International Congress of Entomology, Orlando Notes: Add in Plazi and the idea of the treatment server Terry Catapano September 26, 2016 International Congress of Entomology, Orlando

Extracting Linked Open Data from Taxonomic Publications Notes: Add in Plazi and the idea of the treatment server Plazi Extracting Linked Open Data from Taxonomic Publications Terry Catapano Plazi, New York (http://plazi.org)

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

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.

Plazi TreatmentBank: Million Treatment Goal For 1M Treatments, at minimum: Identify with HTTP URIs in form of http://treatment.plazi.org/id/[UUID] Metadata Taxon Concept Publication Information Representations HTML RDF [XML] Exports Biodiversity Literature Repository EOL GBIF WikiData Notes: Add in Plazi and the idea of the treatment server

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) Notes: Add in Plazi and the idea of the treatment server

TreatmentBank

Plazi: TreatmentBank: Treatment stubs: adding content Notes: Add in Plazi and the idea of the treatment server

Sources Legacy publications Print  Digitization  Text Capture  XML Digitized  Text Capture  XML Born Digital  Text Extraction  XML Prospective publishing Pensoft Journals TaxPub XML  RDF Notes: Add in Plazi and the idea of the treatment server

Plazi conversion workflow TreatmentBank find scan text extraction markup store Notes: Add in Plazi and the idea of the treatment server

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

TreatmentBank: HTML Representation Notes: Add in Plazi and the idea of the treatment server

Treatment Text: XML Representation

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) Notes: Add in Plazi and the idea of the treatment server

Nomenclature Section and Taxon Name Notes: Add in Plazi and the idea of the treatment server

Treatment Citation Notes: Add in Plazi and the idea of the treatment server

Material Citation Notes: Add in Plazi and the idea of the treatment server

TreatmentBank: online editing: material citation Notes: Add in Plazi and the idea of the treatment server

Semantic XML Publishing: TaxPub Notes: Add in Plazi and the idea of the treatment server

Treatment Data: RDF Representation

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 Notes: Add in Plazi and the idea of the treatment server

Treatment Data: Vocabularies, Ontologies, and Identifiers Treatment Ontology https://github.com/plazi/treatmentontologies 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… Notes: Add in Plazi and the idea of the treatment server

Treatment Data: Taxon Concept Notes: Add in Plazi and the idea of the treatment server

Treatment Data: Publication Information Notes: Add in Plazi and the idea of the treatment server

Biodiversity Literature Repository: DOIs for Legacy Literature Access, archive, DOI Who are we?

Treatment Data: Treatment Citations Notes: Add in Plazi and the idea of the treatment server

TreatmentBank: Taxonomic data: linking treatments

Treatment Data: Material Citations Notes: Add in Plazi and the idea of the treatment server

Treatment Data: Specimen Data Analysis and Outputs Notes: Add in Plazi and the idea of the treatment server

Treatment Data: Other Information Content Notes: Add in Plazi and the idea of the treatment server

Thank you! Terry Catapano catapano@plazi.org Notes: Add in Plazi and the idea of the treatment server