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Sherborn: Penev - ZooKeys: Streamlining the registration – to – publication pipeline
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Sherborn: Penev - ZooKeys: Streamlining the registration – to – publication pipeline


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  • 1. Streamlining theregistration- to-publication pipeline Lyubomir Penev, Teodor Georgiev, Pavel Stoev Sherborn Meeting, NHM London, 28 Oct 2011 ViBRANT
  • 2. The registration workflow for taxonomic names and acts AUTHOR PUBLISHER AUTHOR PRE-PUBLICATION TAXONOMIC POST-PUBLICATION REGISTRATION PUBLICATION RECORDINGZooBank Index Animalium XMLMycoBank MARK UP Zoological RecordIPNI Index Kewensis, IPNIIndex Fungorum Index Fungorum Structured text (data!) Biblio- Occurr- Taxon treatments Taxon namesARTICLES ence data graphies Plazi Wiki COL BHL
  • 3. XML-based publication and dissemination workflow GBIF-generated Scratchpads- Manuscripts written Manuscripts manuscripts from generated via customized generated frombn metadata descriptions manuscripts online forms authors’ databases Upfront pre-submission marked up manuscriptsMarked up final publication PENSOFT MARK UP TOOL Non-tagged manuscripts in PDF, HTML and XML (PMT) (MS Word, Open Office) formats Peer-review, editorial and publication process Automated dissemination, archiving, indexing, harvesting ARTICLES Occurrence data Taxon treatments Taxon names Plazi Wiki COL BHL
  • 4. But why doing all this ?
  • 5. Semantic enhancements to published texts
  • 6. The challenges of the registration process Four different groups of players: data managers, registry editors, authors, publishers Who will be “allowed” to register new data in electronic registries? Who will control the quality of (validate) registered records? Who will supply the record ID numbers to the publishers? Who and when will add/correct the article metadata after publication?
  • 7. Automated workflow MANUSCRIPT SUBMISSION Peer review XML Query MANUSCRIPT ACCEPTED XML Response XML article metadata ARTICLE PUBLISHEDTaxon name available(effectively published)
  • 8. The technical solution:Pensoft Writing Tool (PWT)
  • 9. PWT – Main functionalities PWT combines: (1) writing of a taxonomic manuscript(2) upfront markup of the text (3) submission to anappropriate journal into one and the same process(tool) PWT is a core module of the forthcoming BiodiversityData Journal (BDJ) Short taxonomic treatments or even singlenomenclatural acts, single records, biological andecological observations, local checklists, largertaxonomic revisions, etc. Compliant to the two Biological Codes (bacteria stillmissing) Can be used as educational environment for thefuture taxonomists
  • 10. AcknowledmentsPlazi ViBRANT
  • 11. All this is not easy, but...... ... it is truly exciting ...but ... is possible only through Open Access!“ Semi-automatically generated semantic, enhanced e-publications are the only way to describe the missing 10 Mspecies, and to deal with an increasing flood of data.” Donat Agosti
  • 12. I Open Access!Thank you for your attention!