WormMart

WormMart updated to WS191

Will Spooner (whs@ebi.ac.uk) — Wed, 25 Jun 2008 09:49:45 -0500

In addition to the data update to the WormBase WS191 release, the underlying BioMart software has been updated to version 0_7. There are a few UI enhancements, and there is also now a button that creates a "permanent" URL link for a mart query.

WormMart updated to WS185

Will Spooner (whs@ebi.ac.uk) — Tue, 08 Jan 2008 11:51:03 -0500

This is a data release. WormMart functionality remains unchanged.

WormMart updated to WS170

Will Spooner (whs@ebi.ac.uk) — Thu, 15 Feb 2007 06:58:28 -0500

A full list of WormMart changes for WS170 follows;

Gene dataset
- Add a filter for RNAi wild-type phenotypes, i.e. the
phenotype_observed_count == 0
- Add phenotype_short_name filter.
- Fix the 'missing' 3'UTR annotation for all single exon genes.
- Remove species other than elegans/briggsae from the species selection
drop down.
- Add links to Gene Regulation Summary page from
gene_trans_target/regulator.
- Fix the peptide sequences for the MtDNA chromosome.
- Add filter for peptide molecular weight thresholds.
- Add gene relationships (SPECIFIC/PRIMARY/SECONDARY) and scored/observed
phenotype counts/info to 'RNAi experiment' attributes and filters.

Phenotype dataset
- Enhance Attribute_of.RNAi filters/attributes.
- Add phenotype_short_name filter.
- Add Attribute_of.Variation filters/attributes.

RNAi dataset
- Add a filter to remove 'not' phenotypes from the RNAi dumps.

Variation dataset
- Add '[Sequence] Status' filters and attributes.
- Add phenotype filters to Variation objects.

WormMart Updated to WS167

Will Spooner (whs@ebi.ac.uk) — Mon, 11 Dec 2006 16:49:43 -0500

Gene Data Set

Sequence export options have been added to dump the 5' or 3' intergenic regions of a gene (the region between a gene's coding region and that of the next upstream/downstream gene on the same strand).
The Transgene filters have been rationalised into a single option, and a 'Transgene type' attribute added.
GO terms annotated on the Gene but not the CDS are now included in the database.
'Merged' attributes have been added for CDS, Transcript and Protein sequence names.

WormMart Updated to WS165

Will Spooner (whs@ebi.ac.uk) — Mon, 06 Nov 2006 09:14:04 -0500

Gene Data Set
- Filters added to restrict by (un)observed phenotypes only/excluded.
- Filter added for restricting by presence/absence of genetic map.
- Attributes added to improve exporting RNAi phenotype info.

RNAi Data Set
- Filter added to remove 'scored but not observed' phenotypes from the RNAi dumps.

Vaitation Data Set
- The origin.species filter has been moved to the top of the page and enabled (C.elegans) by
default.

WormMart updated to WS154

Will Spooner (whs@ebi.ac.uk) — Mon, 13 Mar 2006 07:31:31 -0500

The WormMart database has been updated to WormBase release WS154

New functionality:
WoamMart pages now have a link to a bookmarkable version. This link is found at the bottom of each page.

New documentation:
Walk-through examples of WormMart usage have been published on the WormBase wiki, available ;
[here]

Public mysql database for WormMart

Todd Harris (harris@cshl.edu) — Tue, 10 Jan 2006 12:39:48 -0500

A public MySQL server hosting the WormMart database is now available. Users can connect via any MySQL client, programatic interface (API) or BioMart enabled application. Connection details are;

Host:   aceserver.cshl.org
User:   anonymous
DBName: wormmart_current

E.g. using the MySQL client from the command line;

> mysql --host=aceserver.cshl.org --user=anonymous  wormmart_current

WormMart has been updated to WS151

Todd Harris (harris@cshl.edu) — Wed, 04 Jan 2006 12:38:43 -0500

The latest WormMart database, WS151, has been added to MartView. Other than the new data there are no new features. As a stable release, the WormMart WS150 database remains available

Upcoming service interruption - 26 Aug 2005

Todd Harris (harris@cshl.edu) — Wed, 24 Aug 2005 12:38:00 -0500

Due to scheduled maintenance and performance upgrade, WormBase will be unavailable starting at 5 PM EDT (UTC -4). We hope to have service restored by 9 PM. Should you require access during this period, consult our list of mirrors at the bottom of this page or use the development site

Introducing The WormMart RSS feed at WormBase

Todd Harris (harris@cshl.edu) — Fri, 05 Aug 2005 12:36:43 -0500

WormBase is pleased to introduce the new WormMart news feed. WormMart is the WormBase implementation of BioMart, a tool for retrieving datasets en masse. Subscribe to this feed to learn about new features and datasets at WormMart.