Releases · geneontology/minerva

What's Changed

Remove 'involved in' from allowed extensions relations by @balhoff in #510
Implement option to preserve evidence when copying a model. by @balhoff in #514
Replace CARO anatomical entity with Uberon. by @balhoff in #515
Update tests to run properly by @balhoff in #536
Remove 'enabled by' as an extension relation by @balhoff in #535
Fix obsolete GO terms in test models. by @balhoff in #538
Fix Biopax URL in test. by @balhoff in #543
Add cli option to allow running checks against a graphstore journal. by @balhoff in #542
Add 'has primary input/output' relations to allowed GPAD extensions by @balhoff in #537
Output interacting taxon in correct column. by @balhoff in #548
Bump httpclient from 4.5.9 to 4.5.13 by @dependabot in #387
Bump maven-assembly-plugin from 2.5.3 to 3.6.0 by @dependabot in #516
Bump maven-source-plugin from 2.4 to 3.3.0 by @dependabot in #517
Bump gson from 2.8.5 to 2.8.9 by @dependabot in #485
Bump maven-surefire-plugin from 2.18.1 to 3.1.2 by @dependabot in #520
Bump httpclient from 4.5.13 to 4.5.14 by @dependabot in #521
Bump owl-to-rules_2.12 from 0.3.6 to 0.3.8 by @dependabot in #523

Full Changelog: v0.6.2...v0.6.3

What's Changed

Fix for failure for reasoner to update after undo by @balhoff in #114
Remove evidence requirements for annotation extensions in GPAD output. by @balhoff in #120
Adds an export service to get explanations for all inferred relations. by @balhoff in #123
Remove has-part from whitelist by @cmungall in #122
attempt to add xenbase to jsonld context by @kltm in #125
Allow passing of custom JSON-LD context to StartUpTool. by @balhoff in #129
Only allow root annotations in GPAD export if ND evidence. by @balhoff in #130
Remove regulation_of qualifiers from GPAD. Fixes #126. by @balhoff in #128
Additional tests for expansion of class IDs to class IRIs by @cmungall in #133
Added additional tests to clarify behavior of parsing class IDs pa… by @cmungall in #134
Testing ComplementOf expressions by @cmungall in #135
Testing ComplementOf-SomeValuesFrom expressions by @cmungall in #136
Getting rid of unused utility class with weird catalog use by @cmungall in #137
Add regulates_o_occurs_in to whitelist by @cmungall in #138
Changed model import to load RDF direct into Blazegraph by @balhoff in #144
A testcase that checks revised import and dump functions by @yy20716 in #145
Removed constraint on available memory for test. by @balhoff in #148
Add back annotation extension filtering based on evidence. by @balhoff in #147
Compact test ontology file (go-lego-module.omn.gz) by @yy20716 in #146
Extending BlazegraphMolecularModelManagerTest to test the full processing cycle of Blazegraph by @yy20716 in #150
Extend GPAD generation codes to support negations in the qualifier field of GPAD. by @yy20716 in #153
Add model production status to GPAD. by @balhoff in #157
Use providedBy annotation for 'assigned by' column by @balhoff in #158
Return contributor labels in meta response. by @balhoff in #159
Concatenate multiple sources on a single evidence. by @balhoff in #161
Update arachne version by @balhoff in #163
Use group shorthand for assigned-by. by @balhoff in #165
Throw exception rather than create a GPAD for an inconsistent ontology. by @balhoff in #169
Add new annotation relations to GPAD export. Fixes #170. by @balhoff in #171
Filter out PR:000000001 as subject of GPAD annotations. by @balhoff in #176
Molecular function annotations in GPAD must only use 'enables' or 'contributes to'. by @balhoff in #177
Disallow GPAD annotations to terms in do_not_annotate subsets. by @balhoff in #182
Exclude CARO terms from annotation extensions. by @balhoff in #184
Remove commas from underscore property names. by @balhoff in #183
Disallow equivalent conjunctive expressions in sets. by @balhoff in #189
Don't load models with 'delete' modelstate. by @balhoff in #193
Switch to new JSON-LD context file for identifiers by @cmungall in #194
regenerated, fixed issue with MGI by @cmungall in #198
Remove “MGI:” from MGI prefix expansion. by @balhoff in #201
Implemented SPARQL endpoint service. by @balhoff in #202
Add instructions for creating ontology mirror. by @balhoff in #211
Remove addition of Tbox axioms to model graphs. by @balhoff in #192
SPARQL endpoint in batch service by @balhoff in #222
Filter CHEBI terms from GPAD annotation subjects. by @balhoff in #224
Update version of owl-to-rules to avoid 'indirect rules' for reflexive subclasses. by @balhoff in #232
Update from master by @balhoff in #233
Adding search API at /search to minerva by @goodb in #234
Shex validation by @goodb in #237
Shex validation - #237 - mvn fix for JNI error by @goodb in #238
switched to maven shade plugin by @goodb in #239
Update several dependencies to allow running on Java 11 (and also 8) by @balhoff in #240
Issue 212 validation service response by @goodb in #241
Added explanations for core shape failures by @goodb in #242
Use openjdk on travis. by @balhoff in #244
implements pattern for retrieving canonical identifiers in gpad output by @goodb in #247
adding result count request paramater #235 and #230 by @goodb in #248
Run command-line GPAD export in parallel. by @balhoff in #243
Add validation framework as package an made accessible via minerva cmdline client by @goodb in #251
update cmdrunner with defaults for shex by @goodb in #252
provide for local go-lego in validator by @goodb in #253
Owl cmdline issue254 by @goodb in #255
adding parallel gpad export from master to dev by @goodb in #257
Issue258 remove owltools by @goodb in #259
Conversion to neo lite and golr #260 by @goodb in #261
Search api sparql query template uri curie by @goodb in #264
switched to isa_closure for golr query by @goodb in #263
many additions in here - perhaps most impactful - #261 regarding #260 by @goodb in #262
for step 4 in #260 by @goodb in #265
adding information on the shapes that do match troublesome nodes. by @goodb in #270
add id to order by for #235 by @goodb in #271
fix ordering for model search by @goodb in #272
fix search result for users and groups by @goodb in #273
Performance go shapes199 by @goodb in #274
addressing shape inheritance issue by @goodb in #275
Performance go shapes199 by @goodb in #276
fixing error running command line by @goodb in #277
Switch to refine for validation by @goodb in #278
Add tests for validator and search services by @goodb in #279
implemented POST by @goodb in #280
running command line client as part of travis. by @goodb in #281
Status service 282 by @goodb in #284
Add pipeline report to cmdline validation by @goodb in #285
require golr server specification for command line run by @goodb in #287
hopefully improved clarity of command line usage by @goodb in #288
Blazegraph for go lego experiment by @goodb in #297
Bugfixes on blazegraph conversion by @goodb in #299
Testing model level shex validation by @goodb in #306
think bug dead by @goodb in #307
take out all super types from response. rendering took forever by @goodb in https://github.com/geneontology/mi...