The document discusses Plazi's work on converting biodiversity literature into structured data through text mining and markup. Key points include: - Plazi extracts scientific names, tables, references and geographic data from literature and converts it into semantically enriched text and RDF. - Their pipelines currently have over 50,000 taxonomic treatments life and are providing data to databases like NCBI, GBIF and EOL. - Future plans include collaborating with ContentMine for daily treatment extraction, releasing RDF and text mining versions 1.0, and expanding the biodiversity literature repository to 100,000 references.

1. Donat Agosti Plazi
http://plazi.org
Linked Data Switzerland Workshop
8th October, HES-SO, Sierre
Open Access to Scientific Data

2. Google.maps

3. Search.ch

4. Search.ch

5. food
Search.ch

6. 4min
Search.ch

7. 46°16'57.80"N 7°32'23.11"E46°16'56.81"N 7°32'13.59"E
46°17'3.98"N 7°32'13.00"E
46°17'5.18"N 7°32'18.34"E
203m
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8. locationlocation
location
location
distance
location
location
Search.ch

9. hostgastronomy
gastronomy
gastronomy
welfare
gastronomy
gastronomy
Search.ch

11. Lateinische
Namen als
Zugang zur
Wissenschaft

16. Treatment

19. XML
RDF

20. The «Mehlwurm» lives in dry bread... or the Potential of LOD
has traits
is part of
refers to
has traits
“The larva of the mealworm lives in dry
bread and can be eaten in Switzerland”

21. The Scientific Challenge
1 tnntttccca cgaataaata atataagatt ttgattatta cctccttctt taattttatt
61 attatcaaga agattagttt ataaaggagt aggaacagga tgaactgttt atcctccttt
121 atctaataat ttatatcata atggattttc aactgattta gcaatttttt ctttacatat
181 tgcaggaata tcatcaatta taggagcaat taattttatt tcaacaattt taaatataca
241 tcataaaaat ttatcattag ataaaattcc attgttagtt tgatcaattt taattacagc
301 tattttatta ttattatctt tacctgtatt agcaggtgca attactatat tattaactga
361 tcgaaatcta aatacaactt tttttgatcc ttcgggtgga ggagatccaa ttttatatca
421 acatttattt

22. The Scientific Challenge

23. The Scientific Challenge

24. The Scientific Challenge

25. LODPDF
HNS
H
The Scientific Challenge

26. The Scientific Challenge

27. The Scientific Challenge

28. The Political Vision: Create the LOD-Cloud

29. The Plazi Vision: The Giant Global Biodiversity Graph
Plazi’s intended uses of LOD
• Public discovery by people not otherwise connected to other discovery services such as
Plazi’s own, the GBIF data repository, …. of data about species extracted from the
publications in which they are described
• Public facility for citation of Plazi’s data by arbitrary internet users.
• Plazi creates a new dataset from literature/publications rather than republish existing
data sets

30. The Plazi Vision: The Giant Global Biodiversity Graph
Legal
Social
Technical
Ontologies
Infrastructure
500 M
pages 5*

31. What does this mean?
The Linking Open Data cloud diagram
Linked Open Data Cloud

32. Text
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identifier="193329"/>
<tax:xmldata>
<dc:Genus>Mystrium</dc:Genus>
<dc:Species>leonie</dc:Species>
</tax:xmldata>
Mystrium leonie
</tax:name>
<tax:status>n. sp.</tax:status>
Fig 1 D - F
</tax:nomenclature>
<tax:div type="description">
<tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI
1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margi
to a sharp apical tooth, the apex parallel to the an
(Holotype with material in mandibles, so mandibles a
$ described below from paratypes.) Median clypeus
....
</treatment>
Semantic
enchanced Text
(TaxonX/Taxpub)
… alternatives: From human to machine readable text
RDF

33. Countries (Region)
Australia (Queensland)
Export species materials citations (DwC)
Treatment Content Visualization
10.3897/BDJ.3.e5063

