agosti 20140813 icd8_agosti_global_dipterology-2
DESCRIPTION
lecture presented at 8th International Congress of Dipterology, Potsdam, Germany, 10-15 August 2014, http://www.icd8.info/TRANSCRIPT
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
