Cargando…
A proteomics sample metadata representation for multiomics integration and big data analysis
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 that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Online Artículo Texto |
| Lenguaje: | English |
| Publicado: |
Nature Publishing Group UK
2021
|
| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494749/ https://www.ncbi.nlm.nih.gov/pubmed/34615866 http://dx.doi.org/10.1038/s41467-021-26111-3 |
| _version_ | 1784579382776430592 |
|---|---|
| author | Dai, Chengxin Füllgrabe, Anja Pfeuffer, Julianus Solovyeva, Elizaveta M. Deng, Jingwen Moreno, Pablo Kamatchinathan, Selvakumar Kundu, Deepti Jaiswal George, Nancy Fexova, Silvie Grüning, Björn Föll, Melanie Christine Griss, Johannes Vaudel, Marc Audain, Enrique Locard-Paulet, Marie Turewicz, Michael Eisenacher, Martin Uszkoreit, Julian Van Den Bossche, Tim Schwämmle, Veit Webel, Henry Schulze, Stefan Bouyssié, David Jayaram, Savita Duggineni, Vinay Kumar Samaras, Patroklos Wilhelm, Mathias Choi, Meena Wang, Mingxun Kohlbacher, Oliver Brazma, Alvis Papatheodorou, Irene Bandeira, Nuno Deutsch, Eric W. Vizcaíno, Juan Antonio Bai, Mingze Sachsenberg, Timo Levitsky, Lev I. Perez-Riverol, Yasset |
| author_facet | Dai, Chengxin Füllgrabe, Anja Pfeuffer, Julianus Solovyeva, Elizaveta M. Deng, Jingwen Moreno, Pablo Kamatchinathan, Selvakumar Kundu, Deepti Jaiswal George, Nancy Fexova, Silvie Grüning, Björn Föll, Melanie Christine Griss, Johannes Vaudel, Marc Audain, Enrique Locard-Paulet, Marie Turewicz, Michael Eisenacher, Martin Uszkoreit, Julian Van Den Bossche, Tim Schwämmle, Veit Webel, Henry Schulze, Stefan Bouyssié, David Jayaram, Savita Duggineni, Vinay Kumar Samaras, Patroklos Wilhelm, Mathias Choi, Meena Wang, Mingxun Kohlbacher, Oliver Brazma, Alvis Papatheodorou, Irene Bandeira, Nuno Deutsch, Eric W. Vizcaíno, Juan Antonio Bai, Mingze Sachsenberg, Timo Levitsky, Lev I. Perez-Riverol, Yasset |
| author_sort | Dai, Chengxin |
| collection | PubMed |
| description | 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 that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets. |
| format | Online Article Text |
| id | pubmed-8494749 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2021 |
| publisher | Nature Publishing Group UK |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-84947492021-10-07 A proteomics sample metadata representation for multiomics integration and big data analysis Dai, Chengxin Füllgrabe, Anja Pfeuffer, Julianus Solovyeva, Elizaveta M. Deng, Jingwen Moreno, Pablo Kamatchinathan, Selvakumar Kundu, Deepti Jaiswal George, Nancy Fexova, Silvie Grüning, Björn Föll, Melanie Christine Griss, Johannes Vaudel, Marc Audain, Enrique Locard-Paulet, Marie Turewicz, Michael Eisenacher, Martin Uszkoreit, Julian Van Den Bossche, Tim Schwämmle, Veit Webel, Henry Schulze, Stefan Bouyssié, David Jayaram, Savita Duggineni, Vinay Kumar Samaras, Patroklos Wilhelm, Mathias Choi, Meena Wang, Mingxun Kohlbacher, Oliver Brazma, Alvis Papatheodorou, Irene Bandeira, Nuno Deutsch, Eric W. Vizcaíno, Juan Antonio Bai, Mingze Sachsenberg, Timo Levitsky, Lev I. Perez-Riverol, Yasset Nat Commun Perspective 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 that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets. Nature Publishing Group UK 2021-10-06 /pmc/articles/PMC8494749/ /pubmed/34615866 http://dx.doi.org/10.1038/s41467-021-26111-3 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
| spellingShingle | Perspective Dai, Chengxin Füllgrabe, Anja Pfeuffer, Julianus Solovyeva, Elizaveta M. Deng, Jingwen Moreno, Pablo Kamatchinathan, Selvakumar Kundu, Deepti Jaiswal George, Nancy Fexova, Silvie Grüning, Björn Föll, Melanie Christine Griss, Johannes Vaudel, Marc Audain, Enrique Locard-Paulet, Marie Turewicz, Michael Eisenacher, Martin Uszkoreit, Julian Van Den Bossche, Tim Schwämmle, Veit Webel, Henry Schulze, Stefan Bouyssié, David Jayaram, Savita Duggineni, Vinay Kumar Samaras, Patroklos Wilhelm, Mathias Choi, Meena Wang, Mingxun Kohlbacher, Oliver Brazma, Alvis Papatheodorou, Irene Bandeira, Nuno Deutsch, Eric W. Vizcaíno, Juan Antonio Bai, Mingze Sachsenberg, Timo Levitsky, Lev I. Perez-Riverol, Yasset A proteomics sample metadata representation for multiomics integration and big data analysis |
| title | A proteomics sample metadata representation for multiomics integration and big data analysis |
| title_full | A proteomics sample metadata representation for multiomics integration and big data analysis |
| title_fullStr | A proteomics sample metadata representation for multiomics integration and big data analysis |
| title_full_unstemmed | A proteomics sample metadata representation for multiomics integration and big data analysis |
| title_short | A proteomics sample metadata representation for multiomics integration and big data analysis |
| title_sort | proteomics sample metadata representation for multiomics integration and big data analysis |
| topic | Perspective |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8494749/ https://www.ncbi.nlm.nih.gov/pubmed/34615866 http://dx.doi.org/10.1038/s41467-021-26111-3 |
