Release 2.0

What's Changed

• Enables Docker build for this application by @hlapp in #52
• Query by publications by @balhoff in #54
• Restore TSV output for taxon list output by @balhoff in #60
• Implement preliminary service providing Jaccard similarity score for a pair of character states by @balhoff in #61
• Add missing import. by @balhoff in #62
• Correct services to ignore limit if <1. by @balhoff in #65
• Update from swagger hub to fix study query doc. by @balhoff in #66
• Service for pairwise similarity of list of ontology classes by @balhoff in #67
• Include entity in OntoTrace query including its parts. by @balhoff in #71
• Generated code by SwaggerHub by @balhoff in #72
• Generated code by SwaggerHub by @balhoff in #74
• Created service for computing ancestor matrix by @balhoff in #75
• Issue 77 by @balhoff in #78
• Document subsumer matrix service. by @balhoff in #79
• Make sort case-insensitive by @Shalsh23 in #80
• Swaggerhub by @balhoff in #84
• Update matrix service to take JSON array of IRIs. by @balhoff in #85
• Generated code by SwaggerHub by @balhoff in #86
• Generated code by SwaggerHub by @balhoff in #88
• Support POST for OntoTrace. by @balhoff in #87
• Swaggerhub by @balhoff in #96
• Generated code by SwaggerHub by @balhoff in #97
• Generated code by SwaggerHub by @balhoff in #99
• Generated code by SwaggerHub by @balhoff in #100
• Make ic_disparity query parameter names consistent. by @balhoff in #101
• Generated code by SwaggerHub by @balhoff in #102
• Return matrix for study as application/xml. by @balhoff in #103
• Added method for executing SPARQL ASK queries. by @balhoff in #105
• Generated code by SwaggerHub by @balhoff in #107
• Generated code by SwaggerHub by @balhoff in #108
• Implement services to handle queries for inferred presence/absence. by @balhoff in #110
• New presence absence matrix branch by @Shalsh23 in #111
• Generalize term search. by @balhoff in #115
• Generated code by SwaggerHub by @balhoff in #117
• Generated code by SwaggerHub by @balhoff in #118
• Generated code by SwaggerHub by @balhoff in #120
• Accept JSON array for definedBy. by @balhoff in #119
• Add ui button to get dependency matrix by @Shalsh23 in #114
• Merge master by @balhoff in #123
• Fix query parameter name by @balhoff in #124
• Fix space in sample data. by @balhoff in #125
• Update media type to text/csv. by @balhoff in #126
• Boost match rank of terms with text exactly equal to search text. by @balhoff in #131
• Return only one label for ancestor and descendant queries. Fixes #129. by @balhoff in #132
• Add newline in results EOF by @Shalsh23 in #133
• Provide option to make use of part_of for ancestor and descendant queries. by @balhoff in #134
• Swaggerhub by @balhoff in #135
• Fixes typos in /similarity/matrix documentation by @hlapp in #140
• Use correct media type for ancestor matrix service by @balhoff in #142
• Add POST to /term/labels and /entity/dependency services by @balhoff in #143
• Implement service providing frequency information for an ontology term according to some identified corpus by @balhoff in #151
• Allow caching of POST requests. by @balhoff in #152
• Preserve user specified order of iris in dependency matrix by @Shalsh23 in #150
• Support streaming response for TaxonPhenotypeAnnotations TSV (and more) by @balhoff in #153
• Add documentation for taxon annotations query and annotation sources query. by @balhoff in #155
• Document publication parameter. by @balhoff in #158
• Return character id and label in the results of the study/phenotype kb-service by @Shalsh23 in #156
• Accept JSON arrays for all IRI lists. by @balhoff in #159
• Enable content negotiation with streaming annotations response. by @balhoff in #160
• Migrate matrix renderer test to utest by @Shalsh23 in #164
