ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

About Rice DB

ricedb.plantenergy.uwa.edu.au

Build Version
0.60

Data Date
2013-02-27

Build ID
744b15b

Build Date
2013-10-26

Citation
doi:10.1111/tpj.12357
What are Rice DB’s advantages?

Rice DB makes it easy to find and compare experimental and putative rice data from many well-established and emerging sources. Rice DB does this by consolidating a wide range of public scholarly data into a single search box, giving an overview of Oryza sativa gene knowledge and side-by-side comparisons for thousands of genes on a single screen. This is achieved by extensive data matching and curated cataloguing of disparate sources that haven't previously shared a common identifier scheme. On screen, a convenient summary is shown for each gene by default, and it can be expanded into detailed spreadsheets with the click of a button. In this way, researchers can gain access to many kinds of rice knowledge by simply entering a keyword or identifier.

Rice DB recognises over 40 different identifier formats in bulk so you can search for and convert between the widest range of rice biology databases. Arbitrary identifiers from published research can in many cases be matched back to your preferred identifiers. Rice DB includes obsolete identifiers so that past papers can be reviewed.

Rice DB provides subcellular localisation information for nice, including those both manually curated for Rice DB and the predicted sub-cellular localisation information computed in house.

Data for homologous Arabidopsis thaliana genes can be easily viewed in Rice DB. Since in many cases, a larger body of experimental evidence exists for Arabidopsis genes, the side-by-side viewing with Oryza in Rice DB can provide research leads that would otherwise be hard to find.

Rice DB includes dozens of interactive features and data displays, shown in screenshots below.

How do I use Rice DB?

To begin, simply paste or type any number of rice identifiers, English-language keywords, upstream 1 kb DNA motifs (with up to 2 wildcards), FASTA format (identifiers will be extracted), or Rice DB’s advanced syntax for reproducible searches.

We’ve included extensive examples on the main page — simply scroll past the data entry box. For constructing your own queries, see our advanced search query syntax.

Rice DB also has tools to help you tidy up your lists of identifiers, like looking for typos and duplicates. This functionality is included in the examples.

What data are included?
Rice DB is expanding the number of data sources included. Frequently-used public data sources are included. Data sources are displayed with a minimal of re-interpretation except where required for spelling or comparability.
Can I download Rice DB?
Rice DB results can be downloaded in bulk TSV format by entering your query in our home page. To download the raw files that were imported into Rice DB, visit our data accession pages. Each of these pages is linked to the source’s official website, or in the case of PEB’s original results, the hand-made Excel spreadsheet and author’s e-mail address. A web service URL for TSV downloads may be publicised in future.
How do I get FASTA output?
Click on advanced options and choose one type of sequence (DNA, upstream, peptide) as your only requested data. In your results, FASTA will be offered as an option next to TSV.

Screenshots

Paste Identifiers or FASTA

Single IDs, multiple IDs separated by commas (CSV), spaces or tabs (TSV) or newlines (TXT), or FASTA format.

English Text Search

Handles international spelling and suffix handling.


Top-hits from Published Location Predictors

Choose your favourite predictors: specific coverage is tallied and scores are normalised as percentages.

See experimental, predicted & annotated subcellular location data

Summaries with Popups

View multiple popups side-by-side.

Download as TSV File

Motif Analysis

Search 1kb upstream hexamers as words & download genome frequency stats.


Expandable Summaries

Conditional Searches

Search within specific criteria, or search all criteria at once with boolean logic.


Text Hints

Automatically suggests spelling variations.

Click through to other Databases

Search & show Legacy Identifiers


Advanced Query Syntax

Edit & adapt your searches


Resize & Re-order Columns

Sort & filter Online


Data Source Descriptions

Includes examples of how to search.

Review & re-run


— Added in Version 0.2 —

Arabidopsis thaliana orthologue data

Added in v0.2!

miRNA (micro RNA) targeting data

Added in v0.2!

Experimentally Shown RNA Expression Motifs

Added in v0.2!

Expression Shown RNA Expression Tissues

Added in v0.2!

Phenotype T-DNA Data

Added in v0.2!

Secondary Structure/Domain Annotations

Added in v0.2!


Search for any 1kb upstream motif with wildcards

Added in v0.2!

FASTA Output Format

Added in v0.2!

Additional Identifiers

Novel gene names from published papers.

Added in v0.2!


— Added in Version 0.3 —

This page of screenshots will be updated for public release v1.0.


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