Details
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New Feature Request
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Resolution: Fixed
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Major
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None
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None
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None
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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.
Attachments
Issue Links
- is related to
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NIF-11762 Create view for VISTA Mouse Enhancer Expression
- Closed