OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

AM Altenhoff, CM Train, KJ Gilbert… - Nucleic acids …, 2021 - academic.oup.com
OMA is an established resource to elucidate evolutionary relationships among genes from
currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise …

Lessons learned to boost a bioinformatics knowledge base reusability, the Bgee experience

T Mendes de Farias, J Wollbrett… - …, 2023 - academic.oup.com
Background Enhancing interoperability of bioinformatics knowledge bases is a high-priority
requirement to maximize data reusability and thus increase their utility such as the return on …

Accessing scientific data through knowledge graphs with Ontop

D Calvanese, D Lanti, TM De Farias, A Mosca, G Xiao - Patterns, 2021 - cell.com
In this tutorial, we learn how to set up and exploit the virtual knowledge graph (VKG)
approach to access data stored in relational legacy systems and to enrich such data with …

The Quest for Orthologs benchmark service and consensus calls in 2020

AM Altenhoff, J Garrayo-Ventas… - Nucleic acids …, 2020 - academic.oup.com
The identification of orthologs—genes in different species which descended from the same
gene in their last common ancestor—is a prerequisite for many analyses in comparative …

Enabling semantic queries across federated bioinformatics databases

AC Sima, T Mendes de Farias, E Zbinden… - Database, 2019 - academic.oup.com
Motivation: Data integration promises to be one of the main catalysts in enabling new
insights to be drawn from the wealth of biological data available publicly. However, the …

The SIB Swiss Institute of Bioinformatics Semantic Web of data

Nucleic Acids Research, 2024 - academic.oup.com
Abstract The SIB Swiss Institute of Bioinformatics (https://www. sib. swiss/) is a federation of
bioinformatics research and service groups. The international life science community in …

Exploring Disease Model Mouse Using Knowledge Graphs: Combining Gene Expression, Orthology, and Disease Datasets

T Kushida, T Mendes de Farias, AC Sima, C Dessimoz… - bioRxiv, 2023 - biorxiv.org
Background: The RIKEN BRC develops and maintains the RIKEN BioResource
MetaDatabase to help users explore appropriate target bioresources for their experiments …

[HTML][HTML] A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

AC Sima, C Dessimoz, K Stockinger… - …, 2019 - ncbi.nlm.nih.gov
The increasing use of Semantic Web technologies in the life sciences, in particular the use
of the Resource Description Framework (RDF) and the RDF query language SPARQL …

Federating and querying heterogeneous and distributed Web APIs and triple stores

TM de Farias, C Dessimoz, AA Benitez, C Yang… - arXiv preprint arXiv …, 2022 - arxiv.org
Today's international corporations such as BASF, a leading company in the crop protection
industry, produce and consume more and more data that are often fragmented and …

[PDF][PDF] Enabling Complex Semantic Queries to Bioinformatics Databases Through Intuitive Search Over Data

AC Sima, C Dessimoz, K Stockinger… - 2020 - serval.unil.ch
Data integration promises to be one of the main catalysts in enabling new insights to be
drawn from the wealth of biological data already available publicly. However, the …