A Step Towards (From) Read to Write Access to Taxonomic Publications

Donat Agosti, PlaziISH Conference

Cuzco

23.7.2014, Cuzco

A Step Towards (From) Read to Write Access to

Taxonomic Publications

Acknowledgement

Pensoft

Pro-iBiosphere / EU FP7

Zenodo / CERN

Why do you publish?

What do you expect from a publication?

What might others expect from publications?

What is a taxonomic publication?

DNA

Specimens Observations

Institution

Pharmacology/epidemiology

Publication

Treatment

TreatmentTreatment

Table

Appendix

Biology/ecologyReference to other biota

Publication

Treatment

Publication

Taxonomic publication

Var sections

Bib. refs

Treatment

Treatment

Treatment

Treatment

publications or (more frequently) sections of publications documenting the features or distribution of a related group of organisms (called a “taxon”, plural “taxa”) in ways adhering to highly formalized conventions. Some of these are over a century old. [Catapano, 2011]

Treatment

Each taxonomic name usage has it’s treatment

Treatment

Formica obsoleta Linnaeus, 1758: 580

Treatments as standard containers

http://en.wikipedia.org

Treatment

Plazi treatment elements schemaTreatment text

Cite Treatment 1

Cite DNA sequence 1

Cite Figure 1

Cite Abbreviation 1

Cite Table 1

Cite Appendix 1

Cite Reference 1

Cite supplementary materials

Interaction sp. X

Trait 1 value = Y

Inline table

Treatment text, continued

Materials citation

Species interacted with

Cited by treatment

httpUri

httpUri

Map, Dashboard charts

Abbreviation 1

treatment x GUID

Trait database

Sequence in databasehttpUri

RDF

Treatment citation ontologyTreatment (Plazi)

httpUri ?

Table 1

Appendix 1

Figure caption

Supplementary materials

Reference 1

Plazi treatmentLinked treatment elementsOther online sourceOther linksContent from citations, instancesContent output from treatmentHyperlink

httpUri

Figure image

Treatment

Countries (Region)Australia (Queensland)

Export species materials citations (DwC)

Pseudomyrmex ants and Vachellia ant-acaciasare a classic example of mutualism in biology.

allenii

melanoceras

ruddiae

chiapensis

collinsii

cookii

cornigera

globulifera

hindsii

janzenii

mayana

sphaerocephala

boopis

flavicornis

hesperius

ita

janzenikuenckeli

mixtecus

nigrocinctus

nigropilosus

opaciceps

particeps

peperi

reconditus

satanicus

simulansspinicola

subtilissimus

veneficus

ferrugineus

gentlei

gracilis

Transbiotic link networkAssociated species linked throughreferences 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

Treatment

Linking of treatments using persistent identifiers

Treatment citation

Treatment identifier

Treatment

Linking of treatments to external resources

Treatment

Plazi Search and Retrieval Server: Access to data

DwC-A

You

You

You

human

machine

What are taxonomic publications?

Taxonomic publictationS

Journal of Hymenoptera Research

5170 specimens

4062 plottable specimens from

1138 unique locations

Brazil

All content in Plazi (34,000 treatments)

14,590 specimens

8900 plottable specimens from

1138 unique locations

200,000,000+ printed pages1,900,000 species described20,000,000+ species treatments 17,000 new species per year

BUT: The data are hidden

Incomplete digitization Publications are not semantically enhancedCollections are incompleteData is not linkedMost data are not open

Taxonomic publictationS

Taxonomic publications

PDFs are stupid –only men canunderstand them

but…

GoldenGATE editor

Conversion

Find the right mix of generic and domain specific solutions

Plazi SRS

find scan «OCR» markup store

?domain domaingeneric

Digitization and Markup Workflow:

$$$$ ?

Solution for the future

Publish semantically enhanced:

Journal of Hymenoptera Research

Solution

Open Access

Solution

Blue Listelements of taxonomic information that are not subject to copyright… e.g. treatments

(Patterson et al., 2014)

Solution

Bouchout Declaration

Solution

Support reliable and permanent open access to digital biodiversity records

Create identifiers, link provide direct access to digital objects of biodiversity literature, specimens, multimedia, genes, etc.

Ensure global interoperability and sharing of biodiversity data, information and knowledge

Ongoing dialogue to refine the concept and implementation

As signatories, we encourage an overarching approach to Open Biodiversity Knowledge Management which is based on the following fundamental principles:

http://bouchoutdeclaration

Solution

Institutional: 57; Individual: 58

Large Natural History Institutions (e.g BGBM, Naturalis, MfN, RGBM, INBio, MCZ, CAS)

Scientific Networks (e.g. IUBS, Vertnet, CRIA, TaiBIF, Canadensys, Creative Commons, DataOne)

Scientists

Global

Initial Signatories (June 12, 2014)

Solution

Solution

Solution

Linking

Solution

DOIpersistent identifiers

Solution: Digital object identifiers

Publications

Treatments

Images / digital objects

Data

Solution

DOI for publications

DOI

Solution

DOI: CrossRef

doi/10.5281/zenodo.10693

doi/10.5281/zenodo.10697

doi/10.5281/zenodo.10697

DOI: DataCite (Biodiversity Literature Repository)

DOI for publications

Solution

Solution

ZENODO @CERN

ZENODO builds and operate a simple and innovative service that enables researchers, scientists, EU projects and institutions to share and showcase multidisciplinary research results (data and publications) that are not part of the existing institutional or subject-based repositories of the research communities.

Zenodo is the digital repository of CERN

Zenodo agreed to host and support the Biodiversity LiteratureRepository

Solution

Solution

Solution

Services or what you get:

Wide access

Refindit

Refbank

Legal Issues

Archiving

Distribution of publications resolved

Your legacy literature is for everybody directly fromyour publications accesible

Solution

Why don’t we assure that all the legacy taxonomicliterature is in the

Biodiversity Literature Repository?

The future

Why not assure that all the legacy taxonomicliterature is in the Biodiversity LiteratureRepository?

Why not make our community the first that canpublish in its journal with all publications linkedto a digital copy?

The future

Why not assure that all the legacy taxonomicliterature is in the Biodiversity LiteratureRepository?

Why not make our community the first that canpublish in its journal with all publications linkedto a digital copy?

Links

LinksFurther reading: http://plazi.org/?q=plazi_publicationsCatapano, 2011 (http://www.ncbi.nlm.nih.gov/books/NBK47081/)Bouchout Declaration (http://bouchoutdeclaration.org)Blue List (http://plazi.org/?q=blue_list)Biodiversity Literature Repository (https://zenodo.org/collection/user-biosyslitZenodo (https://zenodo.org/about)Refindit (http://refindit.org)Refbank (http://refbank.org)Pro-iBiosphere (http://pro-ibiosphere.eu/)Introduction to persistent identifiers (http://wiki.pro-ibiosphere.eu/wiki/Best_practices_for_stable_URIs)

Twitter@plazi_treat; @bouchoutdec, @myrmoteras

Thank you!

Donat [email protected]