dipper
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monarch-initiative
Data Ingestion Pipeline for Monarch
we currently only import the "abnormal" phenotypes, but we also need to bring in the "normal" ones. we also need to set up a general model for these kinds of...
IMPC has paths to images for given genotype+phenotype associations. it would be very cool to display this data. it's available in a rest call like: http://www.ebi.ac.uk/mi/impc/solr/images/select?q=*:*&rows=10&wt=json from this, i think...
we need to add gene fusion modeling to the Genotype and/or Genomic Feature. Use this ticket for discussion. @kshefchek can you post an example of a gene fusion that's in...
there currently aren't real evidence codes for the ICE and PCS 3-letter codes used in the HPO data. these have been requested in a ticket here: https://code.google.com/p/evidenceontology/issues/detail?id=32 they are currently...
there doesn't appear to be bands (only chrs) in the rat ideogram file from ucsc: http://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/cytoBandIdeo.txt.gz i have found a paper that describes some high resolution mapping with FISH. maybe...
current implementation skips the remarkably normal (not abnormal) phenotype associations from zfin. we need to add these as proper associations.
there is coordinate info for various zfin items here: transgenics: http://zfin.org/downloads/zfin_tginsertion.gff3 knockdown reagents: http://zfin.org/downloads/E_zfin_knockdown_reagents.gff3 when they become available, add in the sequence alterations. (it appears there is location info for...
we need to add both the negative phenotype and "not model of" genotype-annotations for MGI data. there are call-outs for this in the code.
There's a nice RNAi resource for human (and drosophila). They curate "phenotypes" to their own internal vocabulary...we should see if we can get mappings... (I have enquired to see i...
here's the list of strains: http://www.cbs.umn.edu/sites/default/files/public/files/celelist2.txt there's the elementary pulling in the strains. but we'll want to also parse them into their constituent parts. we've taken a stab at a...