monarch-initiative
add impc images
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 want to include depiction relationships attached to the genotype+phenotype associations. we'll have to build up the genotype again from the image query using the same methods that we used in the other IMPC data (colony_id, phenotyping_center, zygosity, sex). each animal (animal id) having the phenotype:
<animal_id> has_genotype <genotype_id> <animal_id> ??? Literal(image url) <assoc_id> faldo:depiction Literal(image url)
we want to link the image to both the animal and the phenotype. also, we might want to add a caption to the image that includes the genotype and/or a description of the assay that gave rise to the image.
Are you yet ingesting the mouse enhancer expression data from Axel? When it comes time, it would be nice to include those images as well.
On Mon, Feb 23, 2015 at 4:44 PM, Nicole Washington <[email protected]
wrote:
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 want to include depiction relationships attached to the genotype+phenotype associations. we'll have to build up the genotype again from the image query using the same methods that we used in the other IMPC data (colony_id, phenotyping_center, zygosity, sex). each animal (animal id) having the phenotype:
has_genotype ??? Literal(image url) faldo:depiction Literal(image url)
we want to link the image to both the animal and the phenotype. also, we might want to add a caption to the image that includes the genotype and/or a description of the assay that gave rise to the image.
— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/dipper/issues/64.
not as part of IMPC. please add a ticket for Axel's enhancer data, together with the image request.
Are you yet ingesting the mouse enhancer expression data from Axel? When it comes time, it would be nice to include those images as well. => I think it would be great to have this data! -peter
On Mon, Feb 23, 2015 at 4:44 PM, Nicole Washington <[email protected]
wrote:
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 want to include depiction relationships attached to the genotype+phenotype associations. we'll have to build up the genotype again from the image query using the same methods that we used in the other IMPC data (colony_id, phenotyping_center, zygosity, sex). each animal (animal id) having the phenotype:
has_genotype ??? Literal(image url) faldo:depiction Literal(image url)
we want to link the image to both the animal and the phenotype. also, we might want to add a caption to the image that includes the genotype and/or a description of the assay that gave rise to the image.
� Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/dipper/issues/64.
� Reply to this email directly or view it on GitHubhttps://github.com/monarch-initiative/dipper/issues/64#issuecomment-75677275.
Done, issue added.
On Mon, Feb 23, 2015 at 5:00 PM, Nicole Washington <[email protected]
wrote:
not as part of IMPC. please add a ticket for Axel's enhancer data, together with the image request.
— Reply to this email directly or view it on GitHub https://github.com/monarch-initiative/dipper/issues/64#issuecomment-75678308 .
so i've found discrepancies in the data as dumped in the csv, and that which is available through the image server.
for example, I did this query: http://www.ebi.ac.uk/mi/impc/solr/images/select?q=allele_accession:MGI:4129255%20AND%20gender:Male%20AND%20genotype:HET&wt=json&rows=10 (which is for this mouse gene: https://www.mousephenotype.org/data/genes/MGI:1891295)
and i find it has an annotation to this mp id: MP:0010254 (hard cataracts)
but i queried for that MP id in the raw data, and it isn’t there:
grep “MP:0010254" ALL_genotype_phenotype3.csv | wc -l
should these be made into new genotype-phenotype associations, rather than decorating ones that already exist? or am i missing something?
Hi, terry here. Some of our images are directly annotated with a phenotype term yet our overall statistical analysis failed to associate the knockout mouse strain with the phenotype and thus does not show up on the csv report.
