Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / 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