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x-atlas-consortia
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ubkg-etl
A framework that combines data from the UMLS with assertions from other data sources into a set of CSV files that can be imported into neo4j to build a Unified Biomedical Knowledge Graph (UBKG)
MIT License
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update to UBKG model for soft assay
#148
AlanSimmons
opened
1 week ago
4
Update hmfields.py to use new standardized ubkg-api datasets endpoint
#147
AlanSimmons
closed
2 weeks ago
0
update HRA data in UBKG
#146
AlanSimmons
opened
3 weeks ago
1
update CEDAR metadata from new edge/node files
#145
AlanSimmons
opened
3 weeks ago
0
Expand UBKGSOURCE ontology to include data from Data Distillery DCCs in CFDE repo
#144
AlanSimmons
opened
3 weeks ago
2
DISGENET
#143
AlanSimmons
closed
1 month ago
0
sex and weight_unit metadata values
#142
AlanSimmons
closed
3 weeks ago
2
SENNET: Case for "Mammary gland" organs
#141
AlanSimmons
closed
3 weeks ago
1
HMFIELD import uses new ubkg-api endpoints
#140
AlanSimmons
closed
2 months ago
0
HMFIELD ETL should be refactored to use new ubkg-api endpoints
#139
AlanSimmons
closed
2 months ago
0
Standardize descriptions of HubMAP/SenNet dataset types via UBKG
#138
AlanSimmons
closed
2 months ago
3
Build and ingest a "Source" valueset
#137
AlanSimmons
closed
2 months ago
0
bug fixes related to relationship label translation; updates to ontologies
#136
AlanSimmons
closed
3 months ago
0
bug: relationship mapping to Relations Ontology broken because of case issue
#135
AlanSimmons
closed
3 months ago
0
V3.4
#134
AlanSimmons
closed
3 months ago
0
Updates to Azimuth
#133
AlanSimmons
closed
3 months ago
1
Import PCL
#132
AlanSimmons
closed
3 months ago
1
ETL v3.3, which generated the 23Feb2024 Data Distillery
#131
AlanSimmons
closed
4 months ago
0
Modify RefSeq extract to be in blocks of 50K
#130
AlanSimmons
closed
3 months ago
0
Additional code to normalize SAB HPO to HP
#129
AlanSimmons
closed
5 months ago
0
bug fix UniProtKB synonyms
#128
AlanSimmons
closed
5 months ago
0
1. Reformatted relationship names if they violate neo4j naming rules. 2. Standardized code for HPO nodes.
#127
AlanSimmons
closed
5 months ago
0
CEDAR fields should be linked to HUBMAP provenance entities
#126
AlanSimmons
closed
3 months ago
0
CEDAR edge files should associate fields with dataset types
#125
AlanSimmons
closed
3 months ago
0
remove debug prints
#124
AlanSimmons
closed
6 months ago
0
UBKG updates for HuBMAP/SenNet
#123
AlanSimmons
closed
3 months ago
0
Resolve issues with HPO codes
#122
AlanSimmons
closed
3 months ago
1
Synch terms for new Dataset Data Type in UBKG and HRAVS
#121
AlanSimmons
closed
6 months ago
1
Use script to generate edge and nodes files for HRA via hra-ubkg-exporter instead of downloading from repo
#120
AlanSimmons
closed
4 months ago
5
Bug fix to handle use of alt name of 'Light Sheet' in field_assays.yaml
#119
AlanSimmons
closed
7 months ago
0
UNIPROTKB ETL incorrectly parses synonyms that contain parentheses
#118
AlanSimmons
closed
3 months ago
0
Disable copy of existing CSVs to save.X folders
#117
AlanSimmons
closed
3 months ago
0
jas_hmfield_bugs
#116
AlanSimmons
closed
8 months ago
0
Documentation to explain the HMFIELD ontology and the ETL
#115
AlanSimmons
closed
8 months ago
0
HMFIELD ingest, with nodes cross-referenced to nodes in HUBMAP and CEDAR.
#114
AlanSimmons
closed
8 months ago
0
bug fix related to indexes for HMFIELD for relationships other than isa
#113
AlanSimmons
closed
8 months ago
0
HMFIELD ingestion
#112
AlanSimmons
closed
8 months ago
0
GENCODE_VS codeIDs formatted as GENCODE: VS <code>
#111
AlanSimmons
closed
3 months ago
0
Ingest CCF 2D Reference Functional Tissue Unit (FTU) Library ASCT+B 2D FTU mappings into UBKG
#110
AlanSimmons
opened
9 months ago
2
jas_release_note_fix
#109
AlanSimmons
closed
9 months ago
0
jas_dd_bug_and_cedar
#108
AlanSimmons
closed
9 months ago
0
MSIGDB ingest: current base context has old version
#107
AlanSimmons
closed
3 months ago
1
GTEX ingest: duplicate node files
#106
AlanSimmons
closed
3 months ago
3
Changes related to latest generation of Data Distillery
#105
AlanSimmons
closed
9 months ago
0
documentation
#104
AlanSimmons
closed
10 months ago
0
Remove SUI; various bug fixes
#103
AlanSimmons
closed
10 months ago
0
node_definition of 'None' results in null Definition nodes
#102
AlanSimmons
closed
3 months ago
1
Import OMAP info from AVR database
#101
shirey
opened
10 months ago
0
Remove ATUI property from Definition node
#100
AlanSimmons
opened
10 months ago
0
map Orphanet to ORDO
#99
AlanSimmons
closed
3 months ago
1
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