dbrnz / anatomy-lookup

Ontology lookup to UBERON and ILX

anatomy-lookup

Ontology lookup to UBERON and ILX

Install

pip install git+https://github.com/napakalas/anatomy-lookup.git

Lookup use

from anatomy_lookup import AnatomyLookup

al = AnatomyLookup()
al.search('nasophayrnx')

results

('http://purl.obolibrary.org/obo/UBERON_0001728',
 'nasopharynx',
 0.8313473463058472)

can use force

al.search('cochlear g.', force=True)

results

('http://purl.obolibrary.org/obo/UBERON_0000395',
 'cochlear ganglion',
 1.0000001192092896)

Update UBERON and ILX terms

al.update_terms()

Lookup with scope

al.search_with_scope('C1', ['Spinal cord'])

results

[('http://purl.obolibrary.org/obo/UBERON_0006469',
  'C1 segment of cervical spinal cord',
  0.758830189704895),
 ('http://purl.obolibrary.org/obo/UBERON_0007266',
  'intervertebral disk of atlas',
  0.7131606340408325),
 ('http://purl.obolibrary.org/obo/UBERON_0002828',
  'ventral cochlear nucleus',
  0.6487032771110535),
 ('http://purl.obolibrary.org/obo/UBERON_0006489',
  'C2 segment of cervical spinal cord',
  0.5675715208053589),
 ('http://purl.obolibrary.org/obo/UBERON_0006478',
  'Brodmann (1909) area 37',
  0.5620466470718384)]

running with force is also available

al.search_with_scope('C1', ['Spinal cord'], force=True)

Close instance to free resource

al.close()

Rebuild term embedding

al.build_indexes()

This will download the latest release of SCKAN from https://github.com/SciCrunch/NIF-Ontology/releases an then build the index

Running annotation

from anatomy_lookup import AnatomyAnnotator
anno = AnatomyAnnotator()
anno.annotate('annotation.json','name', ['systems', 'organ'])

can use force also

anno.annotate('annotation.json','name', ['systems', 'organ'], force=True)

Save to xlsx

anno.save_to_xlsx('annotation_test.xlsx')

Save to json

anno.save_to_json('annotation_test.json')