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Lecture provided at the 8th International Congress of Hymenopterists, Cuzco, Peru, July 23, 2014. The lectures makes a case to join the bibligraphies and pdf of hymenoptera taxonomy literature on the Biodiersity Literature Repository / Zenodo
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Donat Agosti, PlaziISH Conference
Cuzco
23.7.2014, Cuzco
A Step Towards (From) Read to Write Access to
Taxonomic Publications
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
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
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
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
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
Blue Listelements of taxonomic information that are not subject to copyright… e.g. treatments
(Patterson et al., 2014)
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
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
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
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