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How to publish genomic Data papers based on BOL data - Biodiversity Data Journal

ViBRANT. How to publish genomic Data papers based on BOL data - Biodiversity Data Journal . Lyubomir Penev Bulgarian Academy of Sciences & Pensoft Publishers. ViBRANT Tools for DNA taxonomists, 11 June 2013, Brussels. Any other data. Genomic dada. Occurrence data.

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How to publish genomic Data papers based on BOL data - Biodiversity Data Journal

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  1. ViBRANT How to publish genomic Data papers based on BOL data - Biodiversity Data Journal Lyubomir Penev Bulgarian Academy of Sciences & Pensoft Publishers ViBRANT Tools for DNA taxonomists, 11 June 2013, Brussels

  2. Any other data Genomic dada Occurrence data Life cycle of data associated with biodiversity manuscripts Biodiversity manuscript Phylogenetic data Morphometric data Image galleries Environmental data XML MARK UP Structured text (data!) Taxon names Taxon treatments Occurr-ence data ARTICLES Biblio-graphies COL Plazi Wiki BHL

  3. The problem ?

  4. Drawings: slavenapeneva.com Primary data

  5. RE-USE of CONTENT Publishing and sharing of primary data Primary data

  6. Key features ALL DATA MATTERS! Collaborative article authoring Online peer-review and editing Community peer review; options for “open” and “public” review Standard-compliant (DwC, NLM DTD) Biological Codes compliant article templates No lower/upper limit of manuscript size Semantically enhanced “articles of the future” Integrated with GBIF, EOL, Dryad Scratchpads, etc.

  7. Multiple Data Publishing Model of BDJ Supplementary data files downloadable from the journals’ website Data deposited at specialized data repositories (Dryad, Pangaea) Data published through data repositories but indexed and collatedwith other data (GenBank, GBIF IPT) Data published in the form of marked-up and machine-readable text. Extended use of multimedia and semantic enhancements

  8. Types of genomic data publishing Data papers describing genome datasets Descriptions of “dark taxa” More??

  9. For genomic datalet’s build up on: GBIF-Pensoft workflow for publishing occurrence data:data papers

  10. Metadata based on the Ecological Metadata Language (EML)

  11. Data publishing through Data Papers

  12. We need to:Identify the specific metadata descriptors used for genomic data and integrate these into the data paper concept

  13. Then we need to:Map the existing metadata descriptors for genomic data and automatically generate data paper manuscripts from them

  14. The testbedViBRANT special issue: DNA barcoding: a practical tool for fundamental and applied biodiversity researchEdited b: Zoltan Nagy, Kurt Jordaens, Marc de Meyer, Thierry Backeljau

  15. Rod Page’s ‘Dark Taxa’: R. Page, iPhyloblogspot, 12 April 2011

  16. Cumulative Records in GenBankGrowth of COI BARCODE vs. Cyt B, all taxa Courtesy: David Schindel

  17. BARCODE Records Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological Databases - Provisional sp. Bishop Museum – 19 June 2008

  18. Description of “dark” taxa Pwt – collaborative article authoring tool Dark taxon sequenced manuscript finaliSation&SUBMISSION Automated submission to Pensoft Writing Tool Bdj – peer-review Metadata: voucher specimen, images, locality, etc. MANUSCRIPT PUBLISHED Automated update of bibliographic metadata, taxon name, Zoobank record, etc.

  19. Reverse Taxonomy • Taxonomic Units: • Clusters, OTUs Nomenclatural Precedence Formal Names (sometimes, with varying certainty) • Diagnostic characters In Reference Databases: • GenBank, MorphBank • Diagnostic characters of Study Specimens: • Traits, Sequences Courtesy: David Schindel

  20. We haveSome tools and workflows for that…

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