monarch-initiative/phenol issues and pull requests

#431 - AnnotationFrequency

Issue - State: open - Opened by pnrobinson over 1 year ago - 1 comment

#430 - ontology version

Issue - State: open - Opened by pnrobinson over 1 year ago
Labels: enhancement

#429 - prototype CSR class

Pull Request - State: open - Opened by pnrobinson over 1 year ago - 4 comments

#428 - Let's remove guava from phenol

Issue - State: open - Opened by pnrobinson over 1 year ago - 1 comment
Labels: bug

#427 - Release v2.0.0

Pull Request - State: closed - Opened by ielis over 1 year ago

#426 - deprecating phenotype writer, changing hpoa disease loader to handle …

Pull Request - State: closed - Opened by iimpulse over 1 year ago

#425 - Enhancement/hpoa format

Pull Request - State: closed - Opened by iimpulse over 1 year ago

#424 - obsoleting classes used for the small files and not needed for phenol…

Pull Request - State: closed - Opened by pnrobinson almost 2 years ago - 3 comments

#423 - Obsolete Terms

Issue - State: open - Opened by iimpulse almost 2 years ago

#422 - Allow dropping non-propagating relationships during ontology loading

Pull Request - State: closed - Opened by ielis almost 2 years ago

#421 - Add `precompute-resnik` command

Pull Request - State: closed - Opened by ielis almost 2 years ago

#420 - Release `v2.0.0-RC5`

Pull Request - State: closed - Opened by ielis about 2 years ago

#419 - making qc better, adding tests

Pull Request - State: closed - Opened by iimpulse about 2 years ago

#418 - Offer versions in data containers/resource objects

Pull Request - State: closed - Opened by ielis about 2 years ago

#417 - Use clinical course to determine global onset of a disease.

Pull Request - State: closed - Opened by ielis about 2 years ago

#416 - Clarify alt ID meaning

Pull Request - State: closed - Opened by ielis about 2 years ago - 1 comment

#415 - Split `HpoDisease` loading

Pull Request - State: closed - Opened by ielis about 2 years ago

#414 - Add default `HpoDiseaseAnnotation` implementation with logic for querying number of patients presenting with the feature at a given time.

Pull Request - State: closed - Opened by ielis about 2 years ago

#413 - extended interface of AssociationContainer by new method

Pull Request - State: closed - Opened by pnrobinson about 2 years ago

#412 - Update deployment info

Pull Request - State: closed - Opened by ielis about 2 years ago

#411 - Improve comparison and overlap of the temporal API

Pull Request - State: closed - Opened by ielis about 2 years ago

#410 - Precalculate disease onset interval.

Pull Request - State: closed - Opened by ielis about 2 years ago

#409 - subontology

Issue - State: open - Opened by pnrobinson about 2 years ago
Labels: bug

#408 - Bump h2 from 1.4.200 to 2.1.210

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#407 - Release 2.0.0-RC4

Pull Request - State: closed - Opened by ielis about 2 years ago

#406 - Improve HPOA loading

Pull Request - State: closed - Opened by ielis about 2 years ago

#405 - Move HPO constants to annotations module.

Pull Request - State: closed - Opened by ielis about 2 years ago

#404 - Polish `HpoDiseaseLoaderV2` and `HpoDiseaseAnnotationFactory`.

Pull Request - State: closed - Opened by ielis about 2 years ago

#403 - DEFAULT_COHORT_SIZE = 5;

Issue - State: closed - Opened by pnrobinson over 2 years ago - 2 comments

#402 - HpoDiseaseLoaderOptions

Issue - State: closed - Opened by pnrobinson over 2 years ago - 1 comment

#401 - Move HPO constants from `phenol-core` to `phenol-annotations`

Issue - State: closed - Opened by ielis over 2 years ago - 1 comment

#400 - Imprecise age

Pull Request - State: closed - Opened by ielis over 2 years ago - 6 comments

#399 - Add Puerpural onset, reorder `HpoOnsetTermIds` constants.

