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phenoscape
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pipeline
Build pipeline for the Phenoscape Knowledgebase
MIT License
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Bump scipy from 0.15.1 to 1.10.0 in /resources
#226
dependabot[bot]
opened
1 year ago
0
Bump numpy from 1.7.0 to 1.22.0 in /resources
#225
dependabot[bot]
opened
2 years ago
0
Bump numpy from 1.7.0 to 1.21.0 in /resources
#224
dependabot[bot]
closed
2 years ago
1
Rework patterns to support phenotype_of over relations.
#223
balhoff
opened
2 years ago
0
Add NEXML subdirs text file
#222
johnbradley
closed
2 years ago
0
Allow running pipeline using Slurm/Singularity
#221
johnbradley
closed
2 years ago
0
Reduce duplication in Makefile
#220
johnbradley
closed
2 years ago
0
Replace duplicated rules with pattern rules
#219
johnbradley
closed
2 years ago
0
Remove sed -i argument for portability
#218
johnbradley
closed
2 years ago
0
Add comments to clarify the query steps
#217
Shalsh23
closed
2 years ago
0
Test Makefile using placeholder scripts
#216
johnbradley
closed
2 years ago
4
Update readme with links
#215
Shalsh23
closed
2 years ago
0
Create a test for the Makefile
#214
johnbradley
closed
2 years ago
0
Increase parameterization in Makefile
#213
balhoff
closed
2 years ago
6
Consider importing OMO metadata ontology
#212
balhoff
opened
3 years ago
0
Set up test suite for pipeline
#211
Shalsh23
opened
3 years ago
2
Fix named graph for genes corpus; prevented taxon-to-gene search.
#210
balhoff
closed
3 years ago
0
Add labels to generated classes.
#209
balhoff
closed
3 years ago
0
Make sure referenced ontology terms are labeled
#208
balhoff
opened
3 years ago
1
Exclude ZP root phenotype. Causing havoc in semantic similarity.
#207
balhoff
closed
3 years ago
0
Parameterize output file
#206
Shalsh23
opened
3 years ago
0
Serialize the run
#205
Shalsh23
closed
3 years ago
0
Data Model Visualization
#204
Shalsh23
opened
4 years ago
3
Update from master
#203
balhoff
closed
4 years ago
0
Relation graphs need Phenex data phenotype classes
#202
balhoff
closed
4 years ago
0
Provide relations graph to absences and presences target
#201
Shalsh23
closed
4 years ago
0
Use relation graph in presences and absences queries
#200
balhoff
closed
4 years ago
1
Update pipeline-tools docker image version
#199
Shalsh23
closed
4 years ago
0
Issue 125 relation graphs
#198
Shalsh23
closed
4 years ago
0
Resolve some issues with missing ZFIN genes in KB.
#197
balhoff
closed
4 years ago
0
Pipeline fixes
#196
balhoff
closed
4 years ago
0
Use Monarch dev location. Disable human for now.
#195
balhoff
closed
4 years ago
0
Add quiet argument to arq commands
#194
Shalsh23
closed
4 years ago
0
Add labels for MOD taxa.
#193
balhoff
closed
4 years ago
0
Always start from scratch
#192
balhoff
closed
4 years ago
1
Use all subclasses and superclasses of 'anatomical entity' for expression generation
#191
balhoff
closed
4 years ago
0
Add a few remaining inputs to match old KB build.
#190
balhoff
closed
4 years ago
0
Review use of stdout with arq
#189
balhoff
closed
4 years ago
0
Update Jenkinsfile to use jenkins agent user for docker container
#188
balhoff
closed
4 years ago
0
User current user id for run.sh.
#187
balhoff
closed
4 years ago
0
Absence from presence
#186
balhoff
closed
4 years ago
0
Container version must match run.sh
#185
balhoff
closed
4 years ago
0
Update docker image version
#184
Shalsh23
closed
4 years ago
0
Set bg-runner memory; fix corpus size
#183
balhoff
closed
4 years ago
0
Output scores tables directly from pairwise sim command.
#182
balhoff
closed
4 years ago
0
Don't add closures to main KB file.
#181
balhoff
closed
4 years ago
0
Use turtle for bio-ontologies-classified, so we can query it with arq.
#180
balhoff
closed
4 years ago
0
Add Dillman data folder.
#179
balhoff
closed
4 years ago
0
Update robot reason options to reduce redundant output.
#178
balhoff
closed
4 years ago
2
Revise presence/absence.
#177
balhoff
closed
4 years ago
0
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