tkuhn

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.)

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Knowledge Space

— Draft —

Link for sharing: https://w3id.org/knowledge-space/

Vision

You might sometimes ask yourself questions like this:

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Demo/Talk about Nanopub Ecosystem at Nanopub Meeting on 12 February 2021

My demo/talk is based on this sequence of links:

• Official nanopublication website
• An example of a nanopublication
• An example of a nanopublication index
• Nanopub network monitor
• One specific server instance
• An example of a query type on a nanopub service instance

tkuhn

Demo/Talk about Nanopub Ecosystem at Nanopub Meeting on 12 February 2021

My demo/talk is based on this sequence of links:

• Nanopub network monitor
• One specific server instance
• An example of a nanopublication on the server network
• An example of a nanopublication index
• An instance of the grlc-based service (via Tapas interface)
• Querying an instance of the LDF-based service

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@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/> .

tkuhn

\documentclass{beamer}
\usepackage{graphicx}
\usepackage{multicol}
\usepackage{bchart}
\usepackage{wasysym}
\usepackage{amssymb}
\usepackage{multirow}
\usepackage{rotating}
\usepackage{tikz}

tkuhn

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