owlsim-v3
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monarch-initiative
Ontology Based Profile Matching
from discussion with @pnrobinson, this pseudocode gives the basic idea: ``` import org.bla.hpoapi.* ontology hpo = new ontology(bla) annotationset as = new annotationset(hpo,bla); double ic = as.getInformationConent("HP:0001234"); ArrayList as.getGenesAnnotatedTo("Arachnodactly"); ArrayList...
AnalyzePhenotypes (and PhenoGrid) are currently missing a host of possible matches. The OMIA species have been curated, we just need to add them to OwlSim. I'm not sure how involved...
v3 and v2 services layer differ dramatically (v2 was a horrendous quick job put together by me). Client apps like phenogrid assume v2 payloads. Need to either - upgrade all...
Assuming you havn't gone too far down this path, how about using [RoaringBitmaps](https://github.com/RoaringBitmap/RoaringBitmap) for your bitmaps instead of EWAH? Apparently they offer better compression, as well as random access (if...
from the old sim2 codebase, i took a crack at computing a co-annotation matrix using the term frequency-inverse document frequency algorithm (TF-IDF). that code is in these methods: computeTFIDFMatrix getCoannotatedClassesForAttribute...
So, [blue meanie mouse](http://stage.monarchinitiative.org/gene/MGI:5446153) is the top hit for HADZISELIMOVIC syndrome, however [the reciprocal search](http://stage.monarchinitiative.org/gene/MGI:5446153) shows 11 other diseases for which blue meanie is better suited. I'd like to show...
**1. When running phenogrid inside monarch-app**, `phenotype_list.json` provided by monarch-app's disease page is used as the phenogrid data input. For those unmatched (after a simsearch) phenotypes, even though they have...
