Nicole Washington
Nicole Washington
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...
There's a new set of data out for PPI. We should fetch these, which are for human interactions. http://wren.hms.harvard.edu/bioplex/downloadInteractions.php
Right now, we have a testing dataset that is produced any time the tests are run. This set automatically materializes all anonymous nodes (using the nobnodes flag). However, this is...
We need to make sure that OMIM is the authoritative source of ID mappings for omim genes. I think this will help to fix the issues where external sites will...