User:Daniel Mietchen/Talks/Naturalis hackathon 2014

Wikimedia projects, open science and biodiversity information

Reality today

 * A figure from a recent paper: 


 * Two videos providing the basis for an article but not published along with it.


 * Inconsistent XML as a Barrier to Reuse of Open Access Content

How things could be
A specification anyone can edit:


 * 1) Dynamics: Research is a process. The scientific journal of the future provides a platform for continuous and rapid publishing of workflows and other information pertaining to a research project, and for updating any such content by its original authors or collaboratively by relevant communities. Eventually, all scientific records should have a public version history or a public justification for not having one.
 * Research cycle.png
 * example
 * Version of record
 * Updates automatically
 * Editable format (SVG)
 * Data and code on GitHub under open licenses
 * PLOS Computational Biology Topic Pages (list)
 * The workflows include writing of research documents, as piloted by the Biodiversity Data Journal.
 * 1) Scope: Data come in many different formats. The scientific journal of the future interoperates with databases and ontologies by way of open standards and concentrates on the contextualization of knowledge newly acquired through research, without limiting its scope in terms of topic or methodology.
 * Eupolybothrus cavernicolus male paratype.jpg of the centipede Eupolybothrus cavernicolus, a species described with its full transcriptome, micro CT and DNA barcoding, in addition to a morphological description.]]
 * another example: citizen science
 * 1) Access: Free access to scientific knowledge, and permissions to re-use and re-purpose it, are an invaluable source for research, innovation and education. The scientific journal of the future provides legally and technically barrier-free access to its contents, along with options for re-use and re-purposing that are stated clearly for both humans and machines.
 * "Academic publishing is no guarantee of anything, except possibly the paywalled obsolescence of your work." (WebCite copy)
 * Xanthichthys ringens - pone.0010676.g191.png'' is sourced from an open-access scholarly article licensed for re-use (details). ]]
 * Open Access Media Importer Bot (ASAP award winner)
 * Leibniz @Wikimedia
 * Open Access @Wikimedia
 * 1) Replicability: Open access to all relevant core elements of a publication facilitates the verification and subsequent re-use of published content. The scientific journal of the future requires the publication of detailed methodologies &mdash; including all data and code &mdash; that form the basis of any research project.
 * NIH plans to enhance reproducibility
 * 1) Review: The critical, transparent and impartial examination of information submitted by the professional community enhances the quality of publications. The scientific journal of the future supports post-publication peer review, and qualified reviews of submitted content shall always be made public.
 * example
 * public peer review
 * public review of grant proposals
 * 1) Presentation: Digitization opens up new opportunities to provide content, such as through semantic and multimedia enrichment. The scientific journal of the future adheres to open Web standards and creates a framework in which the technological possibilities of digital media can be exploited by authors, readers and machines alike, and content remains continuously linkable.
 * Demo of interactive taxonomic paper from ZooKeys.ogv. Courtesy of Rod Page.]].
 * Interactive presentation using Lens
 * Composition of plates on the fly (as opposed to static composite figures)
 * 1) Transparency: Disclosure of conflicts of interest creates transparency. The scientific journal of the future promotes transparency by requiring its editorial board, the editors and the authors to disclose both existing and potential conflicts of interest with respect to a publication and to make explicit their contributions to any publication.
 * 2) Sustainability: Resources are limited. Ecological considerations are reflected in the design and production of the scientific journal of the future.
 * 3) Flexibility: Innovation is stifled by inflexible rules. Exceptions to the above rules are possible if justified in public.
 * examples

Future of publishing

 * GitHub thread: What should we teach about writing/publishing papers in a webby world?

Kaveh Bazargan, River Valley TV: Academic Publishing in Europe 2012 ]]
 * Talk Transforming the way we publish research at Academic Publishing in Europe 2012:
 * [[File:Transforming the way we publish research - APE 2012 talk.ogv|thumb|center|640px| Video recording of the talk. Also available via Vimeo and YouTube.


 * Talk at User:Daniel Mietchen/Talks/ISMTE 2012/Transforming the way we publish research

WikiProjects

 * WP:SCIENCE
 * WP:BIOLOGY
 * WP:COMPBIO
 * WP:OPENACCESS

Key policies

 * Five pillars
 * Notability
 * No original research
 * Conflicts of interest

Open knowledge

 * Definition of free cultural works
 * Open Definition
 * Open license
 * Open knowledge

Semantic approaches

 * DBpedia
 * Semantic MediaWiki
 * Rod's Linkout wiki
 * Example
 * Wikidata
 * Denny Vrandečić, Markus Krötzsch. Wikidata: A Free Collaborative Knowledge Base. In Communications of the ACM (to appear). ACM 2014.
 * Showcases
 * Cactaceae

MediaWiki API

 * mw:API:Main page

Data dumps

 * WP:DUMPS

Visualizations

 * Listen to Wikipedia
 * Wikipulse
 * Map of recent edits
 * Wikistream
 * Wikimedia project growth animation
 * Wikipedia live monitor
 * Wikimedia counter

Tools
See also wikidata:Wikidata:Tools/External tools.
 * Concept cloud
 * Reasonator
 * Tree of Life
 * BaGLAMa
 * GLAMorous

Robots

 * Telemetrie
 * commons:User:Open Access Media Importer Bot

GLAM

 * outreach:GLAM

About
This talk was given on March 18, 2014 at the Data enrichment hackathon at Naturalis in Leiden.

Contact

 * Institutional
 * @EvoMRI on Twitter
 * Wikipedia talk page
 * Wikipedia email