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  1. NIF
  2. NIF-11683

DISCO: import mouse enhancer expression data

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    • New Feature Request
    • Resolution: Fixed
    • Major
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    • NIF

    Description

      Original request via email from Suzi:
      Would you please ingest these data: http://enhancer.lbl.gov/
      I need the images, anatomical terms associated with those, enhancer IDs, and chromosomal locations of the enhancers.
      Ultimately a GFF3 file would be ideal with the image URLs and anatomical terms wedged in some way.

      Followup from Nicole:
      We'd want the data to be something like:

      element | chr | start | stop | build | expressed_in | expressivity | images

      so, for this specific example:
      http://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&experiment_id=705&organism_id=1

      it would give you ideally:

      hs705 | chr1 | 3,190,581 | 3,191,428 | UCSC hg19 | hindbrain (rhombencephalon) | 5 / 6 | embryo 1: http://enhancer.lbl.gov/pics//p6781.jpg, http://enhancer.lbl.gov/pics//p6782.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6783.jpg, http://enhancer.lbl.gov/pics//p6784.jpg; embryo3: http://enhancer.lbl.gov/pics//p6785.jpg, http://enhancer.lbl.gov/pics//p6786.jpg

      or for

      http://enhancer.lbl.gov/cgi-bin/imagedb3.pl?form=presentation&show=1&experiment_id=698&organism_id=1

      hs698 | chr8 | 53,166,730 | 53,167,836 | UCSC hg19 | dorsal root ganglion | 7 / 9 | embryo1: http://enhancer.lbl.gov/pics//p6723.jpg, http://enhancer.lbl.gov/pics//p6724.jpg, http://enhancer.lbl.gov/pics//p6725.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6726.jpg, http://enhancer.lbl.gov/pics//p6727.jpg, http://enhancer.lbl.gov/pics//p6728.jpg; embryo 3: http://enhancer.lbl.gov/pics//p6729.jpg, http://enhancer.lbl.gov/pics//p6730.jpg, http://enhancer.lbl.gov/pics//p6731.jpg
      hs698 | chr8 | 53,166,730 | 53,167,836 | UCSC hg19 | forebrain | 7 / 9 | embryo1: http://enhancer.lbl.gov/pics//p6723.jpg, http://enhancer.lbl.gov/pics//p6724.jpg, http://enhancer.lbl.gov/pics//p6725.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6726.jpg, http://enhancer.lbl.gov/pics//p6727.jpg, http://enhancer.lbl.gov/pics//p6728.jpg; embryo 3: http://enhancer.lbl.gov/pics//p6729.jpg, http://enhancer.lbl.gov/pics//p6730.jpg, http://enhancer.lbl.gov/pics//p6731.jpg
      hs698 | chr8 | 53,166,730 | 53,167,836 | UCSC hg19 | hindbrain (rhombencephalon) | 7 / 9 | embryo1: http://enhancer.lbl.gov/pics//p6723.jpg, http://enhancer.lbl.gov/pics//p6724.jpg, http://enhancer.lbl.gov/pics//p6725.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6726.jpg, http://enhancer.lbl.gov/pics//p6727.jpg, http://enhancer.lbl.gov/pics//p6728.jpg; embryo 3: http://enhancer.lbl.gov/pics//p6729.jpg, http://enhancer.lbl.gov/pics//p6730.jpg, http://enhancer.lbl.gov/pics//p6731.jpg
      hs698 | chr8 | 53,166,730 | 53,167,836 | UCSC hg19 | midbrain (mesencephalon) | 7 / 9 | embryo1: http://enhancer.lbl.gov/pics//p6723.jpg, http://enhancer.lbl.gov/pics//p6724.jpg, http://enhancer.lbl.gov/pics//p6725.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6726.jpg, http://enhancer.lbl.gov/pics//p6727.jpg, http://enhancer.lbl.gov/pics//p6728.jpg; embryo 3: http://enhancer.lbl.gov/pics//p6729.jpg, http://enhancer.lbl.gov/pics//p6730.jpg, http://enhancer.lbl.gov/pics//p6731.jpg
      hs698 | chr8 | 53,166,730 | 53,167,836 | UCSC hg19 | neural tube | 7 / 9 | embryo1: http://enhancer.lbl.gov/pics//p6723.jpg, http://enhancer.lbl.gov/pics//p6724.jpg, http://enhancer.lbl.gov/pics//p6725.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6726.jpg, http://enhancer.lbl.gov/pics//p6727.jpg, http://enhancer.lbl.gov/pics//p6728.jpg; embryo 3: http://enhancer.lbl.gov/pics//p6729.jpg, http://enhancer.lbl.gov/pics//p6730.jpg, http://enhancer.lbl.gov/pics//p6731.jpg
      hs698 | chr8 | 53,166,730 | 53,167,836 | UCSC hg19 | trigeminal V (ganglion, cranial) | 6 / 9 | embryo1: http://enhancer.lbl.gov/pics//p6723.jpg, http://enhancer.lbl.gov/pics//p6724.jpg, http://enhancer.lbl.gov/pics//p6725.jpg; embryo 2: http://enhancer.lbl.gov/pics//p6726.jpg, http://enhancer.lbl.gov/pics//p6727.jpg, http://enhancer.lbl.gov/pics//p6728.jpg; embryo 3: http://enhancer.lbl.gov/pics//p6729.jpg, http://enhancer.lbl.gov/pics//p6730.jpg, http://enhancer.lbl.gov/pics//p6731.jpg

      or, it could be normalized like:

      element | chr | start | stop | build | fasta

      element | expressed_in | expressed_ratio

      element | embryo | images

      In my real ideal scenario, we'd actually get the expression annotations per individual, but it doesn't appear that they put those up. So we must capture the summary.

      Eventually, we'll be able to get this kind of data from the ENCODE folks (since it's going to be slurped into their project), where they'll do the proper mapping to Uberon.

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              bandrow Anita Bandrowski (use this one!)
              nlw Nicole Washington
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