fRNAdb

2016/03/29

HTTPS Site: https://dbarchive.biosciencedbc.jp/data/frnadb/

The database that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences.

README Content

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

1. Database Component

  1. README
  2. fRNAdb Summary
  3. Database Dump
  4. Sequence Data
  5. Mapping Information
  6. RNA secondary structure image
  7. Supplementary Data
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "fRNAdb" data.
File README_e.html(English)
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2.2 fRNAdb Summary

Data name fRNAdb Summary
Description of data contents Functional RNA Database is a human curated catalog of functional RNAs acquired from journal papers. Each RNA is associated to a base sequence, genomic locus, putative secondary structure, citation, etc.
File frnadb_summary.zip (46.5 MB)

Data items are the following:
Data itemDescription
ID Entry ID
Accession Accession
Description Description
SO name Sequence Ontology
Organism Organism
Xref Cross Reference
Length Sequence Length
Sequence Sequence
Second Structure Thumbnail Thumbnail of RNA secondary structure image
Second Structure (PNG) RNA secondary structure image (PNG)
Second Structure (PDF) RNA secondary structure image (PDF)
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2.3 Database Dump

Data name Database Dump
Description of data contents

Dump data from database in the original site:
- fRNAdb.pdf: description of database schema
- fRNAdb_schema.sql: database schema
- fRNAdb_table.7z: dump data (original)
- fRNAdbtsv.zip: dump data (tab separeted text)

File Database Dump (673 MB)
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2.4 Sequence Data

Data name Sequence Data
Description of data contents

Functional RNA sequence files (FASTA)
- sequence.zip: Aggregation of the following files
- mirna.zip: miRNA sequences
- ncrna.zip: ncRNA sequences
- shortread.zip: Sequences from short read sequencer
- Other: Sequences of 10 species

File Sequence Data (102 MB)
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2.5 Mapping Information

Data name Mapping Information
Description of data contents

Mapping results on genomes of 4 species
- dm3_*.zip: Drosophila_melanogaster
- hg18_*.zip: Homo_sapiens
- mm9_*.zip: Mus_musculus
- rn3_*.zip: Rattus_norvegicus

File Mapping_Information (120 MB)
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2.6 RNA secondary structure image

Data name RNA secondary structure image
Description of data contents

RNA secondary structure images
- png.zip: RNA secondary structure images (PNG)
- pdf.zip: RNA secondary structure images (PDF)
- thumbnail.zip: Thumbnails of RNA secondary structure images

File RNA_secondary_structure_image (9.6 GB)
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2.7 Supplementary Data

Data name Supplementary Data
Description of data contents

- xref.zip: Entry ID, Accession, Mapping Position in genome (only Homo sapiens)
- count_taxon.tsv: list of all species and the number of entries in fRNAdb

File Supplementary_Data (3.8 MB)
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3. License

Last updated : 2016/03/29

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: "fRNAdb © Toutai Mituyama (National Institute of Advanced Industrial Science and Technology) 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.

Toutai Mituyama
E-mail: mituyama-toutai[at]aist[dot]go[dot]jp

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4. Update History

DateUpdate contents
2016/03/29 fRNAdb English archive site is opened.
2006/12 fRNdb (http://www.ncrna.org/) is opened.
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5. Literature

Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences
Nucleic Acids Research/2007/D145-8
PMID: 17099231

Mituyama T, Yamada K, Hattori E, Okida H, Ono Y, Terai G, Yoshizawa A, Komori T, Asai K.
The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs.
Nucleic Acids Research/2009/D89-92
PMID: 18948287

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6. Contact address

When you have any question about "fRNAdb", contact the following:

Toutai Mituyama
E-mail: mituyama-toutai[at]aist[dot]go[dot]jp

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