iProX: an integrated proteome resource

iProX: an integrated proteome resource

2019 | Jie Ma, Tao Chen, Songfeng Wu, Chunyuan Yang, Mingze Bai, Kunxian Shu, Kenli Li, Guoqing Zhang, Zhong Jin, Fuchu He, Henning Hermjakob, Yunping Zhu
iProX is an integrated proteome resource developed to facilitate open access to proteomics data worldwide. It serves as a public platform for collecting, sharing, and managing raw data, analysis results, and standardized metadata from proteomics experiments. The iProX repository employs a web-based data submission process and supports open sharing of mass spectrometry-based proteomics datasets. It uses extensive controlled vocabularies and ontologies to annotate proteomics datasets, enabling efficient data sharing and retrieval. Users can submit their proteomics datasets as public or private datasets, with public datasets immediately accessible and private datasets accessible only to authorized users until a related manuscript is published. iProX is a full member of the ProteomeXchange (PX) consortium and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support. It supports two submission workflows: 'Complete submission' and 'Partial submission'. Complete submissions include all processed data in community standard formats, while Partial submissions provide processed data in formats not yet fully supported by the web interface. iProX uses a fast Aspera-based transfer tool for data submission and provides a RESTful Web Service API for bulk download. The iProX system is built on a hyper-converged architecture with high scalability and high availability, ensuring continuous service through a distributed scale-out design for storage and computing resources. It supports localizable backup of datasets to ensure data security. iProX is compatible with the data sharing policies proposed by PX and ensures that all datasets deposited after July 1, 2017, are released once the corresponding paper is published. The system provides a user-friendly data submission process, structured management of datasets, standardized metadata collection, and visualized data transmission with high speed. It also includes manual verification of submitted data and metadata by curators to ensure data quality and compliance with PX standards. iProX has been used to store and share large-scale proteomics datasets, including those from the Chinese Human Proteome Project (CNHPP), and provides a centralized metadata search interface for all datasets. The system is designed to support the long-term and stable sharing of proteomics data, facilitating global data analysis and sharing of proteomics experiments.iProX is an integrated proteome resource developed to facilitate open access to proteomics data worldwide. It serves as a public platform for collecting, sharing, and managing raw data, analysis results, and standardized metadata from proteomics experiments. The iProX repository employs a web-based data submission process and supports open sharing of mass spectrometry-based proteomics datasets. It uses extensive controlled vocabularies and ontologies to annotate proteomics datasets, enabling efficient data sharing and retrieval. Users can submit their proteomics datasets as public or private datasets, with public datasets immediately accessible and private datasets accessible only to authorized users until a related manuscript is published. iProX is a full member of the ProteomeXchange (PX) consortium and has been deployed as part of the proteomics infrastructure of China, ensuring long-term and stable resource support. It supports two submission workflows: 'Complete submission' and 'Partial submission'. Complete submissions include all processed data in community standard formats, while Partial submissions provide processed data in formats not yet fully supported by the web interface. iProX uses a fast Aspera-based transfer tool for data submission and provides a RESTful Web Service API for bulk download. The iProX system is built on a hyper-converged architecture with high scalability and high availability, ensuring continuous service through a distributed scale-out design for storage and computing resources. It supports localizable backup of datasets to ensure data security. iProX is compatible with the data sharing policies proposed by PX and ensures that all datasets deposited after July 1, 2017, are released once the corresponding paper is published. The system provides a user-friendly data submission process, structured management of datasets, standardized metadata collection, and visualized data transmission with high speed. It also includes manual verification of submitted data and metadata by curators to ensure data quality and compliance with PX standards. iProX has been used to store and share large-scale proteomics datasets, including those from the Chinese Human Proteome Project (CNHPP), and provides a centralized metadata search interface for all datasets. The system is designed to support the long-term and stable sharing of proteomics data, facilitating global data analysis and sharing of proteomics experiments.
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