Utilities

Checkup

The checkup.py script loads the OBO version of the ontology, detects missing is_a parents, definitions, and start/end stages, and flags any inconsistencies in the stage ranges of related terms. Open a terminal, navigate to the root xao directory and run:

$ ./utilities/checkup.py

Dictionary

The 'parseont' module constructs a Python dictionary of all anatomy and stage terms in the ontology OBO file. You can load it via the command line after navigating to the utilities directory, starting Python, and running:

> import parseont
> ont = parseont.dict()

Access term data by specifying its ID:

> print(ont["XAO:0002000"])
{'namespace': 'xenopus_anatomy', 'subset': ['frequent_anatomy_items'], 'synonym': ['head kidney', 'pronephros', 'vorniere'], 'name': 'pronephric kidney', 'def': 'Transient embryonic organ that serves as a kidney, providing osmoregulation during early developmental stages, and then degenerates during metamorphosis (starting at NF stage 53) as the mesonephric kidney develops and becomes functional.', 'xref': 'UBERON:0002120', 'is_a': 'XAO:0005243', 'develops_from': ['XAO:0000264'], 'end_stage': 'XAO:1000076', 'part_of': ['XAO:0004521'], 'start_stage': 'XAO:1000044'}

To find the most recently used anatomy ID, run:

> ont = parseont.dict(rm_obsoletes=False)
> ids = [k for k in ont.keys() if ont[k]["namespace"] != "xenopus_developmental_stage"]
> max(ids)