jPOST repository metadata

2018/02/28

Web Site: https://repository.jpostdb.org/
FTP Site: ftp://ftp.biosciencedbc.jp/archive/jpost/

The repository of mass spectrometry (MS) raw data, peak lists and analyzed data.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Metadata
  3. File list
  4. Profile list
  5. Sample list
  6. Fractionation list
  7. Enzyme/Mod. List
  8. MS mode List
  9. Original metadata
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "jPOST repository metadata" data.
File README_e.html (English)
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2.2 Metadata

Data name Metadata
Description of data contents

The main body of jPOST repository metadata
File jpost_metadata.zip (25.3 KB)

Data items are the following:
Data itemDescription
jPOST ID Project ID
PXID ProtemoeXchange (PX) ID
Project title Project title
Keywords Keywords
Description Description
Mode Data analysis mode ("Complete" or "Partial")
PubMed ID(s) PubMed ID(s) if articles are published
PubMed Info References if articles are published
Principal investigator Principal investigator
Created date Data registration date
Announcement date Data publication date
Contact Contact
Files Registered file list (Only simple search)
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2.3 File list

Data name File list
Description of data contents

The list of files registered in jPOST repository
File jpost_file_list.zip (85.4 KB)

Data items are the following:
Data itemDescription
jPOST ID Project ID
File ID File ID
File Name File Name
Download page Link to download page (project entry page)
(Only simple search)
Profiles The list of profiles in this file (Only simple search)
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2.4 Profile list

Data name Profile list
Description of data contents

The list of expeerimental profiles such as sample or enzymes etc.
It is refered from "metadata".
File jpost_profile_list.zip (74.7 KB)

Data items are the following:
Data itemDescription
jPOST ID Project ID
File ID File ID
Profile plex Profile name
Sample - ID Sample ID
Sample - Title Sample name
Fractionation - ID Fractionation ID
Fractionation - Title Fractionation name
Enzyme/Mod. - ID Enzyme/Mod. reaction ID
Enzyme/Mod. - Title Enzyme/Mod. reaction name
MS mode - ID MS mode ID
MS mode - Title MS mode name
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2.5 Sample list

Data name Sample list
Description of data contents

The list of experimental samples
It is refered from "profile list".
File jpost_sample_list.zip (7.37 KB)

Data items are the following:
Data itemDescription
ID Sample ID
Title Sample name
Species Species
Tissue Tissue
Cell type Cell type
Disease Disease
Note Note
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2.6 Fractionation list

Data name Fractionation list
Description of data contents

The list of fractionations
It is refered from "profile list".
File jpost_fractionation_list.zip (5.39 KB)

Data items are the following:
Data itemDescription
ID Fractionation ID
Title Fractionation name
Subcellular Subcellular
Protein Protein
Peptide Peptide
Note Note
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2.7 Enzyme/Mod. List

Data name Enzyme/Mod. List
Description of data contents

The list of enzyme/mod.
It is refered from "profile list".
File jpost_enzyme_mod_list.zip (2.83 KB)

Data items are the following:
Data itemDescription
ID Enzyme/Mod. reaction ID
Title Enzyme/Mod. reaction name
Enzyme Enzyme
Fixed modification Modification prepared before the experiment
Variable modification Other modifications
Taxonomy Taxonomy
Note Note
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2.8 MS mode List

Data name MS mode List
Description of data contents

The list of MS mode
It is refered from "profile list".
File jpost_ms_mode_list.zip (2.58 KB)

Data items are the following:
Data itemDescription
ID MS mode ID
Title MS mode name
Instrument Instrument
Instrument mode Instrument mode
Purpose Purpose
Quantification platform Quantification platform
Plex Plex
Label Label
Note Note
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2.9 Original metadata

Data name Original metadata
Description of data contents

Original jPOST metadata (XML format)
File jpost_original_metadata.zip (584 KB)
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3. License

Last updated : 2018/02/28

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

 

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "jPOST repository metadata © Yasushi Ishihama (Kyoto Univ.) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

E-mail: jpostdb[at]gmail[dot]com

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

DateUpdate contents
2018/02/28 jPOST repository metadata English archive site is opened.
2016/05/02 jPOST (https://repository.jpostdb.org/) is opened.
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5. Literature

Shujiro Okuda, Yu Watanabe, Yuki Moriya, Shin Kawano, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Naoyuki Sugiyama, Susumu Goto, Yasushi Ishihama
jPOSTrepo: an international standard data repository for proteomes
Nucleic Acids Research, Volume 45, Issue D1, 4 January 2017, Pages D1107–D1111
PMID: 27899654

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6. Contact address

When you have any question about "jPOST repository metadata", contact the following:

E-mail: jpostdb[at]gmail[dot]com

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