- Added type annotation to all methods
Ontology.get_hpo_object
now behaves as documented and raises an error if the term is not found instead of silently returning None
- Refactored Gene and Disease annotations
- Added proper hashing methods to
HPOTerm
,Disease
andGene
- Bugfix for similarity score when one set does not contain any HPOTerm
- 2.6.1: Re-add (Gene/Omim).get method for single gene/disease fetching. Needed in pyhpoapi
- Added combination methods for HPOset similarities
- Added Matrix module for row/column based operations
- Data update to
hp/releases/2020-10-12
- HPO: 15530 ==> 15656
- Genes: 4366 ==> 4484
- OMIM: 7801 ==> 7860
- Negative OMIM: 652 ==> 660
- ORPHANET: 3956 ==> 3989
- Negative ORPHANET: 255 ==> 259
- DECIPHER: 47 ==> 47
- Negative DECIPHER: 0 ==> 0
- Data update to
- Data update to
hp/releases/2020-08-11
- HPO: 15332 ==> 15530
- Genes: 4317 ==> 4366
- OMIM: 7675 ==> 7801
- Negative OMIM: 638 ==> 652
- ORPHANET: 3889 ==> 3956
- Negative ORPHANET: 240 ==> 255
- DECIPHER: 47 ==> 47
- Negative DECIPHER: 0 ==> 0
- Data update to
- Added GraphIC similarity measure
- Added Orphanet diseases to Annotation
- Added Decipher diseases to Annotation
- Reworked BasicHPOSet
- Added omim_diseases to HPOSet
- Added distance method to similarity measurement
- Added equal measurement to HPOSet similarity
- Refactored Ontology to act as a singleton - Able to remove some weird dependencies when creating HPOSets - Refactored some unit tests to only temporarily mock methods
- Performance improvements through using more cached objects
- Making HPOSet an actual set
- Adding BasicHPOSet
- Handling obsolete terms
- Added serialization to HPO Term and HPO Set
- Option to remove modifier from HPO Set
- Changed Omim and Gene to be Singletons
- Data update
- HPO: 14961 ==> 15332
- Genes: 4312 ==> 4317
- OMIM: 7623 ==> 7675
- Negative OMIM: 634 ==> 638
- Data update
- HPO: 14832 ==> 14961
- Genes: 4293 ==> 4312
- OMIM: 7758 ==> 7623
- Negative OMIM: 631 ==> 634
- Switched to new annotation files from HPO Team (
phenotype.hpoa
)
- Only data update
- No code changes
- Removed daemon and client scripts since they are not yet part of the package and aren't working.
- Restructured some metadata for packaging and documentation
- Adding annotation automatically to the Ontology by default.
- This should not break backwards compatibility, since all annotation data is stored in the repo itself and thus always present
- Include data (HPO-Ontology and Annotation) directly in the repo
- Data updates:
- HPO: hp/releases/2019-09-06
- Added HPO terms: 14647 ==> 14831
- Genes: Added genes 4073 ==> 4231
- OMIM: Added diseases 7665 ==> 7677
- OMIM excluded: Added excluded diseases 614 ==> 623
- First stable release