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From Open Access to
Open Science
from the Viewpoint
of a Scholarly Publisher
Lyubomir Penev
Bulgarian Academy of Sciences ...
Some facts about Pensoft
• Founded in 1992
• Headquarters in Sofia
• Now 25 permanent employees
Pensoft’s Open Access Journals
Pensoft’s Open Books Program
More than 1000 book titles since 1994 Advanced Open Access Books
WHY?
CLAIM of this Presentation:
Academic publishers
create some bottlenecks
that hamper progress in
science!
Do publishers really follow the
extraordinarily rapid progress in science?
Probably the best answer…
Academic Publishing in Transition
Open access Open science
Human-readable Machine-readable
Data publishing Data re-use
Imp...
Modernise
or
perish!
Publisher’s Dilemma
In the beginning was the Open Access…
Open Access
Open Science
Open Data
The Simplistic View on Open Access
Traditional publishing Open access publishing
Open Access PDF: Nice, but not enough!
The PDF/paper is an Impediment!
(even if they are Open Access)
The XML as the first step to
open content
<taxon-name-part taxon-name-part-type="genus">Nixonia</taxon-name-part>
<taxon-n...
Why do XML markup?
Frequently Asked Question
Automated mapping
Species Profiles on the Fly (1)
Species Profiles on the Fly (2)
This is how it started
Descriptions
Images
Occurrences
Nomenclature
Literature
Text is not just structured, it is machine-...
All fine, but where are the data?
The (mis)fortune of research data
Primary
data
Drawings: Slavena Peneva
DNA sequencer image:
Wikimedia
The Second Day: Let data be open …
Open Access
Open Science
Open Data
How open data should look...
Credit: Scottish Government, http://www.gov.scot/Publications/2016/08/5556/6
5. Maintain
4. P...
Four Models of Open Data Publishing
• Supplementary data files published
with the article
• Data deposited in repositories...
Now comes ARPHA
Two Journal Publishing Workflows:
ARPHA-XML & ARPHA-DOC
• Authoring
• Data import
• Peer review
• Publication
• Dissemination
+
Next-Gen taxonomy requires Next-Gen publishing
All...
The first
Open Science Journal
publishing the
entire research cycle!
Forthcoming in March 2017
Metabarcoding and
Metagenomics
journal
Step 1: Start a manuscript
Step 2: Select article template
Step 3: Manuscript opened
Invite Co-authors
Work with your co-authors & peers online
Import a Figure or a Video
Cited figures (rе-)placed automatically
Direct Search & Import of References
Mandatory Validation Step
‘Embedded’ Copy-editor
Revision History
Truly unique: Update your article anytime!
Update your article
Toolbox for scholarly publishing and dissemination
of biodiversity data (ARPHA-BioDiv)
Online Import of Structured Data
Species Occurrence Data
Data Structured within the Text
Harvest and Re-use Data
Import an Entire Manuscript through API
Create a Data Paper from GBIF EML Metadata
Create a Data Paper from GBIF EML Metadata
Create a Data Paper from EML Metadata
Novel Article Formats
Flexible Article Templates
The IUCN Red List Species Page
The IUCN GISD Species Page
IUCN Species Page = Scholarly Publication?
Why publish SCPs and ASPs?
• A permanent scientific record in a peer-reviewed journal
• Citation and credit
• Collaborativ...
Open Access
Open Science
The Third Day: Let there be Open Science
…
Open Data
What is Open Science?
Open
peer
review
Open
funding
Open
innovation
Open
science
evaluation
Credit: John Parsons, Library ...
The Open Science Taxonomy
What is Open Science?
• Allows for the reproduction of research
findings.
• Enables transparency in research
methodology.
...
EU Open Science Policy Platform (OSPP)
https://ec.europa.eu/research/swafs/pdf/pub_open_science/new_policy_initiative.pdf
Publish the Whole Research Cycle
Credit: CC-BY Cameron Neylon, modified by Daniel Mietchen (Wikimedia.org)
Teaching
Teachi...
The first
Open Science Journal
publishing the
entire research cycle!
The RIO Journal
https://www.youtube.com/watch?v=2QKp4Ttpemw
Six Unique Features of RIO
• RIO publishes all outputs of the research cycle
• Published on ARPHA, the first online collab...
One Year of Success
• 1st birthday on 2 Nov
2017
• More than 100 articles
published so far
• Dedicated collections for
pro...
Open Peer Review
Giving back to the Community
Publish your project or research group
outputs in a special collection
What can you publish?
...
