provide detailed information on proteome metadata. This is not a
research article, but an article about the metadata used in the
measurements for that research, so that the researchers will be
able to submit a new paper. The function to generate the output
file of the metadata of the registered data in the jPOST repository in
the MS Excel format for the JPDM data descriptor article type is
already implemented in the repository.
This chapter introduces the details of data registration of shotgun proteomics studies to the repository database using the jPOST
repository as an example.
2 Materials
The submission system of the jPOST repository is organized as a
web application and uses multiple open-source JavaScript libraries
to implement the user interface (Fig. 1). Backbone.js (https://
backbonejs.org/) and jQuery (https://jquery.com/) were adopted
as the foundation frameworks. However, taking into account the
expansion of functions at the request of the PX Consortium and the
advancement of the JavaScript framework, replacement with React
(https://reactjs.org/) framework is in progress. For file transfer, a
library improved by using Flow.js (http://flowjs.github.io/ngflow/) was used. Flow.js is a JavaScript library that expands the
file upload function of the Web browser and facilitates the highspeed transfer by dividing a file into small pieces and sending them.
The library has also improved the problem of memory consumption that occurs when the file size is too large and limited to the
functions needed for the jPOST repository. We have released a file
transmission library called presto.js (https://prestotools.github.io/
) that clearly reflects these improvements. Metadata registered by
the users and the transmitted files that are stored on the server are
managed by the jPOST project [10]. Nginx (https://nginx.org/)
was used as the webserver and MySQL (https://www.mysql.com/)
as the database server.
3 Methods
Here, we introduce the submission procedure for proteomics data
to the jPOST repository. At first, user registration is required before
submitting the data to the jPOST repository.
3.1 Types
of Registered Data
Two types of data are allowed to be registered in the jPOST
repository.
How to Deposit your Data in the jPOST Repository
311
research article, but an article about the metadata used in the
measurements for that research, so that the researchers will be
able to submit a new paper. The function to generate the output
file of the metadata of the registered data in the jPOST repository in
the MS Excel format for the JPDM data descriptor article type is
already implemented in the repository.
This chapter introduces the details of data registration of shotgun proteomics studies to the repository database using the jPOST
repository as an example.
2 Materials
The submission system of the jPOST repository is organized as a
web application and uses multiple open-source JavaScript libraries
to implement the user interface (Fig. 1). Backbone.js (https://
backbonejs.org/) and jQuery (https://jquery.com/) were adopted
as the foundation frameworks. However, taking into account the
expansion of functions at the request of the PX Consortium and the
advancement of the JavaScript framework, replacement with React
(https://reactjs.org/) framework is in progress. For file transfer, a
library improved by using Flow.js (http://flowjs.github.io/ngflow/) was used. Flow.js is a JavaScript library that expands the
file upload function of the Web browser and facilitates the highspeed transfer by dividing a file into small pieces and sending them.
The library has also improved the problem of memory consumption that occurs when the file size is too large and limited to the
functions needed for the jPOST repository. We have released a file
transmission library called presto.js (https://prestotools.github.io/
) that clearly reflects these improvements. Metadata registered by
the users and the transmitted files that are stored on the server are
managed by the jPOST project [10]. Nginx (https://nginx.org/)
was used as the webserver and MySQL (https://www.mysql.com/)
as the database server.
3 Methods
Here, we introduce the submission procedure for proteomics data
to the jPOST repository. At first, user registration is required before
submitting the data to the jPOST repository.
3.1 Types
of Registered Data
Two types of data are allowed to be registered in the jPOST
repository.
How to Deposit your Data in the jPOST Repository
311