phenol

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java.lang.IllegalAccessError - MinimalOntologyLoader

3

I am getting some weird errors from fenominal in an application program: ``` Exception in thread "main" java.lang.NoSuchMethodError: 'java.lang.Iterable org.monarchinitiative.phenol.ontology.data.MinimalOntology.nonObsoleteTermIds()' at [email protected]/org.monarchinitiative.fenominal.core.impl.hpo.HpoLoader.loadSimpleHpoTerms(HpoLoader.java:65) (...) ``` However, it appears that this method...

pnrobinson

JGraphT

8

phenol is at version 1.2.0. There are API changes for version 1.5.0 (the current one). Investigate how to update.

pnrobinson

From @pnrobinson on email In the Exomiser, HPO website, Monarch Web app, we find the same medical error. Orphanet associated some diseases with tons of genes [ORPHA:91387](https://hpo.jax.org/app/browse/disease/ORPHA:91387)Familial thoracic aortic aneurysm...

cmungall

Implement a function for calculating probability: ```java public interface HpoDiseaseAnnotation { double observationProbability(TemporalInterval interval) { // TODO - implement return 0; } } ```

ielis

http://www.orphadata.org/cgi-bin/epidemio.html

pnrobinson

Remove the APIs marked for deprecation in `v3.0.0`.

ielis

Modernize ontologizer code

2

Review the Ontologizer code and put it into separate phenol module.

ielis

pnrobinson

org.monarchinitiative.phenol.annotations.formats.hpo

1

move the package `org.monarchinitiative.phenol.annotations.formats.hpo` from phenol-annotations to phenol-core. I think that definitions of model objects, such as HpoAnnotation should live either in phenol-core or in some other module, which does...

pnrobinson

Add exact matches to Term data model and parsers

1

@julesjacobsen this is the completely flying blind untested code (24 min work). Can you see if you bring this to conclusion with the appropriate code quality styles etc? cc @cthoyt...

matentzn