1. International Congress of Entomology, Orlando
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Terry Catapano
September 26, 2016
International Congress of Entomology, Orlando

2. Extracting Linked Open Data from Taxonomic Publications
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Plazi
Extracting Linked Open Data from Taxonomic Publications
Terry Catapano
Plazi, New York (

3. 5,000 journals with taxonomic content 1,900,000 species described
Who are we? 3
Plazi
500,000,000+ printed pages
5,000 journals with taxonomic content
1,900,000 species described
20,000,000+ species treatments
BUT: The facts are hidden
Incomplete digitization
Publications are not semantically enhanced
Data are not linked
Most data are not open
Plazi solution:
Linking through taxonomic treatments

4. Taxonomic Treatment Plazi Formica obsoleta Linnaeus, 1758: 580
Who are we? 4
Plazi
Taxonomic Treatment
Formica obsoleta Linnaeus, 1758: 580
name
description
distribution
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).
Linnaeus has to be credited for Latin Binomen AND Treatment.

5. Plazi TreatmentBank: Million Treatment Goal
For 1M Treatments, at minimum:
Identify with HTTP URIs in form of
Metadata
Taxon Concept
Publication Information
Representations
HTML
RDF
[XML]
Exports
Biodiversity Literature Repository
EOL
GBIF
WikiData
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6. Plazi: Output Bibliographic references: > 800,000
Publications (year of publishing): 17,799 (2016: 3,500)
Taxonomic treatments: 165,692 (50,000)
Observation Records: 53099
Observation Records geo-referenced: 23068
Taxonomic names: 152,641 (45,000)
Bibliographic references: > 800,000
RDF triples: > 100 Million (1M)
Scientific illustrations: >140,000 (being uploaded to BLR/Zenodo)
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7. TreatmentBank

8. Plazi: TreatmentBank: Treatment stubs: adding content
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9. Sources Legacy publications Print  Digitization  Text Capture  XML
Digitized  Text Capture  XML
Born Digital  Text Extraction  XML
Prospective publishing
Pensoft Journals TaxPub XML  RDF
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10. Plazi conversion workflow
TreatmentBank
find
scan
text extraction
markup
store
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11. Daily Automated Processing of New Taxa
Notes:
I am afraid, I am going to loose some of you at some point, but I will try to get you all together at the end of the talk

12. TreatmentBank: HTML Representation
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13. Treatment Text: XML Representation

14. XML Representation: Text Markup and Enhancement
Treatments
Treatment Sections
Features of interest
Taxon Names
Treatment Citations
Material Citations (e.g., specimens)
Bibliographic References (w/ citation)
Figures (w/citation)
Tables (w/ ciation)
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15. Nomenclature Section and Taxon Name
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16. Treatment Citation Notes:
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17. Material Citation Notes:
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18. TreatmentBank: online editing: material citation
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19. Semantic XML Publishing: TaxPub
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20. Treatment Data: RDF Representation

21. Treatment Data Published in  Publication
Defines  Taxon Concept [1 and only 1]
Cites  Treatments/Taxon Concepts
Cites  Material (Specimens)
hasInformation  Information Item
[Text] Content
Data
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22. Treatment Data: Vocabularies, Ontologies, and Identifiers
Treatment Ontology
OBKMS Ontology (Viktor Senderov/Pensoft)
Plazi TreatmentBank HTTP URIs
Publication:
Dublin Core, SPAR (FABIO, PRO, FRBR)
DOI (CrossRef, Zenodo/DataCite)
ORCID, ISSN
Taxon Concept
DarwinCore, DarwinCoreSW
ZooBank HTTP URIs
ORCID, ResearcherID, Collection Codes, Repository IDs
Citations: CiTO
Information Item: SPM (+ EOL SPM extensions)
Data: Trait Ontologies; SDD, etc…
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23. Treatment Data: Taxon Concept
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24. Treatment Data: Publication Information
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25. Biodiversity Literature Repository: DOIs for Legacy Literature
Access, archive, DOI
Who are we?

26. Treatment Data: Treatment Citations
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27. TreatmentBank: Taxonomic data: linking treatments

28. Treatment Data: Material Citations
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29. Treatment Data: Specimen Data Analysis and Outputs
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30. Treatment Data: Other Information Content
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31. Thank you! Terry Catapano catapano@plazi.org Notes:
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