2020-11-12 Egon Willighagen open access world Access Publishing... · 2021. 1. 12. · Egon Willighagen 2020-11-12 @egonwillighagen 0000-0001-7542-0286 School of Nutrition and Translational

Open science in an open access world

Egon Willighagen2020-11-12

@egonwillighagen0000-0001-7542-0286

School of Nutrition and Translational Research in Metabolism

Every year in autumn, Open Access receives a lot of attention, and invariably it is conflated with Open

Science. While they both an overlap in intentions, they are quite distinct. This talk will focus on how we can

enable Open Science with Open Access, using scholarly journals as the vehicle. Currently, too many articles

share tiny bits of knowledge that could have been more efficiently shared via a database. The journal article

has, in many cases, effectively become an advertisement: to understand the full experiment, they article is

not always enough. It is not open science. Worse, with the modern fetish around impact factors, we only

recognize and reward the advertisement, which does great damage to open science. For more than 20 years,

Open Science has been about efficient and openly sharing of research output. It does so by allowing other to

reuse, modify, and redistribute that research. Journals used to enable this behavior. How can a journal further

enable Open Science? First and foremost, a scientific journal must recognize and reward all research output.

Research output is not only articles, but also data, software and standards. Journals can recognize and reward

these by adoption of standards for data, software, etc citation. Sustainable and FAIR supplementary

information is essential. Adoption of Open Citations and the Citation Typing Ontology will give more insight in

reuse of output and will support the second urgent need: general improvement of dissemination of

knowledge, for example with semantic web technologies, global unique identifiers, machine readability, etc.

The adoption of Open Science by Open Access journals is slow but steady: a key advantage of Open Science is

that it doesn't go away; it just accumulates. Problems remain, but this talk will give you a good idea of Open

Access can embrace Open Science.

Disclaimer: Editor-in-Chief J. Cheminform.


Acknowledgements


Open Access is not the same as Open Science

Open, Publish, and FAIR


Open Publish

FAIR

Modify

Distribute

Use

Can Open Access support Open Science?

RecognitionandRewarding


Research and Research Output

• Articles• Data (data sets,

databases, …)• Software• Standards

(specifications, policies, …)

• Protocolos• ...


Research and Research Output

• Articles• Data (data sets,

databases, …)• Software• Standards

(specifications, policies, …)

• Protocolos• ...


• Journals, Books• Repositories, “web"

• GitHub/Zenodo• Zenodo•

• ? • ...

Should all RO be published as an article?


Improving knowledge dissemination



Hanspers, K., Riutta, A., Summer-Kutmon, M. et al. Pathway information extracted from 25 years of pathway figures. Genome Biol 21, 273 (2020). https://doi.org/10.1186/s13059-020-02181-2

How FAIR is an article?

https://twitter.com/petermurrayrust/status/1326660269481799680


Availability section (inherited from BMC)



Additional files on Figshare (more FAIR)

ORCID integration


Scholia, ORCID, Wikidata


GitHub


Open Citations & I4OC


Citation distribution


Citation Typing Ontology


Citation Typing Ontology (CiTO) Pilot


CiTO harvested by Wikidata


Uptake (pilot + other)


What is says about a journal?


What is next?


Use Open Access to promote Open Science

• GitHub (etc)• Zenodo/Figshare• code/data review

• built a community

Easy: Manuscript checklists

https://casp-uk.net/School of Nutrition and Translational Research in Metabolism

Figshare: more cheminformatics formats


BMC/Figshare: FAIR biological pathways

Anders Riutta, pvjs → JavaScript viz library for GPMLSchool of Nutrition and Translational Research in Metabolism

Linked chemical data

Samwald et al. (2011), J. Cheminform.10.1186/1758-2946-3-19

Harder


Open Science in an Open Access World



Open Access in an Open Science World



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2020-11-12 Egon Willighagen open access world Access Publishing... · 2021. 1. 12. · Egon Willighagen 2020-11-12 @egonwillighagen 0000-0001-7542-0286 School of Nutrition and Translational