Agosti 20140813 icd8_agosti_global_dipterology-2

Donat Agosti, PlaziICD8

Potsdam

13.8.2014

From Read to Write Access to Taxonomic Publications

Editing and writing privileges

Read Write

Plazi can help you make it happen

Why do you publish?

What do you expect from a publication?

What might others expect from publications?

What is a taxonomic publication?

http://wikisource.org/wiki/File:Brooklyn_Museum_-_Egypt-Gizeh_%28pd%29_%281%29.jpg

What about new insights?

Editing and writing privileges

Read Write

What about questions?

Taxonomic publications

PDFs are stupid – only humen can understand them

Content not Form

What is a taxonomic publication?

Taxonomic publication

Our means to document life on earth

Treatments as standard containers of taxononmic publications

http://en.wikipedia.org

Treatment

Treatment

Treatment

Treatment

Treatmentpublications 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

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)

DNA

Specimens Observations

Institution

Pharmacology/epidemiology

Publication

Treatment

TreatmentTreatment

Table

Appendix

Biology/ecologyReference to other biota

Publication

Treatment

Publication

Treatments in a publication

Var sections

Bib. refs

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 gracilis

Treatment: redescription

Associated ant-acacia: Acacia gentlei

Ants Plants

Photocredits: Alex Wild

Treatment

Treatments linked through citations

Interactions inherent between treatments

Treatment

Linking of treatments using persistent identifiers

Treatment citation

Treatment identifier

Treatment

Linking of treatments to external resources

Treatments

Treatments

Plazi Search and Retrieval Server: Access to data

DwC-A

You

You

You

human

machine

What about questions?

Brazil

All content in Plazi (34,000 treatments)

14,590 specimens8900 plottable specimens from1138 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

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 93, SL 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin strongly curving to a sharp apical tooth, the apex parallel to the anterior clypeal margin. (Holotype with material in mandibles, so mandibles and anterior clypeus $ described below from paratypes.) Median clypeus....</treatment>

Semantically enhanced text

From human to machine readable text

Markup setup: definition of a vocabulary

Taxpub / TaxonX define the XML elements

Markup: Conversion

Plazi SRS

find scan «OCR» markup store

?domain domaingeneric

Plazi Digitization and Markup Workflow:

GoldenGATE

Makup workflow: Biodiversity Literature Repository

Markup: GoldenGATE editor

Markup: linking to external resources

Drag an drop the lin

k: eg CASENT0101073

WINDOW 1 WINDOW 2

Markup: Conversion

Find the right mix of generic and domain specific solutions

Plazi SRS

find scan «OCR» markup store

?domain domaingeneric

Digitization and Markup Workflow:

$$$$ ?

Markup workflows

You External service

Treatment √

Publication √

Corpus √ √

Journal √

Epilogue

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

(Patterson et al., 2014)

Epilogue

Open Access

Epilogue

Bouchout Declaration

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 Agostiagosti@plazi.org