Welcome to the New Era of Scientific Publishing

Tobias Kuhn
VU Amsterdam
http://www.tkuhn.org

IOS Press 35 Year Anniversary, 31 March 2022

These slides: https://tinyurl.com/ios35era

The Scientific Knowledge Cloud

Task for a Developer:

Retrieve all genes that have been found to play a role in a part of the respiratory system in Covid-19 patients. Only include results from randomized controlled trials published in the last seven days.

Task for a Developer:

Problem: Scientific Results are Represented in Plain Text Only

Text Mining in 2015: Not Good Enough

Chemical-disease relation extraction:

Drug-gene relation type extraction:

Named entity recognition/linking of chemicals:

Still Not Good Enough (by far)

Back-of-the-envelope calculation:

Around 60% of retrieved relations are wrong and 60% of existing relations are not retrieved.

"Text mining? ... Why bury it first and then mine it again?" (Barend Mons)

Publishing without Burying

Idea: Let authors publish the main findings of their papers in a machine-interpretable manner right away
Field Study with Special Issue at Data Science

How can we Formally Represent Scientific Findings?

Let's check main findings from 75 random articles across disciplines:

Formally Representing Findings: Super Pattern

Context class: rat brain endothelial cell
Subject class: transient oxidative stress
Qualifier: generally
Relation: affects
Object class: Pgp expression

Main Findings from 75 Random Articles across Disciplines

68 can be represented with the super pattern!
Remaining 7 are simple subject-predicate-object statements

Formalization Papers

Formalization paper: A paper whose novel contribution is the formalization of an existing finding
First step towards the vision of publishing formalized original findings
Represented as nanopublications

Publishing Formalization Papers as Nanopublications: Assertion

Publishing Formalization Papers as Nanopublications: Metadata

15 Formalization Papers

	Authors	CONTEXT	SUBJECT	QUALIFIER	RELATION	OBJECT
1	Joslin	early human adipogenesis	regulatory element within the first intron of FTO	generally	affects	expression of genes IRX3 and IRX5
2	Nichols	human motor neuron	TAR DNA binding protein	can generally	contributes to	transcription of stmn2
3	Mietchen	dejellied fertilizable stage VI Xenopus laevis oocyte	strong static magnetic field	generally	affects	cell cortex
4	Ehrhart, Evelo	(no context class)	genes associated with CAKUT	sometimes	is same as	targets of vitamin A
5	Patrinos	patient undergoing PCI	pharmacogenomics guided clopidogrel therapy	generally	enables	cost-effective treatment
6	Martorana	human	smoothened signaling pathway	mostly	affects	astrocyte development
7	Mietchen, Penev, Dimitrova	biodiversity data	license with non-commercial clause	generally	inhibits	data reuse
8	Dimitrova	release of OpenBiodiv knowledge graph	triple in OpenBiodiv knowledge graph	generally	is same as	semantic triple extracted from biodiversity literature
9	Brauer	UNC13A	TAR DNA binding protein	generally	inhibits	inclusion of cryptic exon
10	Dumontier	data set	adherence to the FAIR guiding principles	can generally	enables	automated discovery
11	Queralt Rosinach	human	NGLY1 deficiency	always	is caused by	dysfunction of ERAD pathway
12	Usbeck	social group	relative neocortex size	never	affects	social group size
13	Bainer	ecm bound cancer cell	glycocayx bulk	generally	increases	integrin clustering
14	Grouès, Vega Moreno, Satagopam	human	STX1B mutation	frequently	co-occurs with	epilepsy
15	de Boer	digital humanities research	usage of Linked Data Scopes	can generally	contributes to	transparency

Formalization Paper (What Humans See)

Formalization Paper (What Machines See)

Welcome to the New Era of Scientific Publishing!

These slides: https://tinyurl.com/ios35era

References/Links:

Cristina-Iulia Bucur, Tobias Kuhn, Davide Ceolin, Jacco van Ossenbruggen. Expressing high-level scientific claims with formal semantics. In Proceedings of K-CAP '21. ACM, 2021.
Cristina-Iulia Bucur, Tobias Kuhn, Davide Ceolin, Jacco van Ossenbruggen. Nanopublication-Based Semantic Publishing and Reviewing: A Field Study with Formalization Papers. arXiv 2203.01608, 2022.
Special Issue: https://content.iospress.com/journals/data-science/5/1
Nanobench: https://github.com/peta-pico/nanobench