| work_keys_str_mv | AT daichengxin aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT fullgrabeanja aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT pfeufferjulianus aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT solovyevaelizavetam aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT dengjingwen aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT morenopablo aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT kamatchinathanselvakumar aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT kundudeeptijaiswal aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT georgenancy aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT fexovasilvie aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT gruningbjorn aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT follmelaniechristine aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT grissjohannes aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT vaudelmarc aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT audainenrique aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT locardpauletmarie aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT turewiczmichael aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT eisenachermartin aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT uszkoreitjulian aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT vandenbosschetim aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT schwammleveit aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT webelhenry aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT schulzestefan aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT bouyssiedavid aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT jayaramsavita aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT dugginenivinaykumar aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT samaraspatroklos aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT wilhelmmathias aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT choimeena aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT wangmingxun aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT kohlbacheroliver aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT brazmaalvis aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT papatheodorouirene aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT bandeiranuno aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT deutschericw aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT vizcainojuanantonio aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT baimingze aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT sachsenbergtimo aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT levitskylevi aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT perezriverolyasset aproteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT daichengxin proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT fullgrabeanja proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT pfeufferjulianus proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT solovyevaelizavetam proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT dengjingwen proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT morenopablo proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT kamatchinathanselvakumar proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT kundudeeptijaiswal proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT georgenancy proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT fexovasilvie proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT gruningbjorn proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT follmelaniechristine proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT grissjohannes proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT vaudelmarc proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT audainenrique proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT locardpauletmarie proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT turewiczmichael proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT eisenachermartin proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT uszkoreitjulian proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT vandenbosschetim proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT schwammleveit proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT webelhenry proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT schulzestefan proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT bouyssiedavid proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT jayaramsavita proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT dugginenivinaykumar proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT samaraspatroklos proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT wilhelmmathias proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT choimeena proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT wangmingxun proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT kohlbacheroliver proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT brazmaalvis proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT papatheodorouirene proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT bandeiranuno proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT deutschericw proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT vizcainojuanantonio proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT baimingze proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT sachsenbergtimo proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT levitskylevi proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis AT perezriverolyasset proteomicssamplemetadatarepresentationformultiomicsintegrationandbigdataanalysis |