PATRIC May 2013 Release Features New Data, Improved Metadata-Site Integration and Updated KEGG Maps

Published on 2013-06-01

Website Enhancement

******Genome Metadata in Protein Family Sorter**

Selected genome metadata fields are now visible in the Genome Filtering Panel of the Protein Family Sorter.  This helps sort and/or select genomes based on metadata attributes, such as country of isolation, host, disease, collection date, and completion date.  Using available metadata and filtering options, users can now search for protein families that are present in genomes isolated from host A but absent in genomes from host B.  Both the Table and Heatmap tabs may be filtered using this panel.

New Genomes and Annotations

In the May 2013 data release, 810 new genomes have been added to PATRIC, 798 new genomes have been annotated using RAST, and 13 genomes have been updated.

A summary of the genomes available on the PATRIC website through May, 2013 is provided in the table below:

PATRIC

RefSeq

Number of genomes

8903

7134

Number of Complete genomes

2189

2132

Number of WGS genomes

6710

4603

Number of Plasmid only genomes

4

399

Featured: New 106 Brucella genomes from USDA available exclusively at PATRIC.

These genomes were sequenced by USDA and subsequently assembled and annotated by PATRIC using RAST. View or download all 106 genomes here.

Genome Metadata

In addition to curating metadata for new genomes, significant effort was made to clean up genome metadata, make it consistent across the genomes, and collect missing metadata from literature, which has resulted in incorporation of bacterial isolation related metadata for an additional 926 genomes.

Updated KEGG Pathways

We have recently updated KEGG pathway maps and pathway annotations at PATRIC using the latest version of pathways available from KEGG. Pathway download files have been updated for all the genomes to reflect the latest pathway annotations.

New Transcriptomics Datasets

155 new GEO experiments have been curated and incorporated into PATRIC.  Below is the summary of the new experiments and curated comparisons added to PATRIC since the Dec 2012 release.

  <table class="basic stripe" width="236" border="0" cellspacing="0" cellpadding="0">
    <tr>
      <th valign="bottom" nowrap="nowrap" width="106">
        <b>Organism</b>
      </th>

      <th valign="bottom" nowrap="nowrap" width="64">
        <b>Experiments</b>
      </th>

      <th valign="bottom" nowrap="nowrap" width="66">
        <b>Comparisons</b>
      </th>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Bdellovibrio
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Bifidobacterium
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          13
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Bradyrhizobium
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          8
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          18
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Caldicellulosiruptor
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          3
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          24
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Caulobacter
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Cupriavidus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          3
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          26
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Dehalococcoides
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          10
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Deinococcus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Desulfovibrio
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          2
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          2
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Enterococcus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          7
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Frankia
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          5
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Geobacter
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          11
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          11
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Haemophilus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          4
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Lactococcus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          7
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          15
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Legionella
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          16
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Leptospira
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          2
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          2
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Magnetospirillum
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          8
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Methylibium
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Mycoplasma
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          86
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Myxococcus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          3
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          14
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Neisseria
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          2
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          2
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Nitrosomonas
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          2
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          7
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Pectobacterium
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Pelobacter
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Photorhabdus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          2
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Porphyromonas
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          1
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Prevotella
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          34
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Proteus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          6
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Pseudomonas
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          40
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          148
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Psychrobacter
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          12
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Rhizobium
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          2
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          2
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Rhodobacter
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          10
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          74
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Rhodopirellula
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          3
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          14
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Rhodopseudomonas
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          3
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          5
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Salmonella
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          2
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Synechococcus
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          23
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Synechocystis
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          4
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          43
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Thermoanaerobacter
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          6
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Xanthomonas
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          1
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          6
        </p>
      </td>
    </tr>

    <tr>
      <td valign="bottom" nowrap="nowrap" width="106">
        Xylella
      </td>

      <td valign="bottom" nowrap="nowrap" width="64">
        <p align="right">
          7
        </p>
      </td>

      <td valign="bottom" nowrap="nowrap" width="66">
        <p align="right">
          33
        </p>
      </td>
    </tr>
  </table>
</div>

<h3>
</h3>