Markup in the mobilization of biodiversity literature

•

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A contribution to the pro-iBiosphere Final Conference on June 12, 2014 in Meise, Belgium. More info via http://wiki.pro-ibiosphere.eu/wiki/Final_Conference .

Wissenschaft Technologie

Daniel Mietchen
Markup in the mobilization of
biodiversity literature
Museum für Naturkunde Berlin

● hundreds of millions of pages
○ ca. 20k treatments of new taxa per year
○ 50-100k re-descriptions annually
○ scattered across thousands of journals
and books
Biodiversity literature

● geared towards the human reader
● not machine-readable (scans/ PDF)
● accumulated over three centuries
● includes much of what is published
today
Legacy literature

● digital > paper-only
● open access > hidden
● with > without open data
● soon: machine readable > PDF
● these biases may skew analyses
Use & citation

● identifying concepts
● linking them using controlled vocabularies
● integrating with other sources of information
Markup

Reis et al. (2008), marked up by Shotton et al. (2009). CC BY 2.5

● automated markup of prospective literature
● crowdsourced markup of legacy literature
● semi-automated markup with expert
assistance
Scaling up

● mark up taxonomic publications henceforth
● focus on revisionary works (biotas)
● adjust granularity to concrete use cases
● follow standards
● automate workflows
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Image credit: Playingwithbrushes, CC BY 2.0

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Markup in the mobilization of biodiversity literature

1. Daniel Mietchen Markup in the mobilization of biodiversity literature Museum für Naturkunde Berlin

2. ● hundreds of millions of pages ○ ca. 20k treatments of new taxa per year ○ 50-100k re-descriptions annually ○ scattered across thousands of journals and books Biodiversity literature

3. ● geared towards the human reader ● not machine-readable (scans/ PDF) ● accumulated over three centuries ● includes much of what is published today Legacy literature

4. ● digital > paper-only ● open access > hidden ● with > without open data ● soon: machine readable > PDF ● these biases may skew analyses Use & citation

5. ● identifying concepts ● linking them using controlled vocabularies ● integrating with other sources of information Markup

6. Reis et al. (2008), marked up by Shotton et al. (2009). CC BY 2.5

7. ● automated markup of prospective literature ● crowdsourced markup of legacy literature ● semi-automated markup with expert assistance Scaling up

8. ● mark up taxonomic publications henceforth ● focus on revisionary works (biotas) ● adjust granularity to concrete use cases ● follow standards ● automate workflows Recommendations

9. Image credit: Playingwithbrushes, CC BY 2.0