PATRIC March 2013 Release Offers Multiple Website Enhancements, New Features, and New Data¶
Website Updates¶
*Auto-spelling Suggestions/Corrections in the Global Search*
By leveraging Spell Checking functionality provided by Apache Solr, the Global Search on the PATRIC website now supports auto-spelling corrections. The search automatically detects minor spelling mistakes by comparing user supplied keywords against the database dictionary and automatically resubmits the user query with corrected spelling. Users still have option to search with their original query, if they wish to do so.
*Persistent Table Preferences and Customizations Throughout the PATRIC Website*
All of the PATRIC tables are highly customizable. Users can add/remove columns, move column locations, resize them, and change the number of rows in a table to see the data they are interested in and make the best use of the computer screen space. Now, all of the changes made by a user persist throughout the session. In addition, if you are a registered PATRIC user and logged in, the table customizations are saved permanently (or until you make another change).
*Community Annotations for Mycobacterium tuberculosis H37Rv Genome from TBCAP*
The first Tuberculosis Community Annotation Project (TBCAP) Jamboree was held in March, 2012 to improve the annotation of Mycobacterium tuberculosis H37Rv genome.
One of the major outcomes of the jamboree was ~25,000 annotation notes provided by the TB research community. The annotation notes included improved annotations, protein function and metabolic pathway assignments, protein-protein interactions, and literature references. We have incorporated all of these annotation notes into PATRIC and they are now available on the Mtb H37Rv gene/protein pages on the PATRIC website.
*New MLST Data*
Multi-locus Sequence Tags have been assigned to 2,420 genomes. The MLST data has been incorporated as an additional genome Metadata Attribute. Users can search for genomes with MLST or with specific MLST signature using the Global Search, Genome Finder, or Genome List page on the PATRIC website. The MLST is also presented under genome Metadata on the Genome Overview page.
** _**Protein Family Sorter: Multi-keyword Search_
A multi-keyword search box has been added on the Protein Family Sorter Page. This allows users to enter multiple keywords representing different protein functions as a list and search for those functions.
*Protein Family Page: Keyword Search*
Added a simple keyword search box on the protein family members page. This allows users to quickly find subsets of protein family members/homologs using simple keywords, such as organism/genome name, locus tag, or gene name.
* Updated Protein Functions and FIGfam Assignments*
The function of all the proteins annotated by RAST has been recalled and synchronized based on the current set of FIGfams. This has also resulted in the updated FIGfam assignments for all the proteins. Also, the average FIGfam coverage per genome has improved by ~10% (up from 78% in the last release to 88% in this release).
New Genomes and Annotations¶
In the March 2012 data release, 899 new genomes have been added to PATRIC and 1093 new genomes have been annotated using RAST. A total of 268 genomes have been updated or replaced with the newer versions.
A summary of the genomes available on the PATRIC website through March, 2013 is provided in the table below:
PATRIC | RefSeq | |
|---|---|---|
Number of genomes | 8105 | 6651 |
Number of Complete genomes | 2118 | 2061 |
Number of WGS genomes | 5982 | 4190 |
Number of Plasmid only genomes | 5 | 400 |
New Transcriptomics Datasets¶
In the March 2013 data release, 86 new GEO experiments have been curated and incorporated into PATRIC. Below is the summary of the new experiments and curated comparisons added to PATRIC between November 2012 and March 2013.
Organism | Experiments | Comparisons |
|---|---|---|
Actinobacillus | 1 | 3 |
Agrobacterium | 1 | 4 |
Bacillus | 19 | 264 |
Bacteroides | 1 | 1 |
Burkholderia | 2 | 48 |
Campylobacter | 5 | 127 |
Chlamydophila | 1 | 24 |
Cupriavidus | 1 | 1 |
Ehrlichia | 1 | 3 |
Escherichia | 3 | 15 |
Francisella | 3 | 40 |
Helicobacter | 5 | 66 |
Lactobacillus | 16 | 121 |
Rickettsia | 2 | 2 |
Vibrio | 25 | 139 |
Total | 86 | 858 |