Project Output Collections
EU BON Project Collection
Today’s presentation published in RIO
We look forward to receiving
your inspiring ideas and
research outputs!
riojournal.com
But even this is not
the end …
Information from Literature
Linked Open Data (LOD)
The Open Biodiversity Knowledge
Management System (OBKMS)
What is a Nanopublication?
The smallest unit of
publishable
information: an
assertion about
anything that can be
uniquely ...
Anatomy of a Nanopublication
Credit: nanopub.org
Tree RDF named graphs
1.The assertion: a statement
linking two concepts (...
Acknowledgements
• Our numerous authors, reviewers, editors and partners
• The staff of Pensoft and Plazi
• Slavena Peneva...
I Open Science!
PLAZI
iDiv Lecture, 15 Feb 2017
From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher
From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher
From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher
From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher
From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher
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From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher

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A presentation held by Lyubomir Penev in the iDiv Seminar Series at the Biodiversity Informatics Unit of the German Centre for Integrative Biodiversity Research (iDiv) Leipzig, 15 February 2017.

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From Open Access to Open Science: from the Viewpoint of a Scholarly Publisher

  1. 1. From Open Access to Open Science from the Viewpoint of a Scholarly Publisher Lyubomir Penev Bulgarian Academy of Sciences & Pensoft Publishers, Sofia iDiv, Leipzig, 15 Feb 2017
  2. 2. Some facts about Pensoft • Founded in 1992 • Headquarters in Sofia • Now 25 permanent employees
  3. 3. Pensoft’s Open Access Journals
  4. 4. Pensoft’s Open Books Program More than 1000 book titles since 1994 Advanced Open Access Books
  5. 5. WHY? CLAIM of this Presentation: Academic publishers create some bottlenecks that hamper progress in science!
  6. 6. Do publishers really follow the extraordinarily rapid progress in science?
  7. 7. Probably the best answer…
  8. 8. Academic Publishing in Transition Open access Open science Human-readable Machine-readable Data publishing Data re-use Impact Factor Article-Level Metrics Publishing Technology-Driven Service Technology Critical for journals’ survival
  9. 9. Modernise or perish! Publisher’s Dilemma
  10. 10. In the beginning was the Open Access… Open Access Open Science Open Data
  11. 11. The Simplistic View on Open Access Traditional publishing Open access publishing
  12. 12. Open Access PDF: Nice, but not enough!
  13. 13. The PDF/paper is an Impediment! (even if they are Open Access)
  14. 14. The XML as the first step to open content <taxon-name-part taxon-name-part-type="genus">Nixonia</taxon-name-part> <taxon-name-part taxon-name-part-type="species">masneri</taxon-name-part> </taxon-name> - <taxon-author> <string-name>van Noort & Johnson</string-name> </taxon-author> <taxon-status>sp. n.</taxon-status> <xref>Figures 1A-F</xref> a
  15. 15. Why do XML markup? Frequently Asked Question
  16. 16. Automated mapping
  17. 17. Species Profiles on the Fly (1)
  18. 18. Species Profiles on the Fly (2)
  19. 19. This is how it started Descriptions Images Occurrences Nomenclature Literature Text is not just structured, it is machine-readable!
  20. 20. All fine, but where are the data?
  21. 21. The (mis)fortune of research data Primary data Drawings: Slavena Peneva DNA sequencer image: Wikimedia
  22. 22. The Second Day: Let data be open … Open Access Open Science Open Data
  23. 23. How open data should look... Credit: Scottish Government, http://www.gov.scot/Publications/2016/08/5556/6 5. Maintain 4. Publish 1. Start with a plan 2. Select your data 3. Create your data Open Data Process
  24. 24. Four Models of Open Data Publishing • Supplementary data files published with the article • Data deposited in repositories and linked to the article they underpin • Data papers, describing data • Integrated data and narrative publishing
  25. 25. Now comes ARPHA
  26. 26. Two Journal Publishing Workflows: ARPHA-XML & ARPHA-DOC
  27. 27. • Authoring • Data import • Peer review • Publication • Dissemination + Next-Gen taxonomy requires Next-Gen publishing All within a single online collaborative platform ARPHA-XML Workflow
  28. 28. The first Open Science Journal publishing the entire research cycle!
