lecture provided at the Systematicas Association Biennial meeting, Oxford, 28.8.2015 http://systass.org/biennial2015/

1. Donat Agosti Plazi
http://plazi.org
Systematics Association
Oxford, 28. August 2015
Nothing in taxonomy makes sense
except in the light of Open Access

3. I want to be able at anytime, anywhere to access, mine and analyse a
significant body of published and digitized taxonomic knowledge.
I want to build by machine the catalogue of life.
I hope taxonomiy communications arrives in the 21st century
Vision and hope

4. 1. The demand
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).
2004

5. 2. The corpus of taxonomic literature

6. Build and establish a TreatmentBank, such as Plazi, as basis for
content mining of and linking to the taxonomic literature
3. The core corpus of taxonomic knowledge: Treatments

7. 4. Make use of the semantic linked WWW
Avoid all the waistful actual publishing!
• Publish structured data
• Publish open access
• Make taxonomic literature first class literature by minting
DOIs and making digital copies accessible
• Add links to names, treatments, articles, DNA sequences,
digital objects
• Help by building your own public corpus of citable data
Pensoft journals (e.g. Biodiversity Data Journal, Zookeys,
Phytokeys) are the gold standard.

8. Surfing or the seduction of science (for a young kid)

9. Surfing or the seduction of science (for a young kid)

10. Surfing or the seduction of science (for a young kid)

11. Surfing or the seduction of science (for an adult)

12. Get a copy of the Cyclothone paper
Surfing or the seduction of science (for an adult)

13. Surfing or the imperative for science

14. Surfing or the imperative for science

15. Linking treatments and data with external resources
NCBI
Surfing or the imperative for science

16. Establish Plazi as, or use Plazi to build TreatmentBank as source for content mining of the
taxonomic literature
TreatmentBank

17. What are the species in Amazonia?
TreatmentBank

18. Countries (Region)
Australia (Queensland)
Export species materials citations (DwC)

19. Text mining tools: Visualization of treatment content
Summary of content of 37 Zootaxa spider publications and 8
Biodiversity Data Journal. (Miller et al., 2015)

20. 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
Text mining tools: Visualization of treatment content

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

22. The demand: scientists and citizen scientists
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

23. Online catalogue
The interest of big science
2004
2005

24. The demand: scientists and citizen scientists

25. The scientific challenge: Bridging the gap
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

26. Where do we stand?

28. The bristlemouths are a rapacious
family of deep-sea fishes that include
the wildly successful genus
Cyclothone
In contrast, ichthyologists put the
likely figure for bristlemouths at
hundreds of trillions — and perhaps
quadrillions, or thousands of
trillions.

29. The bristlemouths are a rapacious
family of deep-sea fishes that include
the wildly successful genus
Cyclothone

31. Taxonomy?
Source?

33. Issue USD 266.00
Article USD 48.00

34. Get a copy of the Cyclothone paper
Our contribution for a better understanding of biodiversity

35. Access to ant taxonomic publications through antbase.org /Smithsonian Institution, including currently the entire
body of non-copyrighted publications since 1758 (>4,000 publications or 85,000 pages. Source: (Agosti 2005)
Access

36. • Limited access (copyright)
• Limited discoverability of content
• Research results cannot be cited
• Data mining does not work
Issues of access

37. Provide an open access, linked corpus of taxonomic literature
A solution

38. Surfing at breakfast table

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

40. Surfing or the imperative for science

41. Surfing or the imperative for science

42. Surfing or the imperative for science

43. LODPDF
HNS
H
Surfing or the imperative for science: Use of name services

44. The goal

45. Create a citable open corpus of taxonomic publications

47. Biodiversity Literature Repository: Record

48. Biodiversity Literature Repository: RecordTreatment
Illustration

49. http://plazi.org/wiki/Blue_ListPatterson et al., 2014: http://dx.doi.org/10.1186/1756-0500-7-79
Legal issues

50. Workflow
Plazi
SRS
find scan «OCR» markup store +
access

51. 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>
Semantisch
erweiterter Text
(TaxonX)
… alternatives: From human to machine readable text
RDF

52. Plazi tools: table extraction
«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

53. Plazi tools: discovering of scientific names

54. Plazi tools: discovering and parsing of bibliographic references

55. Plazi tools: discovering and parsing of observation data

56. Plazi tools: discovering of treatments

57. Treatment: a well defined part of an article that
defines the particular usage of a scientific name
by an authority at a given time (a page(s) in a
publication).
Treatment
The special case taxonomic literature: The citated elements are
treatments, not article
Formica obsoleta Linnaeus, 1758: 580

58. Treatment

59. Original combinations
Reference to an orginal combination
Subsequent useages of names cite the referenced treatment
What is a treatment?

60. Treatment and treatment reference and citation
Treatmentcitation
Treatment
references

61. Treatment
Citing of treatments or linking of treatments to treatments
By minting persistent httpURIs for treatments, treatments
can be cited like a bibliographic reference
http://treatment.plazi.org/id/A9FFD1FC-4629-FFB4-968F-AD38386521BA

62. Status quo
• 50,000+ treatments life, daily growth
• RDF in Betaversion
• GoldenGate Imagine (PDF and text mining tool) in betaversion
• Provider for data for NCBI, Wikidata, GBIF, EOL, antweb
• Biodiversity Literature Repository functional

63. Next steps
• Collaborate with ContentMine to extract >50
treatments/day

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

65. Next steps
• Collaborate with ContentMine to extract 50 treatments/day
• 1 Million treatments life
• RDF Version accessibl
• GoldenGate Imagine (Text mining tool)
• Provider für Daten für NCBI, GBIF, EOL, antweb
• Biodiversity Literature Repository mit 100,000 bibliographic
references and digital copies (PDF, images, etc.)

66. Next steps
BUT

67. Next steps
Avoid all this waste (our next generation will have to clean up)!
Publish structured data
Publish open access
Publish in journals with DOI
Add links to names, treatments, articles, DNA sequences, digital
objects
Help build your own corpus of citable data
Pensoft journals (e.g. Biodiversity Data Journal, Zookeys,
Phytokeys) are the gold standard.

68. Thanks!
Donat Agosti
agosti@plazi.org
Acknowledgment: Pensoft, Zenodo/CERN, NCBI, Wikidata, ContentMine