• Fix #26: Annotate ontotrace matrix with variable status by @Shalsh23 in #166
• Order text search results consistently for different values of limit by @balhoff in #168
• Document acceptance of json array of IRIs for kb services by @Shalsh23 in #169
• Make character IRI and label available where needed. by @balhoff in #178
• Combine character id and label into a single json object by @Shalsh23 in #180
• Issue 139 - merge term labels by @Shalsh23 in #170
• Add ‘phenotype’ parameter to query endpoints. For issue #148. by @balhoff in #181
• Implement phenotype info service. by @balhoff in #185
• Refinements to phenotype info service. by @balhoff in #186
• Document phenotype info service. by @balhoff in #187
• Retrieve dependency matrix with a single query. by @balhoff in #204
• Fixes #167: Adds missing author to ontotrace matrix by @Shalsh23 in #205
• Add implementation for similarity/frequency for genes corpus by @Shalsh23 in #206
• Return null if label doesn't exist by @Shalsh23 in #209
• Only show states that are linked to taxon in /phenotype/info. by @balhoff in #208
• Update sparql-interpolator. by @balhoff in #213
• Return only one label for a term. by @balhoff in #211
• Convert None responses for Option values into 404. by @balhoff in #212
• Change MinimalTerm label to Option[String]. by @balhoff in #214
• Fix null pointer exception in query result. by @balhoff in #215
• Update sbt to 1.3.8 by @scala-steward in #235
• Update scalaz-core to 7.2.30 by @scala-steward in #236
• Update scowl to 1.3.4 by @scala-steward in #234
• Update phenoscape-kb-ingest to 1.6.2 by @scala-steward in #233
• Update groovy-all to 2.4.19 by @scala-steward in #231
• Update apache-jena-libs to 3.14.0 by @scala-steward in #230
• Update owlapi-distribution to 4.2.9 by @scala-steward in #229
• Update sbt-native-packager to 1.3.25 by @scala-steward in #226
• Update utest to 0.7.4 by @scala-steward in #223
• Update scala. Remove guava. by @balhoff in #237
• Update sbt-native-packager to 1.7.0 by @scala-steward in #238
• Update groovy-all to 2.5.10 by @scala-steward in #240
• Update owlapi-distribution to 4.5.15 by @scala-steward in #239
• Update commons-io to 2.6 by @scala-steward in #227
• Update to JavaConverters, remove warnings. by @balhoff in #241
• Update akka-stream-alpakka-xml to 1.1.2 by @scala-steward in #222
• Update owlet to 1.6.2 by @scala-steward in #232
• Update akka-actor, akka-slf4j, akka-stream to 2.5.30 by @scala-steward in #224
• Update spray-json to 1.3.5 by @scala-steward in #228
• Update akka-http-cors to 0.3.4 by @scala-steward in #219
• Update logback-classic to 1.1.11 by @scala-steward in #220
• Update results json in api docs by @Shalsh23 in #248
• Update akka-actor, akka-slf4j, akka-stream to 2.6.4 by @scala-steward in #246
• Update akka-http-cors to 0.4.2 by @scala-steward in #244
• Update logback-classic to 1.2.3 by @scala-steward in #245
• Update akka-http, akka-http-caching, ... to 10.1.11 by @scala-steward in #225
• Update owlet to 1.7 by @scala-steward in #247
• Fix missing results in ancestors & descendants services by @balhoff in #218
• Return 0 count for frequency query when term is not matched in SPARQL query by @balhoff in #216
• Include character, state, and cell IRIs in matrix output. by @balhoff in #217
• Fixes #188: Return term source ontology by @Shalsh23 in #249
• Update sbt to 1.3.9 by @scala-steward in #250
• Remove println by @balhoff in #251
• Update groovy-all to 2.5.11 by @scala-steward in #253
• Update sbt to 1.3.10 by @scala-steward in #255
• Update owlet to 1.8.1 by @scala-steward in #259
• Update akka-http-cors to 0.4.3 by @scala-steward in #256
• Update owlapi-distribution to 4.5.16 by @scala-steward in #257
• Issue 179 kb metadata by @Shalsh23 in #252
• Update sbt-native-packager to 1.7.1 by @scala-steward in #264
