Open TG-GATEs Pathological Image Database

2012/05/24

HTTPS Site: https://dbarchive.biosciencedbc.jp/data/open-tggates-pathological-images/

The database of high-resolution whole slide digital pathological images of liver and kidney pathological specimens which were obtained through animal tests using 160 compounds.

README Content

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

1. Database Component

  1. README
  2. Pathological Image Information
  3. Pathological Images (SVS format)
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Open TG-GATEs Pathological Image Database" data.
File README_e.html(English)
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2.2 Pathological Image Information

Data name Pathological Image Information
Description of data contents Information regarding each high-resolution digital image in the "Pathological Images (SVS format)" section.
File open_tggates_pathological_image.zip (370 KB)
Data items are the following:
Data item Description
EXP_ID ID assigned to each test which is defined mainly as a combination of COMPOUND_NAME, SPECIES, EXP_TEST_TYPE, and SINGLE_REPEAT_TYPE. IDs for in vivo tests are #0040 or larger.
GROUP_ID ID assigned to each group which is defined mainly as a combination of DOSE_LEVEL and SACRIFICE_PERIOD. IDs are in double digits. (e.g. 01, 16)
INDIVIDUAL_ID ID assigned to each individual within a group. IDs are in single digit.
COMPOUND_NAME Compound name
ORGAN Organs evaluated in tests. Liver or Kidney.
FILE_LOCATION HTTPS server path to the pathological images.
CAPTURE_NO/NO_OF_SAMPLE(n/n) The sequence number of scanned images with the total number. 1/2 means that 2 glass slides were scanned for an organ and that the image is the first one.
SPECIES Species
SINGLE_REPEAT_TYPE Type of in vivo test. Single-dose test or 28-day repeat-dose test.
ADMINISTRATION_ROUTE_TYPE Administration route
ANIMAL_AGE(week) Age of animal (weeks).
SACRIFICE_PERIOD Sampling time or period on in vivo test.
DOSE Dose
DOSE_UNIT Unit of dose

2.3 Pathological Images (SVS format)

Data name Pathological Images (SVS format)
Description of data contents High-resolution whole slide digital images of liver and kidney pathological specimens stained with hematoxylin-eosin dyes. The specimens were obtained through animal tests.
File File name: Pathological Images in SVS format
File URL: https://dbarchive.biosciencedbc.jp/data/open-tggates-pathological-images/LATEST/images/
File size: 25 TB (Total amount of SVS files)
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3. License

Last updated : 2012/05/24

You may use this database in compliance with the terms and conditions of the Standard License and the Additional License described below. The Standard License specifies the license terms regarding the use of this database and the requirements you must follow in using this database. The Additional License specifies those items that are exceptionally permitted even though they are generally prohibited in the Standard License.

Standard License

Creative Commons License

The Standard License for this database is the license specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "Toxicogenomics Project and Toxicogenomics Informatics Project under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan 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 derivative works based on part or whole of the data from this database,

under the Standard 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 derivative work.
  2. You must distribute any derivative work based on part or whole of the data from this database under this License.

Additional License

  1. You must display this Additional License along with the Standard License when distributing any derivative work based on part of whole of the data from this database.
  2. When you conduct research by using this database, and describe the research results in an article or paper, you always need to cite this database, and specify the name and URL of this database in the article or paper.
  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 Standard License and the above Additional License.

National Institute of Biomedical Innovation
7-6-8 Saito-Asagi, Ibaraki City, Osaka 567-0085, Japan
Tel: +81-72-641-9826
E-mail: opentggates[at]nibio[dot]go[dot]jp

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

Date Update contents
2012/05/24 Open TG-GATEs Pathological Image Database English archive site is opened.
2012/03/30 Open TG-GATEs Pathological Image Database(http://toxico.nibio.go.jp/) is released.
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5. Literature

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6. Contact address

When you have any question about "Open TG-GATEs Pathological Image Database", contact the following:

Toxicogenomics Informatics Project, National Institute of Biomedical Innovation
7-6-8, Saito-asagi, Ibaraki-city, Osaka 567-0085, Japan
Tel: +81-72-641-9826
E-mail: opentggates[at]nibio[dot]go[dot]jp

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