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.