Dataset Information

WikiPathways 2024: next generation pathway database.

ABSTRACT: WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight the continuing efforts supporting WikiPathways, content growth and collaboration among pathway researchers. As an evolving database, there is a growing need for WikiPathways to address and overcome technical challenges. In this direction, WikiPathways has undergone major restructuring, enabling a renewed approach for sharing and curating pathway knowledge, thus providing stability for the future of community pathway curation. The website has been redesigned to improve and enhance user experience. This next generation of WikiPathways continues to support existing features while improving maintainability of the database and facilitating community input by providing new functionality and leveraging automation.

SUBMITTER: Agrawal A

PROVIDER: S-EPMC10767877 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Publications

WikiPathways 2024: next generation pathway database.

Agrawal Ayushi A Balcı Hasan H Hanspers Kristina K Coort Susan L SL Martens Marvin M Slenter Denise N DN Ehrhart Friederike F Digles Daniela D Waagmeester Andra A Wassink Isabel I Abbassi-Daloii Tooba T Lopes Elisson N EN Iyer Aishwarya A Acosta Javier Millán JM Willighagen Lars G LG Nishida Kozo K Riutta Anders A Basaric Helena H Evelo Chris T CT Willighagen Egon L EL Kutmon Martina M Pico Alexander R AR

Nucleic acids research 20240101 D1

WikiPathways (wikipathways.org) is an open-source biological pathway database. Collaboration and open science are pivotal to the success of WikiPathways. Here we highlight the continuing efforts supporting WikiPathways, content growth and collaboration among pathway researchers. As an evolving database, there is a growing need for WikiPathways to address and overcome technical challenges. In this direction, WikiPathways has undergone major restructuring, enabling a renewed approach for sharing a ...[more]

PMID: 37941138

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Project description:BackgroundCurrent proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also be improved to solve this issue.ResultsWe developed a state-of-the-art toolkit (SeqWiz) for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. First, we proposed two derived data formats: SQPD (a well-structured and high-performance local sequence database based on SQLite), and SET (an associated list of selected entries based on JSON). The SQPD format follows the basic standards of the emerging PEFF format, which also aims to facilitate the search of complex proteoform. The SET format is designed for generating subsets with with high-efficiency. These formats are shown to greatly outperform the conventional FASTA or PEFF formats in time and resource consumption. Then, we mainly focused on the UniProt knowledgebase and developed a collection of open-source tools and basic modules for retrieving species-specific databases, formats conversion, sequence generation, sequence filter, and sequence analysis. These tools are implemented by using the Python language and licensed under the GNU General Public Licence V3. The source codes and distributions are freely available at GitHub ( https://github.com/fountao/protwiz/tree/main/seqwiz ).ConclusionsSeqWiz is designed to be a collection of modularized tools, which is friendly to both end-users for preparing easy-to-use sequence databases as well as bioinformaticians for performing downstream sequence analysis. Besides the novel formats, it also provides compatible functions for handling the traditional text based FASTA or PEFF formats. We believe that SeqWiz will promote the implementing of complementary proteomics for data renewal and proteoform analysis to achieve precision proteomics. Additionally, it can also drive the improvement of proteomic standardization and the development of next-generation proteomic softwares.

Dataset Information

WikiPathways 2024: next generation pathway database.

Publications

WikiPathways 2024: next generation pathway database.

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