• Update akka-actor, akka-slf4j, akka-stream to 2.6.5 by @scala-steward in #263
• Add synonym detail to taxon info by @Shalsh23 in #266
• Fix some deprecation warnings. by @balhoff in #265
• Reformat with new scalafmt configs by @Shalsh23 in #271
• Update to new sparql-utils. by @balhoff in #276
• Change scalafmt align setting by @Shalsh23 in #283
• Update akka-http, akka-http-caching, ... to 10.1.12 by @scala-steward in #269
• Update apache-jena-libs to 3.15.0 by @scala-steward in #273
• Update groovy-all to 2.5.12 by @scala-steward in #275
• Update Scala version for Travis by @balhoff in #285
• Update sbt-native-packager to 1.7.2 by @scala-steward in #270
• Test automatic SPARQL result derivation. by @balhoff in #279
• Update akka-actor, akka-slf4j, akka-stream to 2.6.6 by @scala-steward in #291
• Update akka-stream-alpakka-xml to 2.0.1 by @scala-steward in #292
• Update scalafmt-core to 2.5.3 by @scala-steward in #278
• Update sbt-native-packager to 1.7.3 by @scala-steward in #289
• Update sbt to 1.3.12 by @scala-steward in #288
• Update commons-io to 2.7 by @scala-steward in #284
• Update scalafmt-core to 2.6.0 by @scala-steward in #293
• Update akka-http-cors to 1.0.0 by @scala-steward in #277
• Make tests actually run. by @balhoff in #295
• Update scalafmt-core to 2.6.1 by @scala-steward in #296
• Change phenotypic profiles method to work with the new monarch schema by @Shalsh23 in #183
• Updates for new Gene model by @balhoff in #297
• Update owlapi-distribution to 4.5.17 by @scala-steward in #301
• Update sbt to 1.3.13 by @scala-steward in #299
• Update sbt-native-packager to 1.7.4 by @scala-steward in #302
• Update apache-jena-libs to 3.16.0 by @scala-steward in #306
• Update scalafmt-core to 2.6.4 by @scala-steward in #308
• Update groovy-all to 2.5.13 by @scala-steward in #309
• Update akka-actor, akka-slf4j, akka-stream to 2.6.8 by @scala-steward in #307
• Update groovy-all to 3.0.5 by @scala-steward in #311
• Fixes #90 - add option to include subclasses, or not, for entity and … by @Shalsh23 in #290
• Update sbt to 1.4.0 by @scala-steward in #335
• Update scalafmt-core to 2.7.5 by @scala-steward in #341
• Bug fix; rewrite query using sparql interpolator by @Shalsh23 in #344
• Update sbt-native-packager to 1.7.6 by @scala-steward in #340
• Update owlapi-distribution to 4.5.18 by @scala-steward in #345
• Update sbt to 1.4.1 by @scala-steward in #343
• Update commons-io to 2.8.0 by @scala-steward in #322
• Update utest to 0.7.5 by @scala-steward in #318
• Update sbt to 1.4.4 by @scala-steward in #356
• Update utest to 0.7.7 by @scala-steward in #375
• Update scalaz-core to 7.2.31 by @scala-steward in #373
• Don’t return owl:Thing in ancestor results. by @balhoff in #383
• Update sbt to 1.4.7 by @scala-steward in #381
• Update sbt-native-packager to 1.8.0 by @scala-steward in #369
• Update akka-actor, akka-slf4j, akka-stream to 2.6.12 by @scala-steward in #379
• Update sparql-utils, sparql-utils-owlapi to 1.3 by @scala-steward in #360
• Update spray-json to 1.3.6 by @scala-steward in #350
• Roll back changes to taxon info return format. by @balhoff in #384
• Create scala.yml by @balhoff in #385
• Update scala.yml by @balhoff in #386
• Services new data model by @Shalsh23 in #329
• Update scala-library to 2.12.13 by @scala-steward in #394
• Allow return of all search results using limit < 1. by @balhoff in #395
• Update sparql-utils, sparql-utils-owlapi to 1.3.1 by @scala-steward in #396
• Update apache-jena-libs to 3.17.0 by @scala-steward in #357
• Update akka-http, akka-http-caching, ... to 10.1.14 by @scala-steward in #392
• Update akka-stream-alpakka-xml to 2.0.2 by @scala-steward in #327
• Support search and info for genes without phenotype annotations in switch to Monarch data. by @balhoff in #399

Full Changelog: v0.5...v2.0