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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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How does ingestion work for entity that only has an identifier?
#184
wrosko
closed
2 years ago
2
Transform KGX file to Neo4J data dump
#183
putmantime
closed
2 years ago
2
Dictybase Gene2Phenotype Ingest
#182
putmantime
closed
2 years ago
11
Remove nodes from association ingests, remove source from remaining nodes
#181
kevinschaper
closed
2 years ago
0
Fix 'MGI:MGI:' ids in GO ingest
#180
kevinschaper
closed
2 years ago
1
Exclude marker/mechanism rows from ctd_chemical_to_disease
#179
kevinschaper
closed
2 years ago
0
update reactome ingest to chemicaltopathwayassociation
#178
victoriasoesanto
closed
2 years ago
0
CTD Chemical to Disease ingest
#177
kevinschaper
closed
2 years ago
0
Add GitHub action to deploy docs
#176
kevinschaper
closed
2 years ago
1
tutorial docs update + use latest downloader
#175
kevinschaper
closed
2 years ago
0
Jenkins job to run pipeline merge & build neo4j & blazegraph datastores
#174
kevinschaper
closed
2 years ago
1
Run individual ingests in Jenkins w/upload to bucket
#173
kevinschaper
closed
2 years ago
3
Reactome Chemical 2 Pathway ingest is using the association for Gene 2 Pathway
#172
putmantime
closed
2 years ago
0
Update downloader & tutorial
#171
kevinschaper
closed
2 years ago
0
WIP Update Biolink Model Pydantic to latest
#170
glass-ships
closed
2 years ago
1
Tagged downloads
#169
kevinschaper
closed
2 years ago
0
MGI gene to pub ingest
#168
glass-ships
closed
2 years ago
2
Upgrade koza, handle node only ingests nicely, plus formatting changes
#167
kevinschaper
closed
2 years ago
3
Chemical Entity Ingest
#166
putmantime
closed
2 years ago
1
NCBI Ingest
#165
putmantime
closed
2 years ago
1
Test Monday.com Issue
#164
putmantime
closed
2 years ago
0
Source File Cloud Storage
#163
putmantime
closed
1 year ago
1
Upgrade monarch-ingest to latest Koza & kgx
#162
kevinschaper
closed
2 years ago
0
added chemical to pathway files for reactome ingest, added docs for reactome, modified download and ingest pipeline yaml files
#160
victoriasoesanto
closed
2 years ago
0
added gene to pathway files for reactome ingest
#159
victoriasoesanto
closed
2 years ago
1
Gene Orthology (Panther) ingest
#158
RichardBruskiewich
closed
2 years ago
7
Depdency tweaks: numpy to ^1.22, python to ^3.8
#157
kevinschaper
closed
2 years ago
0
Panther Ingest
#156
putmantime
closed
1 year ago
5
Reactome Ingest
#155
putmantime
closed
2 years ago
1
Update to latest biolink-model-pydantic & fix gene to pub associations
#153
kevinschaper
closed
2 years ago
1
GO annotations ingest
#152
RichardBruskiewich
closed
2 years ago
4
Pombase phenotype_annotations.pombase.phaf.gz now has a FYECO prefix for gene names
#151
putmantime
closed
2 years ago
8
Ingests need edge (node?) knowledge source provenance fixed?
#150
RichardBruskiewich
closed
2 years ago
2
Gene 'source' value should be entrez infores, for consistency with associations
#149
RichardBruskiewich
closed
2 years ago
0
Could source data download.yaml file specs be parameterized?
#148
RichardBruskiewich
opened
2 years ago
0
String database ingest
#147
RichardBruskiewich
closed
2 years ago
0
Create initial StringDB koza ingest from original dipper ingest / koza example
#146
putmantime
closed
2 years ago
1
Minor changes from getting the ingest to run on gcp
#145
kevinschaper
closed
2 years ago
0
Adds the monarch ontology
#144
kevinschaper
closed
2 years ago
0
Downloader Module
#143
putmantime
closed
2 years ago
0
Run Dagster on GCP for ingest & graphdb deploy
#142
kevinschaper
closed
2 years ago
1
Ingest should make versioned output
#141
kevinschaper
closed
1 year ago
1
Initial downloader
#140
kevinschaper
closed
2 years ago
0
Remove category from edge_properties for all transforms
#139
kevinschaper
closed
2 years ago
1
Create ingest cache
#138
kevinschaper
closed
1 year ago
3
Add download support to Monarch Ingest
#137
kevinschaper
closed
2 years ago
2
Add drug/chemical to disease/phenotype associations from non-human databases
#136
kshefchek
opened
2 years ago
1
First pass at a Dagster pipeline
#135
kevinschaper
closed
2 years ago
0
Consider adding Dictybase gene to phenotype associations
#134
kevinschaper
closed
1 year ago
3
added gene2publication py, yaml, metadata yaml and test files for HGNC ingest
#133
victoriasoesanto
closed
2 years ago
0
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