biolink / ontobio

python library for working with ontologies and ontology associations

https://ontobio.readthedocs.io/en/latest/

biolink/ontobio Issues

Current version of ontobio, in some cases, has trouble parsing GAF(?)
Updated 2 months ago1
ontobio is not HTTPS-safe
Updated 3 months ago1
ontobio pull request failing workflow actions due to Monarch
Updated 7 months ago1
Import breaks on >=Python3.7 because of dataclasses package
Closed a year ago1
sqlite3.DatabaseError: file is not a database
Updated a year ago
enrichment_test() function not returning anything
Updated 2 years ago
Move this repo to the GO organization?
Closed 2 years ago
EcoMap should parse eco.owl as ontology
Updated 2 years ago1
Use behind proxy
Updated 2 years ago2
GO-CAM translation should convert 'transports or maintains localization of' and other relations
Closed 2 years ago3
Converting GPAD to GAF can result in blank evidence codes if no ECO-to-GAF mapping exists
Closed 2 years ago2
Use gaf-eco-mapping-derived.txt in EcoMap in GpadParser and GafWriter
Closed 2 years ago2
"category" field in Token should be "categories"
Updated 3 years ago
Obsolete GO term with no replacement breaks with/from validation
Closed 3 years ago2
Emit creation-date on Evidence individuals
Closed 3 years ago1
Cannot render subgraphs using GraphRenderer
Updated 3 years ago
error in gocamgen
Closed 3 years ago1
ogr bug?
Updated 3 years ago1
ontobio output to obograph?
Updated 3 years ago
loading local json files fails
Updated 3 years ago1
pyparsing upgrade causes AttributeError
Closed 3 years ago1
generate reports on differences in two gpad2.0 files
Updated 3 years ago5
ModuleNotFoundError: No module named ‘ontobio.graph_io'
Updated 3 years ago
get_minimal_subgraph gives "RecursionError: maximum recursion depth exceeded"
Updated 3 years ago
Unknown GAF qualifier/relation breaks parser
Closed 3 years ago1
GAF evidence code to ECO conversion: always use gaf-eco-mapping.txt PURL
Closed 3 years ago
Changes to rdfgen/gocamgen for handling new date fields
Closed 3 years ago
Graph.node removed in networkX 2.4
Closed 3 years ago5
What does this repo do? Please improve the readme
Updated 3 years ago
Add missing chardet dependency for PyShEx module
Closed 3 years ago4
Report should only receive strings and not objects
Closed 3 years ago1
Run GO rule 20 (obsolete term repair) before GO rule 28 (term aspect check)
Updated 3 years ago2
Change CURIE of exists_during in lookup
Closed 3 years ago1
Add ns2:evidence-with property to models that have been converted to 'has_input' edges.
Closed 3 years ago
Add missing relations to relations.py
Closed 3 years ago3
Default rule_set in validate.py produce is parsed as list ['a', 'l', 'l']
Closed 3 years ago2
Fix circular import reference between collapsed_assoc and errors
Closed 3 years ago
param to run ALL GO rules in ontobio-parse-assocs does not run all rules
Closed 3 years ago2
There should be a way to exclude some GO rules when parsing a GAF file
Updated 4 years ago6
question about owl:DatatypeProperty
Updated 4 years ago14
synonym parsing skips synonyms with xsd:string declared
Updated 4 years ago2
requirements.txt requiring networkx 2.2
Closed 4 years ago3
Annotation properties should allow multiple values of the same key
Closed 4 years ago1
GAF 2.2 output generates extensions using CURIE for relations instead of underscore labels
Closed 4 years ago1
Separate out unit and integration tests
Updated 4 years ago1
Test notebooks along side the usual suite of tests
Updated 4 years ago
Fix filepaths for resources in tests
Updated 4 years ago
Ontology.merge() should copy logical definitions and property chain axioms
Closed 4 years ago
GPI 2.0 support with GPAD 2.0
Updated 4 years ago
handling multiple rdfs labels
Updated 4 years ago