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biolink
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ontobio
python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
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adding github action to run tests
#492
dougli1sqrd
closed
3 years ago
0
setting networkx version back to 2.2
#491
dougli1sqrd
closed
3 years ago
1
gpad parser now takes taxon element out of the list instead of passing on the entire list
#490
dougli1sqrd
closed
3 years ago
1
Taxon Curie objects are being leaked into the GPAD output
#489
dustine32
closed
3 years ago
7
Fix slimmer sort bug
#488
kshefchek
closed
3 years ago
0
curies should not parse with spaces in them, tests for new validation
#487
dougli1sqrd
closed
3 years ago
2
add support for q param to golr association fx for monarch
#486
kshefchek
closed
3 years ago
0
Association collections
#485
dougli1sqrd
closed
3 years ago
7
Go site 1453 gpad 2 parser
#484
dougli1sqrd
closed
3 years ago
3
Ensure that GO Rules test cases and test parsing can handle GAF 2.2
#483
kltm
closed
3 years ago
1
Ontobio should not pin dependencies to a particular version
#482
deepakunni3
closed
2 years ago
4
gpad now correctly sets the relation when parsing
#481
dougli1sqrd
closed
3 years ago
2
Adding gocamgen emitter code
#480
dustine32
closed
3 years ago
2
Issue 477 curie leaking
#479
dougli1sqrd
closed
3 years ago
2
adding synonymType field to the Synonym class to fix parse bug
#478
dougli1sqrd
closed
3 years ago
1
Taxon Curie objects are being leaked into the Report object during gpad parsing
#477
dougli1sqrd
closed
3 years ago
1
gpad 2.0 writer for geneontology/go-site#1453
#476
dougli1sqrd
closed
3 years ago
1
GPAD parser should set the relation in GoAssociation using the qualifier field
#475
dougli1sqrd
closed
3 years ago
1
GoRule 57 update and test for issue #473
#474
dustine32
opened
3 years ago
5
GoRule57 filter lines by provided_by
#473
dustine32
opened
3 years ago
0
qualifiers from gpad to gaf that are outside the gaf spec just blank out the field
#472
dougli1sqrd
closed
3 years ago
4
Logging configuration in __init__ file takes precedence over user configuration
#471
valearna
opened
3 years ago
0
Gaf 2.1 writer should emit blank qualifiers if the underlying GoAssociation qualifier is not in the allowed gaf 2.1 quafier set
#470
dougli1sqrd
closed
3 years ago
1
adding gorule55 in qc and a test
#469
dougli1sqrd
closed
4 years ago
1
ontobio doesn't work with obographs 0.2.1
#468
cmungall
closed
3 years ago
7
Issue 450 parse use association
#467
dougli1sqrd
closed
3 years ago
18
Fix for issue #465
#466
dustine32
closed
4 years ago
2
ontobio-parse-assocs.py omits version header line from output
#465
dustine32
closed
3 years ago
1
Update README-developers.md
#464
deepakunni3
closed
4 years ago
4
Option to allow IBAs for geneontology/go-site#1531
#463
dustine32
closed
4 years ago
2
ontobio hard failing on monarch rgd ingest
#462
kshefchek
closed
3 years ago
3
Annotation parsing for large files can become intractable
#461
kltm
opened
4 years ago
0
caching in ontol_factory.py
#460
saramsey
opened
4 years ago
0
updating go association model and needed refactoring elsewhere. Tests added for new functionality
#459
dougli1sqrd
closed
4 years ago
0
WithFrom field in all Parsers should be ensured they conform to the spec
#458
dougli1sqrd
closed
3 years ago
2
Qualifier field in GoAssociation Model should be removed in favor of just using negated + relation
#457
dougli1sqrd
opened
4 years ago
0
GoAssociation Model Updates
#456
dougli1sqrd
closed
3 years ago
1
add clinical mod test back
#455
kshefchek
closed
3 years ago
0
setting PASS variant of example type enum to pass, rather than fail
#454
dougli1sqrd
closed
4 years ago
0
Rule validation tests only parse rule examples as FAIL types
#453
dougli1sqrd
closed
4 years ago
0
Test tests/unit/test_clinical_mod failing
#452
dougli1sqrd
closed
3 years ago
0
adding option to give ontobio-parse-assocs a gaf inferences file
#451
dougli1sqrd
closed
4 years ago
3
Ontobio parsers and writers should use the underlying `GoAssociation` model
#450
dougli1sqrd
closed
3 years ago
2
add require_tld=False to EndpointSchema
#449
kshefchek
closed
4 years ago
1
config schema validation returns 'not a valid URL' in docker-compose
#448
kshefchek
closed
4 years ago
0
ontobio now respects gaf 2.2 and parses qualifiers dependent on versions
#447
dougli1sqrd
closed
4 years ago
10
Ontobio should support gaf 2.2 - Qualifiers update
#446
dougli1sqrd
closed
3 years ago
1
Add/finish API docs for Ontology methods
#445
jclerman
opened
4 years ago
0
fixing NOT| bug
#444
dougli1sqrd
closed
4 years ago
2
Adjust window expansion for IEAs in GAF QC
#443
kltm
closed
4 years ago
6
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