A proteomics sample metadata representation for multiomics integration and big data analysis

C Dai, A Füllgrabe, J Pfeuffer, EM Solovyeva… - Nature …, 2021 - nature.com
The amount of public proteomics data is rapidly increasing but there is no standardized
format to describe the sample metadata and their relationship with the dataset files in a way …

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Y Perez-Riverol, J Bai, C Bandla… - Nucleic acids …, 2022 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is …

The PRIDE database at 20 years: 2025 update

Y Perez-Riverol, C Bandla, DJ Kundu… - Nucleic Acids …, 2025 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's leading mass spectrometry (MS)-based proteomics data repository and one of …

Proteomics standards initiative at twenty years: current activities and future work

EW Deutsch, JA Vizcaíno, AR Jones… - Journal of proteome …, 2023 - ACS Publications
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been
successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the …

The PRIDE database and related tools and resources in 2019: improving support for quantification data

Y Perez-Riverol, A Csordas, J Bai… - Nucleic acids …, 2019 - academic.oup.com
Abstract The PRoteomics IDEntifications (PRIDE) database (https://www. ebi. ac. uk/pride/) is
the world's largest data repository of mass spectrometry-based proteomics data, and is one …

iProX: an integrated proteome resource

J Ma, T Chen, S Wu, C Yang, M Bai, K Shu… - Nucleic acids …, 2019 - academic.oup.com
Sharing of research data in public repositories has become best practice in academia. With
the accumulation of massive data, network bandwidth and storage requirements are rapidly …

[HTML][HTML] Ontology mapping for semantically enabled applications

I Harrow, R Balakrishnan, E Jimenez-Ruiz, S Jupp… - Drug discovery today, 2019 - Elsevier
Highlights•Ontology mapping enables data analytics through interoperability and
integration.•Mapping between ontologies expands coverage across large domains such as …

The European Bioinformatics Institute in 2017: data coordination and integration

CE Cook, MT Bergman, G Cochrane… - Nucleic acids …, 2018 - academic.oup.com
Abstract The European Bioinformatics Institute (EMBL-EBI) supports life-science research
throughout the world by providing open data, open-source software and analytical tools, and …

OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database

B Le Roux, G Lenaers, X Zanlonghi… - Orphanet journal of rare …, 2019 - Springer
Background The dysfunction of OPA1, a dynamin GTPase involved in mitochondrial fusion,
is responsible for a large spectrum of neurological disorders, each of which includes optic …

MicroPhenoDB associates metagenomic data with pathogenic microbes, microbial core genes, and human disease phenotypes

G Yao, W Zhang, M Yang, H Yang… - Genomics …, 2020 - academic.oup.com
Microbes play important roles in human health and disease. The interaction between
microbes and hosts is a reciprocal relationship, which remains largely under-explored …