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BioStor Next

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Talk given at BioDiversity Next, Leiden, 23 October 2019

Published in: Science
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BioStor Next

  1. 1. BioStor Next (AKA: Text-mining BHL: towards new interfaces to the biodiversity literature) @rdmpage https://iphylo.blogspot.com
  2. 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. 3. BHL makes stuff available… but where are the articles?
  4. 4. BHL Item 261937 before BioStor...
  5. 5. … and after BioStor
  6. 6. An article from BHL Item 261937 on BioStor 200K+ articles from BHL, running since 2009 (new version last week), https://biostor.org
  7. 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. 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. 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. 10. Map of localities extracted from BioStor article
  11. 11. H3: A Hexagonal Hierarchical Geospatial Indexing System https://github.com/uber/h3
  12. 12. Biodiversity knowledge graph
  13. 13. 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!
  14. 14. 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)
  15. 15. Extract more articles Geographic search Atomise articles Embed in knowledge graph

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