Arabidopsis Phenome Database

2017/02/27

Web Site: http://jphenome.info/?page_id=95
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/arabid_pheno/

The database is Arabidopsis Phenome Database that consist of “RIKEN Phenome Integration of Arabidopsis Mutants”and“Database of Curated Plant Phenome”.

README Content

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

1. Database Component

  1. README
  2. Plant phenotype
  3. Observation of Arabidopsis phenotype
  4. Image of Arabidopsis phenotype
  5. Phenotype-gene
  6. Phenotype abnormality
  7. Experimental Condition
  8. Reference
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Arabidopsis Phenome Database" data.
File README_e.html (English)
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2.2 Plant phenotype

Data name Plant phenotype
Description of data contents

Phenotypes mentioned in the presented database, such as "long leaf", can be expressed as combinations of "entity" and "quality". Terms of entities and qualities are expressed with ontology terms, to standardize phenotype information. Entities: Names of organs, tissues, development stages. The vocabulary is defined in Plant Ontology(PO). Qualities: Characteristics, attributes of entities. The vocabulary is defined in Phenotype Ontology(PATO).

File riken_piam_phenome.zip (2.3 KB)

Data items are the following:
Data itemDescription
Entry URI Entry URI
Entry name Entry name
Entity in PO Entity (defined in PO)
Quality in PATO Quality (defined in PATO)
Num of observation data The number of entries where the phenotype is used in "Observation of Arabidopsis phenotype"
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2.3 Observation of Arabidopsis phenotype

Data name Observation of Arabidopsis phenotype
Description of data contents

Observation data are distinguished by phenotype, method of mutation, mutant ID etc., and standardized with appropriate ontology terms. The listed observation data are correspond to original observation data one-to-one,which are presented in databases including Ds tagging line, activation tagging line, and Fox-hunting line.

File riken_piam_main.zip (367 KB)

Data items are the following:
Data itemDescription
Entry URI Entry URI
Image Mutant image
Entry name Entry name
Original data name Name in the original database
Observed phenotype Observed phenotype
Phenotype URI Phenotype URI
Modified gene Modified gene
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2.4 Image of Arabidopsis phenotype

Data name Image of Arabidopsis phenotype
Description of data contents

Mutant images in "Observation of Arabidopsis phenotype"

File piam_image.tar.gz (8.4 GB)
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2.5 Phenotype-gene

Data name Phenotype-gene
Description of data contents

Combination of phenotype observation and gene modification found by literature curation

File cpp_main.zip (39 KB)

Data items are the following:
Data itemDescription
Entry URI Entry URI
Entry name Entry name
Reference Curated reference
Reference URI Reference URI
Pheno abnormality Pheno abnormality
Abnormality URI Abnormality URI
Muteted gene Muteted gene
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2.6 Phenotype abnormality

Data name Phenotype abnormality
Description of data contents

We have collected various kind of phenotypes, including those of morphology, responsibility to environmental factors. They are standardized by combination of ontology terms and properties. Phenotypes for morphology are standardized using Plant Ontology (PO) or Trait Ontology (TO), with Phenotype Ontology (PATO). PATO is the vocabulary covering terms of characcteristics such as "large" and "long". PO and TO are the vocabularies covering names of organs and developmental stages. Phenotypes of biochemical characteristics or stress tolerance can be expressed using Gene Ontology (GO), ChEBI etc. Some phenotypes are observed under some specific environements such as "long-day condition". Such phenotypes have links to environmental factors standardized and listed in another class.

File cpp_abnormality.zip (12 KB)

Data items are the following:
Data itemDescription
Entry URI Entry URI
Entry name Entry name
Experimental condition Experimental condition
Condition URI Condition URI
Quality in PATO Quality (defined in PATO)
In organ named In organ named
In period of In period of
In response to organism In response to organism
In situation of In situation of
After After
Under influence of Under influence of
During process named During process named
Exhibited by Exhibited by
For quantity of For quantity of
For state of For state of
For trait of For trait of
Num of phenotype gene The number of entries where the abnormality is used in "Phenotype-gene"
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2.7 Experimental Condition

Data name Experimental Condition
Description of data contents

Environmental factor necessary to express phenotypes
- Light condition etc.
Plant Environment Ontology (EO) is used for standardization.
- Existence or absence of specified substances
The focused factors are standardized with ChEBI for substance names, and some properties.

File cpp_exp_condition.zip (0.8 KB)

Data items are the following:
Data itemDescription
Entry URI Entry URI
Entry name Entry name
Description Description
In environment of In environment of
In presence of In presence of
In absense of In absense of
Num of phenotype abnormality The number of entries where the condition is used in "Phenotype abnormality"
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2.8 Reference

Data name Reference
Description of data contents

Literature as evidence of phenotype information

File cpp_reference.zip (475 KB)

Data items are the following:
Data itemDescription
Entry URI Entry URI
Entry name Entry name
Title Title
Authors Authors
Abstract Abstract
Pubmed ID Pubmed ID
Journal Journal
Volume Volume
Issue Issue
Pages Pages
Publication date Publication date
Num of phenotype gene The number of entries where the reference is used in "Phenotype-gene"
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3. License

Last updated : 2017/02/27

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: "Arabidopsis Phenome Database c Hiroshi Masuya (RIKEN BioResource Center) 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.

RIKEN BioResource Center
Hiroshi Masuya
E-mail:hiroshi[dot]masuya[at]riken[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

DateUpdate contents
2017/02/27 Arabidopsis Phenome Database English archive site is opened.
- Arabidopsis Phenome Database (http://jphenome.info/?page_id=95) is opened.
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5. Literature

-
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6. Contact address

When you have any question about "Arabidopsis Phenome Database", contact the following:

RIKEN BioResource Center
Hiroshi Masuya
E-mail:hiroshi[dot]masuya[at]riken[dot]jp

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