Knowledge-Graph-Hub kg-phenio issues

Knowledge-Graph-Hub / kg-phenio

A graph for accessing and comparing knowledge concerning phenotypes across species and genetic backgrounds.

BSD 3-Clause "New" or "Revised" License

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issues

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Fix issue with missing owl breaking transform

#161 caufieldjh closed 3 hours ago
0
Workaround for #159 - use obojson directly; use ROBOT v1.9.7

#160 caufieldjh closed 4 hours ago
0
`KeyError: 'val'` breaks transform

#159 caufieldjh closed 4 hours ago
2
Decompress phenio source

#158 caufieldjh closed 7 hours ago
0
Do Biolink category assignment to nodes here (rather than in PHENIO)

#157 caufieldjh opened 5 days ago
1
Pin numpy to <2; update deps

#156 caufieldjh closed 3 weeks ago
0
KG build failing in transform step due to numpy issues

#155 caufieldjh closed 3 weeks ago
3
Always capture the ontology relation as original_predicate

#154 kevinschaper opened 3 months ago
0
Use CURIE as name when name is not available

#153 caufieldjh opened 3 months ago
0
Store original relation on original_predicate slot

#152 caufieldjh closed 5 months ago
0
Build fails due to writing `relation` value on `Association`

#151 caufieldjh closed 5 months ago
0
Another fix for predicate assignment

#150 caufieldjh closed 5 months ago
0
Ensure that associations between disease and phenotype get categorized as `DiseaseToPhenotypicFeatureAssociation`

#149 caufieldjh closed 5 months ago
0
Ensure that associations between disease and phenotype get categorized as `DiseaseToPhenotypicFeatureAssociation`

#148 caufieldjh closed 5 months ago
2
Update UPHENO map transform to be compatible with latest Biolink Model

#147 caufieldjh closed 6 months ago
0
Update koza import (koza.cli_runner -> koza.cli_utils)

#146 caufieldjh closed 6 months ago
0
Transforms fail due to missing `koza.cli_runner`

#145 caufieldjh closed 6 months ago
0
Add agent_type and knowledge_level slots to edges

#144 caufieldjh closed 6 months ago
0
Update fields to align with Biolink Model 4.2.0

#143 caufieldjh closed 6 months ago
1
Re-add missing node xrefs

#142 caufieldjh closed 7 months ago
0
Re-add missing node xrefs

#141 caufieldjh closed 7 months ago
3
Add DDPHENO to edge infores sources

#140 caufieldjh closed 8 months ago
0
Repair DDPHENO infores_source; restructure source maps

#139 caufieldjh closed 8 months ago
0
PHENIO node transform can't find infores for DDPHENO

#138 caufieldjh closed 8 months ago
0
Fix for using Biolink Model in PHENIO transform

#137 caufieldjh closed 8 months ago
2
Build fails due to `ModuleNotFoundError: No module named 'biolink'`

#136 caufieldjh closed 8 months ago
0
Split up configs for test and full transform

#135 caufieldjh closed 8 months ago
0
Build fails because it can't find `phenio-test.json`

#134 caufieldjh closed 8 months ago
3
Add transformed test artifact

#133 caufieldjh closed 8 months ago
1
URLs to KGX TSV `tar.gz` files in two builds are 404

#132 justaddcoffee opened 10 months ago
1
Bump koza to >=0.5.3

#131 caufieldjh closed 11 months ago
0
ImportError: cannot import name 'ensure_converter' from 'sssom.context'

#130 caufieldjh closed 11 months ago
2
Further dependency fixes to avoid incompatibilities

#129 caufieldjh closed 11 months ago
2
Build fails during transform due to `ModuleNotFoundError: No module named 'biolink'`

#128 caufieldjh closed 11 months ago
3
Dependency fixes for biolink-model and universalizer

#127 caufieldjh closed 11 months ago
0
Transform stage of build fails due to `ImportError` in `sssom`

#126 caufieldjh closed 11 months ago
3
Repair validation error during transform stage

#125 caufieldjh closed 1 year ago
0
Build fails due to pydantic `ValidationError`

#124 caufieldjh closed 1 year ago
1
Update `biolink-model` dependency to next release (3.5.5)

#123 caufieldjh closed 11 months ago
0
Add `deprecated` column

#122 kevinschaper closed 1 year ago
2
Add config file to specify transform parameters and pass deprecated flag

#121 caufieldjh closed 1 year ago
2
Use config file to specify transform parameters for kgx

#120 caufieldjh closed 1 year ago
0
Update infores dicts in phenio source transforms

#119 caufieldjh closed 1 year ago
0
MOD missing from infores sources

#118 caufieldjh closed 1 year ago
0
Dependency updates

#117 caufieldjh closed 1 year ago
0
Bump kgx to >=2.0.0

#116 caufieldjh closed 1 year ago
0
Switch to explicit looping in koza

#115 kevinschaper closed 1 year ago
1
Rewrite Koza ingest of PHENIO to use updated looping behavior

#114 caufieldjh closed 1 year ago
0
Synchronize with semsql build (i.e., do it here)

#113 caufieldjh opened 1 year ago
0
Get synonyms

#112 caufieldjh closed 1 year ago
6