The database is Arabidopsis Phenome Database that consist of “RIKEN Phenome Integration of Arabidopsis Mutants”and“Database of Curated Plant Phenome”.
Data name | README |
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Description of data contents | HTML file to describe "Arabidopsis Phenome Database" data. |
File | README_e.html (English) |
Data name | Plant phenotype |
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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 item | Description |
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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" |
Data name | Observation of Arabidopsis phenotype |
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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 item | Description |
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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 |
Data name | Image of Arabidopsis phenotype |
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Description of data contents | Mutant images in "Observation of Arabidopsis phenotype" |
File | piam_image.tar.gz (8.4 GB) |
Data name | Phenotype-gene |
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Description of data contents | Combination of phenotype observation and gene modification found by literature curation |
File | cpp_main.zip (39 KB) |
Data item | Description |
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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 |
Data name | Phenotype abnormality |
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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 item | Description |
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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" |
Data name | Experimental Condition |
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Description of data contents | Environmental factor necessary to express phenotypes |
File | cpp_exp_condition.zip (0.8 KB) |
Data item | Description |
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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" |
Data name | Reference |
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Description of data contents | Literature as evidence of phenotype information |
File | cpp_reference.zip (475 KB) |
Data item | Description |
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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" |
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.
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:
under the license, as long as you comply with the following conditions:
RIKEN BioResource Center
Hiroshi Masuya
E-mail:hiroshi[dot]masuya[at]riken[dot]jp
You can freely provide links to all contents in this database. But, contents might be changed without notice.
Date | Update contents |
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2017/02/27 | Arabidopsis Phenome Database English archive site is opened. |
- | Arabidopsis Phenome Database (http://jphenome.info/?page_id=95) is opened. |
RIKEN BioResource Center
Hiroshi Masuya
E-mail:hiroshi[dot]masuya[at]riken[dot]jp