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monarch-initiative
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monarch-ingest
Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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update pombase phaf url
#236
kevinschaper
closed
2 years ago
1
Package into CLI app (sorta)
#235
glass-ships
closed
2 years ago
0
Use new Koza logging feature in ingest pipeline
#234
kevinschaper
closed
1 year ago
1
Update biolink model associations we use to have classes for subject & object
#233
kevinschaper
closed
2 years ago
3
Add a nicer CLI to the ingest pipeline script
#232
kevinschaper
closed
2 years ago
1
Update docs (WIP)
#231
glass-ships
closed
2 years ago
0
BMP update
#230
kevinschaper
closed
2 years ago
0
Properly Map Gene ids in STRING Ingest
#229
putmantime
opened
2 years ago
1
Add edge and node file paths to ingests.yaml
#228
putmantime
closed
1 year ago
1
Create Repository For Applying Mappings to KGX Files
#227
putmantime
opened
2 years ago
3
Script for initializing a new ingest.
#225
putmantime
closed
1 year ago
1
kgx transform of monarch ontology is putting subject, object, predicate columns in nodes file
#224
kevinschaper
closed
2 years ago
1
Ingests may be specifying edge properties in the node prorperties yaml config
#223
putmantime
closed
1 year ago
1
PomBase Ingest Prefix Correction in Panther ingest
#222
putmantime
closed
2 years ago
1
Create Documentation For Each Ingest that declares Preferred namespace, and category for each ingest.
#221
putmantime
closed
1 year ago
1
Post initial QC ingest cleanup
#220
kevinschaper
closed
2 years ago
0
Make panther_ref_genome_orthologs an edge only ingest
#219
kevinschaper
closed
2 years ago
0
Exclude pub to gene & pub nodes from transforms & merge
#218
kevinschaper
closed
2 years ago
0
Add links to data files on ingest documentation pages
#217
kevinschaper
closed
8 months ago
1
ingest script shouldn't re-transform by default, add --force-transform option
#216
kevinschaper
closed
2 years ago
0
Monarch Ingest downloader Jenkins job is writing files in the wrong place
#215
kevinschaper
closed
1 year ago
1
bring in run-all-ingests changes
#214
glass-ships
closed
2 years ago
0
EBI gene to phenotype ingest
#213
RichardBruskiewich
closed
2 years ago
1
Add tsv file to enumerate the species we will include in graph
#212
kevinschaper
closed
1 year ago
1
QC Stats on merged kgx files
#211
putmantime
closed
2 years ago
3
Point downloader at Xenbase downloads.
#210
putmantime
closed
1 year ago
1
EBI Gene 2 Phenotype Ingest
#209
putmantime
closed
2 years ago
3
Mirror latest kg on public data.monarchinitiative.org
#207
kevinschaper
closed
1 year ago
1
Ingest wrapper w/yaml config
#206
kevinschaper
closed
2 years ago
0
Create an ingests.yaml, single python command to run all ingests
#205
kevinschaper
closed
2 years ago
2
Add a custom map for alliance-genes
#204
kevinschaper
closed
1 year ago
1
Update Panther ingest to use new tar.gz "archive" attribute in koza
#203
glass-ships
closed
2 years ago
1
Use alliance schema formatted data in gene expression (site) ingest
#202
RichardBruskiewich
closed
2 years ago
1
add ncbi gene information ingest files
#201
victoriasoesanto
closed
2 years ago
2
Merge updates
#200
kevinschaper
closed
2 years ago
0
fix: move non-runtime dependencies into dev-dependencies section
#199
finswimmer
closed
2 years ago
1
add node to pathway files to be tested
#198
victoriasoesanto
closed
2 years ago
1
Convert from biolink-model-pydantic to linkml pydanticgen classes
#197
kevinschaper
closed
2 years ago
4
Remove GO Annotation Mapping file
#196
putmantime
closed
2 years ago
0
Provide Updated ID-Prefix stats for informing mapping.
#195
putmantime
closed
1 year ago
2
Prefixes, some notes by Nico
#194
matentzn
closed
6 months ago
5
Remove go annotation mapping
#193
kevinschaper
closed
2 years ago
0
Remove mapping from GO Annotation ingest
#192
kevinschaper
closed
2 years ago
0
Odd looking genes in GO Annotation ingest
#191
kevinschaper
closed
2 years ago
2
Preserve original triple in ingests that use maps
#190
kevinschaper
closed
1 year ago
5
Preserve original triples in mapping step
#189
kevinschaper
closed
1 year ago
1
Alliance gene expression ingest
#188
RichardBruskiewich
closed
2 years ago
2
Add Alliance Gene Expression
#187
RichardBruskiewich
closed
2 years ago
1
Reactome pathway node ingest
#186
kevinschaper
closed
2 years ago
2
Edge-only ingests
#185
glass-ships
closed
2 years ago
0
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