34. Treatment Graph for the Malagasy Ants Aphaenogaster

35. Treatment Graph for the Malagasy Ants Aphaenogaster
Original description
Re-description cites
cites/
synonymizes
Re-description
Re-de.
Re-description
cites

36. Treatment Graph for the Ant Azteca alfari
https://github.com/plazi/TreatmentOntologies

37. Pseudomyrmex ants and Vachellia ant-acacias
are a classic example of mutualism in biology.
allenii
melanoceras
ruddiae
chiapensis
collinsii
cookii
cornigera
globulifera
hindsii
janzenii
mayana
sphaerocephala
boopis
flavicornis
hesperius
ita
janzeni
kuenckeli
mixtecus
nigrocinctus
nigropilosus
opaciceps
particeps
peperi
reconditus
satanicus
simulans
spinicola
subtilissimus
veneficus
ferrugineus
gentlei
gracilis
Transbiotic link network
Associated species linked through
references in taxonomic treatments
Acacia-ant species: Pseudomyrmex gracili
Treatment: redescription
Associated ant-acacia: Acacia gentlei
Ants Plants
Photocredits: Alex Wild
Treatment
Treatments linked
through citations
Treatment opportunities

38. Treatment
Verlinkung der Daten mit externen Referenzen
5*
2014
NCBI

39. Zugang zu wissenschaftlicher Literatur: DOI via Zenodo/CERN

40. Open Access as Necessity
Before antbase.org, Harvard‘s Museum of Comparative Zoology could claim to be the
only location with a complete set of ant systematics publications from 1758 - present.
Through antbase.org‘s
digital library, access
to this body of
literature is worldwide,
and it is actively used
(>10,000 visits in one
month only).
Online catalogue
Open access
Online library
2004

41. Conversion Workflows: Plazi
Plazi
SRS
find scan «OCR» markup store +
access
Swiss exceptions to copyright law to extract data is an advantage for the sciences
in Switzerland

42. Conversion Workflows: Plazi: Scientific Names

43. Conversion Workflows: Plazi: Tables
«Treatment»
Wissenschaftliche Artname
Verbreitungsnachweis
Cataglyphis tartessica workers
Variable mean ± SD
Head length 11.23 ± 0.12
Head width 11.15 ± 0.12
Scape length 11.47 ± 0.12
Mesosoma length 11.94 ± 0.16
Femur length 12.03 ± 0.14
Cephalic index 0 93.60 ± 3.940
Scape index 128.10 ± 7.660

44. Conversion Workflows: Plazi: Bibliographic References

45. Conversion Workflows: Plazi: Geographic data

46. Conversion Workflows: Plazi: Pipelines

47. Status quo
• 50,000+ treatments life
• RDF in Betaversion
• GoldenGate Imagine (Text mining tool) in Betaversion
• Provider für Daten für NCBI, GBIF, EOL, antweb
• Biodiversity Literature Repository functional

48. Trait information
machine ready
ResolutionReconciliation
TreatmentBank
NAMES
MANAGEMENT
CITATION
MANAGEMENT
REFBANK
TREATMENT
MANAGEMENT
ATOMIZATION &
SEMANTICIZATION
OF CONTENT MARKUP / initial
trait extraction
Specialist taxonomic
databases
Next steps: HES-SO, HEG Geneva

49. Next steps: CotentMine
Planned collaboration with ContentMine to extract treatments on a
daly bases
http://www.slideshare.net/petermurrayrust/?
BioDiv

50. article
treatment
Cites
httpURI
cites (DOI)
Scientific name
https://www.wikidata.org/wiki/
Property:P1992
Feed Wikipedia with taxonomic data

51. Publications, one of our footprints

52. Next steps
• 1 Million treatments life
• RDF Version 1
• GoldenGate Imagine (Text mining tool) Version 1
• Provider für Daten für NCBI, GBIF, EOL, antweb
• Biodiversity Literature Repository mit 100,000
Bibliographischen Referenzen und digitalen Versionen

53. Danke!
Donat Agosti
agosti@plazi.org