Pull Request - State: closed - Opened by ielis over 2 years ago

#398 - Add `HGNC` prefix and corresponding IRI into `curie_map.yml`

Issue - State: closed - Opened by ielis over 2 years ago - 1 comment

#397 - Documentationv2

Pull Request - State: open - Opened by pnrobinson over 2 years ago

#396 - Implement `equals` and `hashCode` on XRefs

Pull Request - State: closed - Opened by ielis over 2 years ago

#395 - Manage dependency versions in the `dependencyManagement` section of the parent POM

Pull Request - State: closed - Opened by ielis over 2 years ago

#394 - Remove non-modular `curie-util` dependency.

Pull Request - State: closed - Opened by ielis over 2 years ago

#393 - Fix bounds of the fetal and embryonal periods.

Pull Request - State: closed - Opened by ielis over 2 years ago
Labels: bug

#392 - Functionality for age to hpo onset

Pull Request - State: closed - Opened by iimpulse over 2 years ago

#391 - Add iterables with present and absent disease annotations to `HpoDisease`.

Pull Request - State: closed - Opened by ielis over 2 years ago

#390 - Release `v2.0.0-RC3`

Pull Request - State: closed - Opened by ielis over 2 years ago

#389 - Ratio and frequency are non-null in `HpoDiseaseAnnotation`.

Pull Request - State: closed - Opened by ielis over 2 years ago

#388 - Make `ratio` and `frequency` to non-null attributes of `HpoDiseaseAnnotation`

Issue - State: closed - Opened by ielis over 2 years ago

#387 - Provide `Iterable` over `HpoDiseaseAnnotation`s instead of an `Iterator`.

Pull Request - State: closed - Opened by ielis over 2 years ago

#386 - Speed up the build.

Pull Request - State: closed - Opened by ielis over 2 years ago

#385 - Implement `isAnnotatedTo` on `HpoDisease`.

Pull Request - State: closed - Opened by ielis over 2 years ago

#384 - Rename `globalOnset()` to `diseaseOnset()` in `HpoDisease`.

Pull Request - State: closed - Opened by ielis over 2 years ago

#383 - Add new onset terms.

Pull Request - State: closed - Opened by ielis over 2 years ago - 2 comments

#382 - Implement `HpoDiseaseAnnotation.isAbsent()`.

Pull Request - State: closed - Opened by ielis over 2 years ago - 2 comments

#381 - Update HPO disease, add annotation sources, implement aggregated disease loader.

Pull Request - State: closed - Opened by ielis over 2 years ago - 2 comments

#380 - Fix gene info loading

Pull Request - State: closed - Opened by ielis over 2 years ago - 4 comments

#379 - "negative terms"

Issue - State: closed - Opened by pnrobinson over 2 years ago - 4 comments

#378 - isAnnotatedTo

Issue - State: closed - Opened by pnrobinson over 2 years ago

#377 - globalOnset

Issue - State: closed - Opened by pnrobinson over 2 years ago

#376 - public Iterator<HpoDiseaseAnnotation> phenotypicAbnormalities() { return phenotypicAbnormalities.iterator(); }

Issue - State: closed - Opened by pnrobinson over 2 years ago

#375 - this.modesOfInheritance = Objects.requireNonNull(modesOfInheritance, "Modes of inheritance must not be null");

Issue - State: closed - Opened by pnrobinson over 2 years ago - 5 comments

#374 - HpoDiseaseAnnotationMetadata should contain source

Issue - State: closed - Opened by pnrobinson over 2 years ago - 4 comments

#373 - Add new onset terms

Issue - State: closed - Opened by pnrobinson over 2 years ago - 3 comments

#372 - Cannot load Mondo file

Issue - State: closed - Opened by mabeckwith over 2 years ago - 24 comments

#371 - Salvage v1 API

Pull Request - State: closed - Opened by ielis over 2 years ago - 2 comments

#370 - Constants in Phenol

Pull Request - State: closed - Opened by ielis over 2 years ago

#369 - Clean up annotation IO

Pull Request - State: closed - Opened by ielis over 2 years ago

#368 - Add `release` metadatum entry.

