GenBank 2024 update

EW Sayers, M Cavanaugh, K Clark… - … Acids Research, 2024 - academic.oup.com
2023 as a Year of Open Science, GenBank in 2023 … we have introduced an increasing set
of automations that accelerate … If you use the GenBank database in your published research

Comparative toxicogenomics database (CTD): update 2021

AP Davis, CJ Grondin, RJ Johnson… - … acids research, 2021 - academic.oup.com
data-tabs for both the corresponding chemical and phenotype (6,14). We have increased
the utility of chemical–phenotype data by integrating it with CTD’s chemical–disease data-set

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

Y Perez-Riverol, J Bai, C Bandla… - … acids research, 2022 - academic.oup.com
… PRIDE Archive pipelines (2) perform a set of validation and quality checks to … problem,
we will be working in developing a tailored infrastructure for sensitive human proteomics data

OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs

EV Kriventseva, D Kuznetsov, F Tegenfeldt… - … acids research, 2019 - academic.oup.com
… comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO
assessments of gene set completeness and mapping of the uploaded data to OrthoDB to …

LncRNA2Target v2. 0: a comprehensive database for target genes of lncRNAs in human and mouse

L Cheng, P Wang, R Tian, S Wang, Q Guo… - … acids research, 2019 - academic.oup.com
collected all lncRNA papers and datasets published from 1 August 2014 to 30 April 2018 by
searching the PubMed literature database … lncRNA–target relationship data through our web …

MODOMICS: a database of RNA modifications and related information. 2023 update

A Cappannini, A Ray, E Purta, S Mukherjee… - … Acids Research, 2024 - academic.oup.com
… The MODOMICS database was updated with recent data … , which commonly caused problems
for computational parsing … We also plan to expand the collection of synthetic modifications…

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

I Rauluseviciute, R Riudavets-Puig… - … Acids Research, 2024 - academic.oup.com
… To address this issue, multiple database solutions have been developed to collect and store
… provide programmatic access to the data stored in the JASPAR database. Specifically, the …

Lnc2Cancer v2. 0: updated database of experimentally supported long non-coding RNAs in human cancers

Y Gao, P Wang, Y Wang, X Ma, H Zhi… - … acids research, 2019 - academic.oup.com
… In Lnc2Cancer 2.0, we have updated the database with more data and several new features…
methylation were collected. For lncRNAs regulated by miRNA and TF, we only collected the …

The European nucleotide archive in 2021

C Cummins, A Ahamed, R Aslam, J Burgin… - … acids research, 2022 - academic.oup.com
… in the event of validation errors or other issues. Additional tools are offered to support … set,
(a) a master record (which is still loaded into the relational database) and (b) a FASTA data

PLSDB: advancing a comprehensive database of bacterial plasmids

GP Schmartz, A Hartung, P Hirsch, F Kern… - … Acids Research, 2022 - academic.oup.com
… In order to address this issue, another filtering step was set in place specially … data of PLSDB,
was to clean it up. In this update, we integrated a part of this process into our data collection