begoniaceae) from Sumbawa Island, Indonesia
(extracted from BioStor PDF, ABBYY OCR)
Fig 1. Distribution of
Begonia sumbawaensis
Girm. (triangles), B.
brangbosangensis
Ginn,(circles) and B.
jaranpusangensis Girm.
(square).
Fig. 4. Begonia
jaranpusangensis Ginn. A.
Habit. B. Male flower. C. Male
flower tepal. D.Stamen. E.
Female flower. F. Female
flower tepal. G. Fruit. H. Style.
Drawn by A. Kusumawati&
Wahyudi.
Fig. 3. Begonia
brangbosangensis Ginn. A.
Habit. B. Male flower. C.
Stamen. D. Femaleflower. E.
Style. F. Stipule. G. Seed. H.
Fruit in cross section. I. Fruit.
J. Ovary. Drawn by
A.Kusumawati.
Scanned content not so easy 

10. Map of localities extracted from BioStor article

12. H3: A Hexagonal Hierarchical Geospatial Indexing System
https://github.com/uber/h3

14. Biodiversity knowledge graph

15. Linking BHL
Begonia sumbawaensis
https://www.ipni.org/n/77157221-1
BHL doesn’t know
that this is a new
species…
… but IPNI knows that
Begonia sumbawaensis
is described on this page!

16. Time to join the dots…
• Linking BHL to databases (in both directions)
• Link BHL entities to Wikidata (e.g., authors, journals,
articles) (happening already)
• Represent BHL content as linked data (e.g.,
annotations, cf. International Image Interoperability
Framework, IIIF)

17. Extract more articles
Geographic search
Atomise articles
Embed in knowledge graph