Pull Request - State: closed - Opened by ielis over 2 years ago - 1 comment

#367 - Calculate probability of observing a phenotype feature in an `HpoDiseaseAnnotation` in a temporal interval

Issue - State: open - Opened by ielis over 2 years ago

#366 - Improve `HpoDisease` model

Pull Request - State: closed - Opened by ielis over 2 years ago - 10 comments
Labels: enhancement

#365 - Indicate deprecation for `getId()` in `Identified` implementors

Pull Request - State: closed - Opened by ielis over 2 years ago

#364 - Release 2.0.0 RC1

Pull Request - State: closed - Opened by ielis over 2 years ago

#363 - Bump h2 from 1.4.199 to 2.1.210 in /phenol-io

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#362 - java.lang.NoClassDefFoundError: org/apache/commons/io/input/BOMInputStream

Issue - State: closed - Opened by pnrobinson over 2 years ago - 3 comments

#361 - adding method to get total raw annotations

Pull Request - State: closed - Opened by pnrobinson over 2 years ago

#360 - Bump h2 from 1.4.199 to 2.0.206 in /phenol-io

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#359 - correcting container error

Pull Request - State: closed - Opened by pnrobinson almost 3 years ago

#358 - org/yaml/snakeyaml/Yaml not found

Issue - State: closed - Opened by pnrobinson almost 3 years ago - 2 comments

#357 - Go gaf22

Pull Request - State: closed - Opened by pnrobinson almost 3 years ago - 1 comment

#356 - TermAnnotation interface

Issue - State: open - Opened by pnrobinson almost 3 years ago - 1 comment

#355 - Support for GO GAF format 2.2

Issue - State: closed - Opened by pnrobinson almost 3 years ago

#354 - fix of picocli error

Pull Request - State: closed - Opened by pnrobinson almost 3 years ago

#353 - Setup CI

Pull Request - State: closed - Opened by ielis almost 3 years ago

#352 - Upgrade to Java 11

Pull Request - State: closed - Opened by ielis almost 3 years ago - 7 comments

#351 - Refactor `HpoDiseaseAnnotationParser`

Issue - State: closed - Opened by ielis almost 3 years ago - 1 comment

#350 - adding getter to MpGeneModel

Pull Request - State: closed - Opened by pnrobinson almost 3 years ago

#349 - Cleanup analysis

Pull Request - State: closed - Opened by pnrobinson almost 3 years ago

#348 - Remove the "#" from the header line of Phenol

Issue - State: open - Opened by pnrobinson almost 3 years ago

#347 - Use enum for disease database

Issue - State: closed - Opened by pnrobinson almost 3 years ago - 1 comment

#346 - next release

Issue - State: closed - Opened by pnrobinson almost 3 years ago - 1 comment

#345 - TermAnnotation

Issue - State: open - Opened by pnrobinson almost 3 years ago

#344 - GoAssociationContainer

Issue - State: closed - Opened by pnrobinson almost 3 years ago - 1 comment
Labels: bug

#343 - Drop OWL/OBO support from `phenol-io` in favor of JSON format

Pull Request - State: closed - Opened by ielis almost 3 years ago - 11 comments

#342 - Remove OWL/OBO support from `phenol-io`

Issue - State: closed - Opened by ielis almost 3 years ago - 1 comment
Labels: enhancement

#341 - Modularize the codebase

Issue - State: closed - Opened by ielis almost 3 years ago

#340 - Modernize ontologizer code

Issue - State: open - Opened by ielis almost 3 years ago - 2 comments

#339 - Upgrade the disease model to include temporal elements

Issue - State: closed - Opened by ielis almost 3 years ago - 6 comments

#338 - Work on `phenol-annotations`

Pull Request - State: closed - Opened by ielis about 3 years ago - 2 comments

#336 - Mycurieutil

Pull Request - State: closed - Opened by pnrobinson over 3 years ago - 2 comments

#335 - Set min version to Java 9/11

Issue - State: closed - Opened by pnrobinson over 3 years ago

#334 - CurieUtil

Issue - State: closed - Opened by pnrobinson over 3 years ago - 1 comment

#333 - snakeyaml

Issue - State: closed - Opened by pnrobinson over 3 years ago - 3 comments

#317 - Java 14

Issue - State: closed - Opened by pnrobinson almost 4 years ago - 1 comment
Labels: bug

#315 - Support GAF 2.2 format

Issue - State: closed - Opened by pnrobinson almost 4 years ago - 1 comment
Labels: future release

GitHub / monarch-initiative/phenol issues and pull requests