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Patpat: a public proteomics dataset search framework
SUMMARY: As the FAIR (Findable, Accessible, Interoperable, Reusable) principles have become widely accepted in the proteomics field, under the guidance of ProteomeXchange and The Human Proteome Organization Proteomics Standards Initiative, proteomics public databases have been providing Application...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933831/ https://www.ncbi.nlm.nih.gov/pubmed/36744907 http://dx.doi.org/10.1093/bioinformatics/btad076 |
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author | Liao, Weiheng Zhang, Xuelian |
author_facet | Liao, Weiheng Zhang, Xuelian |
author_sort | Liao, Weiheng |
collection | PubMed |
description | SUMMARY: As the FAIR (Findable, Accessible, Interoperable, Reusable) principles have become widely accepted in the proteomics field, under the guidance of ProteomeXchange and The Human Proteome Organization Proteomics Standards Initiative, proteomics public databases have been providing Application Programming Interfaces for programmatic access. Based on generating logic from proteomics data, we present Patpat, an extensible framework for searching public datasets, merging results from multiple databases to help researchers find their proteins of interest in the vast mass spectrometry. Patpat’s 2D strategy of combining results from multiple databases allows users to provide only protein identifiers to obtain metadata for relevant datasets, improving the ‘Findable’ of proteomics data. AVAILABILITY AND IMPLEMENTATION: The Patpat framework is released under the Apache 2.0 license open source, and the source code is stored on GitHub (https://github.com/henry-leo/Patpat) and is freely available. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-9933831 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-99338312023-02-17 Patpat: a public proteomics dataset search framework Liao, Weiheng Zhang, Xuelian Bioinformatics Applications Note SUMMARY: As the FAIR (Findable, Accessible, Interoperable, Reusable) principles have become widely accepted in the proteomics field, under the guidance of ProteomeXchange and The Human Proteome Organization Proteomics Standards Initiative, proteomics public databases have been providing Application Programming Interfaces for programmatic access. Based on generating logic from proteomics data, we present Patpat, an extensible framework for searching public datasets, merging results from multiple databases to help researchers find their proteins of interest in the vast mass spectrometry. Patpat’s 2D strategy of combining results from multiple databases allows users to provide only protein identifiers to obtain metadata for relevant datasets, improving the ‘Findable’ of proteomics data. AVAILABILITY AND IMPLEMENTATION: The Patpat framework is released under the Apache 2.0 license open source, and the source code is stored on GitHub (https://github.com/henry-leo/Patpat) and is freely available. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2023-02-06 /pmc/articles/PMC9933831/ /pubmed/36744907 http://dx.doi.org/10.1093/bioinformatics/btad076 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Liao, Weiheng Zhang, Xuelian Patpat: a public proteomics dataset search framework |
title | Patpat: a public proteomics dataset search framework |
title_full | Patpat: a public proteomics dataset search framework |
title_fullStr | Patpat: a public proteomics dataset search framework |
title_full_unstemmed | Patpat: a public proteomics dataset search framework |
title_short | Patpat: a public proteomics dataset search framework |
title_sort | patpat: a public proteomics dataset search framework |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9933831/ https://www.ncbi.nlm.nih.gov/pubmed/36744907 http://dx.doi.org/10.1093/bioinformatics/btad076 |
work_keys_str_mv | AT liaoweiheng patpatapublicproteomicsdatasetsearchframework AT zhangxuelian patpatapublicproteomicsdatasetsearchframework |