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 ViBRANT
Life cycle of data associated with biodiversity manuscripts Occurrence data Any other data Genomic dada Morphometric data
BIODIVERSITY MANUSCRIPT Phylogenetic data Image galleries XML MARK UP Environmental
data Structured text (data!) ARTICLES Bibliographies Occurrence data
Taxon treatments Plazi BHL Taxon names Wiki COL
The problem ? Primary data Drawings: slavenapeneva.com RE-USE of CONTENT Publishing and sharing of primary data
Primary data Key features 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,
ALL DATA MATTERS! Multiple Data Publishing Model of BDJ 1. 2. 3. 4.
5. Supplementary data files downloadable from the journals website Data deposited at specialized data repositories (Dryad, Pangaea) Data published through data repositories but indexed and collated with other data (GenBank, GBIF IPT) Data published in the form of marked-up and
machine-readable text. Extended use of multimedia and semantic enhancements Types of genomic data publishing Data papers describing genome datasets Descriptions of dark taxa More??
For genomic data lets build up on: GBIF-Pensoft workflow for publishing occurrence data: data papers Metadata based on the Ecological Metadata Language (EML)
Data publishing through Data Papers We need to: Identify the specific metadata descriptors used for genomic data and integrate these into the data paper concept Then we need to:
Map the existing metadata descriptors for genomic data and automatically generate data paper manuscripts from them The testbed ViBRANT special issue: DNA barcoding: a practical tool for fundamental and applied
biodiversity research Edited b: Zoltan Nagy, Kurt Jordaens, Marc de Meyer, Thierry Backeljau Rod Pages Dark Taxa: R. Page, iPhylo blogspot, 12 April 2011 Cumulative Records in GenBank Growth of COI BARCODE vs. Cyt B, all taxa
Courtesy: David Schindel BARCODE Records Specimen Metadata Georeference Habitat Character sets Images Behavior Other genes
Other Databases Phylogenetic Popn Genetics Ecological Voucher Specimen Barcode
Sequence Trace files Primers Literature (link to content or citation) Bishop Museum 19 June 2008 Species
Name Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species
Databases - Provisional sp. Description of dark taxa PWT COLLABORATIVE ARTICLE AUTHORING TOOL Dark taxon sequenced MANUSCRIPT FINALISATION &SUBMISSION
Automated submission to Pensoft Writing Tool Metadata: voucher specimen, images, locality, etc. BDJ PEER-REVIEW
MANUSCRIPT PUBLISHED Automated update of bibliographic metadata, taxon Reverse Taxonomy Taxonomic Units:
Clusters, OTUs Diagnostic characters of Study Specimens: Traits, Sequences Diagnostic characters
In Reference Databases: Nomenclatural Precedence Formal Names (sometimes, with varying certainty)
GenBank, MorphBank Courtesy: David Schindel We have Some tools and workflows for that
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