Release 2.1.4

What's Changed

• Add another taxon corpus for annotated-taxa. Rename taxa corpus to taxon-variation. by @balhoff in #579

Full Changelog: v2.1.3...v2.1.4

Release 2.1.3

What's Changed

• Update utest to 0.8.0 by @scala-steward in #574
• Update owlapi-distribution to 4.5.22 by @scala-steward in #559
• Implement genes corpus for similarity queries. by @balhoff in #578

Full Changelog: v2.1.2...v2.1.3

Release 2.1.2

What's Changed

• Update sbt to 1.6.2 by @scala-steward in #551
• Update scowl to 1.4.1 by @scala-steward in #554
• Use ancestral phenotype profiles for taxa corpus. by @balhoff in #570
• Use QLever endpoint for similarity frequencies query. by @balhoff in #573

Full Changelog: v2.1.1...v2.1.2

Release 2.1.1

What's Changed

• Move FILTER to where it will not always fail. by @balhoff in #566

Full Changelog: v2.1...v2.1.1

Release 2.1

What's Changed

• Rewrite query using sparql interpolator by @Shalsh23 in #332
• Updates to gene/eq service to work with relations graphs by @Shalsh23 in #326
• Taxon phenotypes updates by @Shalsh23 in #346
• Update entity/presence/evidence service to work with relation graphs by @Shalsh23 in #354
• Update taxon-with-phenotype service to work with relation graphs by @Shalsh23 in #352
• Update entity-dependency service to use relation graphs by @Shalsh23 in #353
• Update phenotype/query service to work with relation graphs by @Shalsh23 in #366
• Update study/query service to work with relation graphs by @Shalsh23 in #365
• Update relation-graphs branch with latest fixes on services-new-data-model by @balhoff in #359
• Update taxon/annotations service to work with relation graphs by @Shalsh23 in #368
• Updates to gene/affecting_entity_phenotype service to work with relat… by @Shalsh23 in #363
• Update term/property_neighbors/subject to work with relation graph by @Shalsh23 in #388
• Update relation-graphs branch from main branch by @balhoff in #390
• Update term/property_neighbors/object service to use relation graph. by @Shalsh23 in #387
• Update phenotype info service to use relation-graphs by @balhoff in #389
• Update relation-graphs branch from master by @balhoff in #420
• Update sbt to 1.4.9 by @scala-steward in #402
• Update utest to 0.7.9 by @scala-steward in #415
• Update sbt-native-packager to 1.8.1 by @scala-steward in #403
• Update akka-http, akka-http-caching, ... to 10.2.4 by @scala-steward in #400
• Similarity/matrix updates for relation graph by @Shalsh23 in #418
• Similarity jaccard by @Shalsh23 in #427
• WIP add classification to term info result. by @balhoff in #419
• Update similarity/profile_size service to work with relation graphs by @Shalsh23 in #432
• Migrate to Scala 2.13. by @balhoff in #444
• Update from master by @balhoff in #446
• Update utest to 0.7.10 by @scala-steward in #429
• Update frequency service to use term paths and handle relational terms by @balhoff in #423
• Add latest relation graphs changes to master by @balhoff in #458
• Update logback-classic to 1.2.5 by @scala-steward in #456
• Update commons-io to 2.11.0 by @scala-steward in #452
• Update scalaz-core to 7.2.33 by @scala-steward in #449
• Update sbt-scalafmt to 2.4.3 by @scala-steward in #450
• Update sbt to 1.5.5 by @scala-steward in #451
• Update scowl to 1.4.0 by @scala-steward in #447
• Update akka-http-cors to 1.1.1 by @scala-steward in #361
• Update akka-http, akka-http-caching, ... to 10.2.5 by @scala-steward in #457
• Update akka-stream-alpakka-xml to 3.0.2 by @scala-steward in #448
• Update groovy-all to 3.0.8 by @scala-steward in #416
• Provide swagger api docs as a static file by @Shalsh23 in #467
• Update owlapi-distribution to 4.5.20 by @scala-steward in #460
• Implement corpus size using term paths by @balhoff in #422
• Add similarity/profile service. by @balhoff in #470
• Fix handling of part_of for ancestors/descendants. by @balhoff in #472
• Align GET and POST docs. by @balhoff in #473
• Fix some symbol deprecation warnings. by @balhoff in #474
• Add specifier pattern parameters for semantic similarity. by @balhoff in #475
• Fix null pointer bug in matrix. by @balhoff in #476
• Reject request if both specifier parts are not provided. by @balhoff in #479
• Change specifier parameters to 'subject_filter'. by @balhoff in #481
• Submit a query for each term in frequency service, rather than as a single VALUES block. by @balhoff in #489
• Add subject property and and value as parameters to jaccard and mat… by @Shalsh23 in #485
• Update logback-classic to 1.2.7 by @scala-steward in #500
• Minor cleanup and warnings fixes. by @balhoff in #506
• Port some swagger fixes to master branch by @balhoff in #549
• Update sbt to 1.5.8 by @scala-steward in #518
• Update logback-classic to 1.2.11 by @scala-steward in #547
• Update sbt-native-packager to 1.9.9 by @scala-steward in #545
• Update akka-http-cors to 1.1.3 by @scala-steward in #532
• Update utest to 0.7.11 by @scala-steward in #530
• Remove log4j completely. Unify logging to logback via slf4j. by @balhoff in #511
• Update scala-library to 2.13.8 by @scala-steward in #524
• Update akka-actor, akka-slf4j, akka-stream to 2.6.18 by @scala-steward in #517
• Update scala.yml by @balhoff in #550
• Improve performance of OntoTrace query. by @balhoff in #560
• Update akka-http, akka-http-caching, ... to 10.2.9 by @scala-steward in #546
• Modify services to use simplified similarity corpora by @balhoff in #562
• Revert main queries to use generated relation classes. by @balhoff in #563
• Remove redundant relation graph by @balhoff in #564

