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CHANGELOG.rst

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Changelog

2.7

  • 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

2.6

  • Refactored Gene and Disease annotations
  • Added proper hashing methods to HPOTerm, Disease and Gene
  • 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

2.5

  • 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

2.4

  • 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

2.3

  • Added GraphIC similarity measure

2.2

  • Added Orphanet diseases to Annotation
  • Added Decipher diseases to Annotation

2.1

  • Reworked BasicHPOSet
  • Added omim_diseases to HPOSet
  • Added distance method to similarity measurement
  • Added equal measurement to HPOSet similarity

2.0

  • 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

1.4

  • Added serialization to HPO Term and HPO Set
  • Option to remove modifier from HPO Set
  • Changed Omim and Gene to be Singletons

1.3

  • Data update
    • HPO: 14961 ==> 15332
    • Genes: 4312 ==> 4317
    • OMIM: 7623 ==> 7675
    • Negative OMIM: 634 ==> 638

1.2

  • 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)

1.1.2

  • Only data update

1.1.1

  • 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

1.1

  • 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

1.0.1

  • 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

1.0

  • First stable release