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Welcome to the New Era of Scientific Publishing

— by Tobias Kuhn, 4 April 2022; reporting on work with Cristina Bucur, Davide Ceolin, and Jacco van Ossenbruggen [1,2] —

I believe we have made the first steps venturing into a new era of scientific publishing. Let me explain. [Update: At what point exactly a new era begins and what counts as first steps are of course subject to debate. I therefore added a section on related initiatives and further reading below.]

Science is nowadays communicated in a digital manner through the internet. We essentially have a kind of "scientific knowledge cloud", where researchers with the help of publishers upload their latest findings in the form of scientific articles, and where everybody who is interested can access and retrieve these findings. (This is in fact only true for articles that are published as Open Access, but that is not the point here.)

View knowledgespace.md
@tkuhn
tkuhn / nanopub.trig
Created Mar 8, 2018
Trusty nanopub from elton
View nanopub.trig
@prefix this: <http://purl.org/np/RADSgVXXsYOBvrcaidzewWQ29PajKWZZ1i7j7JLMzRkzQ> .
@prefix sub: <http://purl.org/np/RADSgVXXsYOBvrcaidzewWQ29PajKWZZ1i7j7JLMzRkzQ#> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix opm: <http://purl.org/net/opmv/ns#> .
@prefix pav: <http://swan.mindinformatics.org/ontologies/1.2/pav/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
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tkuhn / trustyuris-presentation.tex
Created Oct 9, 2014
Trusty URI presentation sources
View trustyuris-presentation.tex
\documentclass{beamer}
\usepackage{graphicx}
\usepackage{multicol}
\usepackage{bchart}
\usepackage{wasysym}
\usepackage{amssymb}
\usepackage{multirow}
\usepackage{rotating}
\usepackage{tikz}
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tkuhn / 4postulates.md
Created Feb 11, 2014
Four Postulates for Diagrams as Semantic Data Carriers in Scientific Publications
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Four Postulates for Diagrams as Semantic Data Carriers in Scientific Publications

(this is an excerpt of the paper linked below)

We would like to take the opportunity to postulate the following actions, which we think should be carried out to make the content of images in biomedical articles more accessible:

  • Stop pressing diagrams into bitmaps! Unless the image only consists of one single photograph, screenshot, or another kind of picture that only has bitmap representation, vector graphics should be used for article figures.
  • Let data and metadata travel from the tools that generate diagrams to the final articles! Whenever the specific tool that is used to generate the diagram "knows" that a certain graphical element refers to an organism, a gene, an interaction, a point in time, or another kind of entity, then this information should be stored in the image file, passed on, and finally published with the articl