Full Changelog: v2.0.3...v2.1

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 https://github.com/phe...

Release 1.0

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 https://github.com/phe...

Release v0.5

Major changes include the following:

• Application configuration
  • 7c103c2 Make hostname configurable.
• Moved API description from Apiary.io to Swagger
• Various improvements and additions to querying, in particular:
  • 0e83da9, 231ae05 option for including parts of entity in taxon phenotypic profiles
  • c0928dc Services for reasoner-computed existential relations.
  • aba3f1c Services for retrieving EQ terms for phenotypes, and retrieving taxon and gene annotations.
  • 19ebaef New services: count of annotated taxa within taxon; list taxa for a rank.
  • b3a40dd Added service to get EQ annotations for taxon phenotype.
  • 1f3f73f Taxa and phenotype services for a study.
  • 1282343 Service for citation for study IRI.
  • ac98f28 New service for taxa with phenotype, for entity page.
  • dbb2e2f Service for parsing label-based expressions.
  • d1606a9 Services for returning all ancestors or all descendants (via subClassOf) of a term.
  • 48579ef Added service to query for studies.
  • 759c4f7 New API for least common subsumers.
  • 9875a3a Added service for annotation report as TSV.
  • 492c14e Added include parts option for OntoTrace service.
• Varios improvements to query answering performance:
  • 130ce45, 46d3b83 Speed up for queries for genes affecting phenotype.
  • 3ee39a3 Much faster taxon-with-phenotype queries.
  • 7fd1aeb Faster to use distinct in subquery.
  • 40bc49d use named subquery for attributes for annotation report
  • 54d863b, 2bd5e39, a6adf5f, dc733ae, bfda557, c9d1a85 use precomputed closure
  • 2e81bd0 Performance improvement for corpus size query.
• Implement historical and serial homology axioms
• Improved logging

Bug fixes include the following:

• 4179747 Fixed bug in pattern connecting phenotypes via parts.
• ae5d367 Fix OWL API class path problem.
• e1d72b2 Fix part_of queries to handle non-reflexive part_of.
• ffebb51 Fixed error in query for genes expressed in structure.
• ae7af38 Fixed returning owl:Class for expression locations.
• d24c903 Fixed character encoding problem.
• 299ce0f Fix to gene for phenotype query.
• 31e4e12 Fix for incorrect counts of phenotypic profile size.
• 4e9be40 Fixed missing IDs for polymorphic states.
• be43b3b Fix to annotation summary service.

phenoscape-kb-services: Release 0.4

Web services application for the Phenoscape Knowledgebase.

Release 0.3

v0.3

Version 0.3