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Download Data

Here you may download the complete dataset contained in the YRC Public Image Repository.

Image Repository Data

strain_genotypes.xml
This xml file contains a mapping of strain names to genotypes. It contains the following structure:
  • <strainData>
    • <strainList>
      • <strain name="" id="" speciesID="" genotype="">
        • <plasmidList>
          • <plasmid markers="">
The explanation for each label as follows:
  • strain id - unique numerical identifier for a particular strain
  • strain name - unique string identifier for a particular strain (used in YRC PIR web site)
  • species id - NCBI taxonomy ID for a particular strain
  • genotype - the genotype for a particular strain
proteins.fasta
A FASTA-formatted file containing protein names (used in YRC PIR), NCBI taxonomy IDs, descriptions and sequences.
Complete Data Download:
The entire YRC PIR has been archived into ten tarred and gzipped files for download. Each .tgz file may be uncompressed on Windows using WinZip, Apple OS X using Stuffit Expander and on Linux using the command line syntax "tar -xzf full_download_0.tgz".

The files will uncompress in the following format (this example assumes an experiment ID that ends in "123" and an experiment that includes 3 channels and 3 z-sections):

experiments/1/2/3/YRCPIR_ex123/
metadata.txt
images/
YRCPIR_123_p0_z0_c0_t0.ome.tiff
YRCPIR_123_p0_z0_c0_t0.txt
YRCPIR_123_p0_z0_c1_t0.ome.tiff
YRCPIR_123_p0_z0_c1_t0.txt
YRCPIR_123_p0_z0_c2_t0.ome.tiff
YRCPIR_123_p0_z0_c2_t0.txt
YRCPIR_123_p0_z1_c0_t0.ome.tiff
YRCPIR_123_p0_z1_c0_t0.txt
YRCPIR_123_p0_z1_c1_t0.ome.tiff
YRCPIR_123_p0_z1_c1_t0.txt
YRCPIR_123_p0_z1_c2_t0.ome.tiff
YRCPIR_123_p0_z1_c2_t0.txt
YRCPIR_123_p0_z2_c0_t0.ome.tiff
YRCPIR_123_p0_z2_c0_t0.txt
YRCPIR_123_p0_z2_c1_t0.ome.tiff
YRCPIR_123_p0_z2_c1_t0.txt
YRCPIR_123_p0_z2_c2_t0.ome.tiff
YRCPIR_123_p0_z2_c2_t0.txt

File definitions:
  • metadata.txt - contains metadata for the experiment. The data are clearly labeled in the text file.
  • images/YRCPIR_1_p0_z0_c0_t0.ome.tiff - an OME TIFF containing the image data. The OME-XML contained in the TIFF header contains image metadata. The filename is formatted to as: YRCPIR_EXPERIMENT ID_pPANEL INDEX_zZ-SECTION INDEX_cCHANNEL INDEX_tTIME INDEX.ome.tiff.
  • images/YRCPIR_1_p0_z0_c0_t0.txt - contains metadata for the given image. The data are clearly labeled in the text file.
Files:

UW
The YRC Public Image Repository is supported by grants P41GM103533 and GM40506 from National Institute of General Medical Sciences at the US National Institutes of Health.