owlsim-v3
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monarch-initiative
Ontology Based Profile Matching
e.g. http://owlsim3.monarchinitiative.org/api/match/phenodigm id=OMIM:612900 returns everything at rank 1. Either 1. the match route should auto-expand an individual ID to its annotated class IDs 2. there should be a separate route...
http://localhost:8080/api/match/jaccard?id=HP:0007280 ``` ontologyUris: - http://purl.obolibrary.org/obo/hp.owl ontologyDataUris: [] dataTsvs: - ./Hs_disease_phenotype.txt curies: # Skolemize Blank Nodes # overwrite iri fragment with '' for unresovable bnodes '_': 'https://monarchinitiative.org/.well-known/genid/' # Monarch-specific '': 'https://monarchinitiative.org/'...
The set `nodesQfPu` is initialized, but it seems that nothing get added to this set. It is later transformed to the Bitmap `nodesQfPuBM` which is used to determine some `andCardinality`...
If `prWeakTrueMiss` is too small (right now it is 0.85), we are introducing `-Inf` in lines 335/336/338 ``` int nQuHuPt = nodesQuPtBM.andNot(nodesHtBM).andNotCardinality(nodesHfBM); double cprQuHuPt = Math.pow(prWeakTrueMiss, nQuHuPt); ``` In my...
``` wget http://purl.obolibrary.org/obo/upheno/data/omim-disease-phenotype.owl -O src/test/resources/data/omim-disease-phenotype.owl --2016-05-16 13:57:07-- http://purl.obolibrary.org/obo/upheno/data/omim-disease-phenotype.owl Resolving purl.obolibrary.org... 52.3.123.63 Connecting to purl.obolibrary.org|52.3.123.63|:80... connected. HTTP request sent, awaiting response... 302 Moved Temporarily Location: http://build.berkeleybop.org/view/Monarch/job/generate-triples-from-nif/lastSuccessfulBuild/artifact/target/omim-disease-phenotype.owl [following] --2016-05-16 13:57:08-- http://build.berkeleybop.org/view/Monarch/job/generate-triples-from-nif/lastSuccessfulBuild/artifact/target/omim-disease-phenotype.owl Resolving...
This returns a list of matchers: http://localhost:8080/api/match/matchers Either change or add a new route to return a list of objects - name - capabilities (e.g. negationAware) - text description All...
E.g on http://owlsim3.monarchinitiative.org/api/match/phenodigm?id=HP%3A0000465 ``` { "message": "There was an error processing your request. It has been logged (ID 9b48bd522075bf1c)." } ```
travis appears to be failing, ca't debug as too much log.info Some may be coming from upstream libs? Can we silence some libs that pollute the info stream with too...
Currently `id` is used for class and `negatedId` for negated class this is potentially confusing as id can also be used for individuals. Consider changing