  29. 29. Forthcoming in March 2017 Metabarcoding and Metagenomics journal
  30. 30. Step 1: Start a manuscript
  31. 31. Step 2: Select article template
  32. 32. Step 3: Manuscript opened
  33. 33. Invite Co-authors
  34. 34. Work with your co-authors & peers online
  35. 35. Import a Figure or a Video
  36. 36. Cited figures (rе-)placed automatically
  37. 37. Direct Search & Import of References
  38. 38. Mandatory Validation Step
  39. 39. ‘Embedded’ Copy-editor
  40. 40. Revision History
  41. 41. Truly unique: Update your article anytime! Update your article
  42. 42. Toolbox for scholarly publishing and dissemination of biodiversity data (ARPHA-BioDiv)
  43. 43. Online Import of Structured Data
  44. 44. Species Occurrence Data
  45. 45. Data Structured within the Text
  46. 46. Harvest and Re-use Data
  47. 47. Import an Entire Manuscript through API
  48. 48. Create a Data Paper from GBIF EML Metadata
  49. 49. Create a Data Paper from GBIF EML Metadata
  50. 50. Create a Data Paper from EML Metadata
  51. 51. Novel Article Formats
  52. 52. Flexible Article Templates
  53. 53. The IUCN Red List Species Page
  54. 54. The IUCN GISD Species Page
  55. 55. IUCN Species Page = Scholarly Publication?
  56. 56. Why publish SCPs and ASPs? • A permanent scientific record in a peer-reviewed journal • Citation and credit • Collaborative peer-review and assessment • Expert engagement (e.g. of taxonomists) • Media-rich descriptions of species of conservation importance • Publication in both human - (semantic HTML, PDF) and machine-readable (XML) format • Article- and Sub-Article-Level Metrics • Streamlined continuous update of IUCN Red List via ARPHA • Dissemination via the journals’ networks • Permanent archiving in PubMedCentral, Zenodo, CLOCKSS
  57. 57. Open Access Open Science The Third Day: Let there be Open Science … Open Data
  58. 58. What is Open Science? Open peer review Open funding Open innovation Open science evaluation Credit: John Parsons, Library Journal 2016, adapted from J.-C. Burgelman’s 2015 presentation.
  59. 59. The Open Science Taxonomy
  60. 60. What is Open Science? • Allows for the reproduction of research findings. • Enables transparency in research methodology. • Increases the researcher’s societal impact. • Saves money and time for both researchers and research institutions. Pontica et al. 2015 Collaborate rather than compete!
  61. 61. EU Open Science Policy Platform (OSPP) https://ec.europa.eu/research/swafs/pdf/pub_open_science/new_policy_initiative.pdf
  62. 62. Publish the Whole Research Cycle Credit: CC-BY Cameron Neylon, modified by Daniel Mietchen (Wikimedia.org) Teaching TeachingOutreach Administration Develop Publish Read Fund Support Plan Idea Process
  63. 63. The first Open Science Journal publishing the entire research cycle!
  64. 64. The RIO Journal https://www.youtube.com/watch?v=2QKp4Ttpemw
  65. 65. Six Unique Features of RIO • RIO publishes all outputs of the research cycle • Published on ARPHA, the first online collaborative platform supporting the full life cycle of a manuscript • Entirely OPEN author-organised pre-submission and community-sourced post-publication peer reviewp • Authors decide how to peer review their manuscripts • Authors can publish article revisions anytime • Emphasises social engagement by mapping research to UN’s Sustainable Development Goals (SDGs)
  66. 66. One Year of Success • 1st birthday on 2 Nov 2017 • More than 100 articles published so far • Dedicated collections for projects and conferences
  67. 67. Open Peer Review
  68. 68. Giving back to the Community Publish your project or research group outputs in a special collection What can you publish? • Abstract • Idea • Presentation • Poster • Video • Infographic • Workshop Report • Hackathon Report • Policy Brief • Research Article • Any other
  69. 69. Project Output Collections
  70. 70. EU BON Project Collection
  71. 71. Today’s presentation published in RIO
  72. 72. We look forward to receiving your inspiring ideas and research outputs! riojournal.com
  73. 73. But even this is not the end …
  74. 74. Information from Literature Linked Open Data (LOD)
  75. 75. The Open Biodiversity Knowledge Management System (OBKMS)
  76. 76. What is a Nanopublication? The smallest unit of publishable information: an assertion about anything that can be uniquely identified and attributed to its author. Groth, Gibson, and Velterop (2010) http://www.nanopub.org
  77. 77. Anatomy of a Nanopublication Credit: nanopub.org Tree RDF named graphs 1.The assertion: a statement linking two concepts (subject and object) via a third concept (predicate). 2.The provenance: some metadata to provide context for the assertion. 3.The publication information: metadata about the actual nanopublication itself.
  78. 78. Acknowledgements • Our numerous authors, reviewers, editors and partners • The staff of Pensoft and Plazi • Slavena Peneva for designing this presentation • EU BON, BIG4, pro-iBiosphere, ViBRANT • iDiv Biodiversity Informatics Unit for inviting me for this lecture
  79. 79. I Open Science! PLAZI iDiv Lecture, 15 Feb 2017

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