Changelogs » Ontoma

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- Bug fixes in the Zooma API querying module: Removed HP as a ontology to search; and correction of a typo from "filters" to "filter"
  - New test: test_find_term_alzheimer()


- New functions get_mondo_label() and get_hp_label() to retrieve MONDO and HP disease labels using the disease id
  - When the match is found in the HP OBO file the function _find_term_from_string() now returns the actual disease label instead of the one that was queried


- New function get_efo_from_xref() to map disease ids from other ontologies to EFO using xrefs


- Query strings are searched as they are, splitting at commas and semicolons and using the largest substring has been removed.
  - Use latest EFO OBO file instead of hard-coded v2018-01-15
  - Updated OT top nodes with current therapeutic areas for checking if mapped term is in OT


- even more weird and wonderful packaging problems


- fix version deploy


- Version bump to 0.0.10
  - restore cache




- pipenv lock to try fixing pypi deploy issues


- add doctest for mondo
  - implement MONDO lookups
  - move fieldnames to constants
  - change messaging and only use longest fragment if long query
  - adding lru cache, though our calls are rarely repeated :(
  - use sessions to take advantage of any connection pooling we can get
  - nicely aligned logging
  - add ability to exclude some API calls


- add details on verbose to readme
  - added a verbose output to find_term
  - ols doctest more robust to changes in underlying ontology
  - document suggest
  - add a suggest mode to find_term
  - add ORDO exact lookup
  - get_ancestors raises a keyerror for an empty response
  - phewascat tests were not being picked up
  - _is_included guesses ontology when not directly specified
  - get_ancestors handles empty responses
  - clean whitespace in mappings file
  - restrict to efo and hp in zooma
  - logging name_to_node parsing
  - improve find_term docs


- output label of match when used in batch mode
  - handle iri to label lookups
  - use dict to return quality, source, action
  - works
  - markdown readme


- fix pylint


- updated docs
  - polishing CLI
  - batch command line interface
  - fix tests
  - save pylint artifact (big otherwise)
  - checking whether node is in the included branch of efo (and LOTS of linting)
  - get ancestors
  - find_efo becomes find_term given that we don't use efo alone
  - return quality in the tuple
  - explain the ot ontology difference
  - exact match logic
  - fix bumpv error msg