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Introduction

This document is a section of the Migration Guide.

For more information about the OWL loader, see Loader Guide.

OWL Loader Enhancements

Substantial changes have been implemented in LexEVS 5.0 during the conversion of the OWL loader. The NCI OWL loader has been decommissioned and replaced with a more generic Protégé OWL loader. All effort has been made to ensure that no previous functionally has been lost during this transition. Priority was given to maintaining existing functionality while improving the OWL loader.

Enhancements and changes made to the OWL loader:

  • Improve OWL model footprint by upgrading to latest Protégé (3.4 w/improved support for database streaming)
  • Provide ability to enable use the Protégé DB support (Protégé database will serve as cache while we build the LexEVS model from OWL)
  • Add support for NCI-based complex props (processing of XML fragments)
  • Add support for preferences
  • Add support for manifest
  • Add support to split role and associations (consider splitat relation container level as done by NCIT loader)
  • When resolving IndividualProperties, changed casting from 'OWLNamedClass' to super interface 'RDFSNamedClass'.
  • When determining the Entity Id, there were some spots that were using the 'getBrowserText()' method on the 'OWLNamedClass' class. The 'getBrowserText()' was intended to give Protege a nice display string – but in order to get the id we wanted we want to use the 'getLocalName()' method.
  • Now we do not create 'domain' and 'range' associations if there is no target of the association.
  • When processing OWLObjectProperties, changed casting from 'OWLObjectProperty' to super interface 'RDFProperty'
  • When processing Instances, changed casting from 'OWLNamedClass' to super interface 'RDFSClass', and 'OWLIndividual' to super interface 'RDFResource'.
  • When determining the the Entity code during load of an association, we now parse the string based on a colon OR hash symbol.
    For example:
    Code Block
    http://someNamespace.org:C12345

...

  •  would 
...
  •  resolve 
...
  •  to 
...
  •  'C12345' 
...
  •  and 
...
  •  Code Block
...
  • http://someNamespace.org#C12345
...
  •  would 
...
  •  also 
...
  •  resolve 
...
  •  to 
...
  •  'C12345'
...

  •  We 
...
  •  used 
...
  •  to 
...
  •  process 
...
  •  only 
...
  •  the 
...
  •  colon.
...
  • The 
...
  •  isDefined() 
...
  •  property 
...
  •  is 
...
  •  now 
...
  •  set 
...
  •  on 
...
  •  created 
...
  •  entities.
...
  • Removed 
...
  •  the 
...
  •  following 
...
  •  OWL 
...
  •  preferences 
...
  •  - 
...
  •  dataTypeNameBoolean, 
...
  •  associatonNameHasType, 
...
  •  and 
...
  •  associationNameHasTypeURN.
...
  • Annotation 
...
  •  properties 
...
  •  are 
...
  •  now 
...
  •  stored 
...
  •  in 
...
  •  terms 
...
  •  of 
...
  •  presentation/comments.
...
  • Manifest 
...
  •  supports 
...
  •  forward 
...
  •  and 
...
  •  reverse 
...
  •  association 
...
  •  names.
...
  • The 
...
  •  codedNodeSet 
...
  •  restriction 
...
  •  added 
...
  •  to 
...
  •  restrict 
...
  •  lucene-based 
...
  •  queries.
...
  • RDF 
...
  •  local 
...
  •  names 
...
  •  are 
...
  •  used 
...
  •  instead 
...
  •  of 
...
  •  'textualPresentation' 
...
  •  and 
...
  •  'comment' 
...
  •  property 
...
  •  names.
...
  • Updated 
...
  •  SupportedCodingScheme.isImported 
...
  •  set 
...
  •  to 
...
  •  "true" 
...
  •  as 
...
  •  default.
...
  • The 
...
  •  previous 
...
  •  NCI 
...
  •  Loader 
...
  •  and 
...
  •  related 
...
  •  dependencies 
...
  •  have 
...
  •  been 
...
  •  removed.
...
  • Non-concept 
...
  •  entities 
...
  •  by 
...
  •  EMF 
...
  •  EntityService 
...
  •  are 
...
  •  being 
...
  •  handled 
...
  •  correctly.
...
  • Memory 
...
  •  profiling 
...
  •  options 
...
  •  0 
...
  •  and 
...
  •  3 
...
  •  removed 
...
  •  from 
...
  •  external 
...
  •  interfaces.
...
  • Instances 
...
  •  are 
...
  •  streamed 
...
  •  under 
...
  •  the 
...
  •  enhanced 
...
  •  memory 
...
  •  profile 
...
  •  options.
...
  • Update 
...
  •  made 
...
  •  to 
...
  •  properly 
...
  •  store/retrieve 
...
  •  the 
...
  •  entity 
...
  •  type 
...
  •  in 
...
  •  lucene 
...
  •  indexing.
...
  • Update 
...
  •  made 
...
  •  for 
...
  •  use 
...
  •  of 
...
  •  association 
...
  •  code 
...
  •  as 
...
  •  the 
...
  •  'id' 
...
  •  in 
...
  •  supported 
...
  •  associations 
...
  •  are 
...
  •  consistent 
...
  •  with 
...
  •  hierarchy 
...
  •  and 
...
  •  general 
...
  •  API 
...
  •  declarations 
...
  •  that 
...
  •  work 
...
  •  with 
...
  •  associations 
...
  •  (same 
...
  •  for 
...
  •  GUI 
...
  •  interfaces).
...
  • Loader 
...
  •  preference 
...
  •  "CreateConceptForObjectProp" 
...
  •  is 
...
  •  added. 
...
  •  It 
...
  •  controls 
...
  •  whether 
...
  •  concept 
...
  •  entities 
...
  •  are 
...
  •  created 
...
  •  for 
...
  •  object 
...
  •  properties 
...
  •  defined 
...
  •  in 
...
  •  the 
...
  •  OWL 
...
  •  source. 
...
  •  The 
...
  •  default 
...
  •  is 
...
  •  false.
...
  • Loader 
...
  •  preference 
...
  •  "DatatypePropSwitch" 
...
  •  is 
...
  •  added. 
...
  •  It 
...
  •  controls 
...
  •  how 
...
  •  data 
...
  •  type 
...
  •  properties 
...
  •  are 
...
  •  converted 
...
  •  to 
...
  •  components 
...
  •  of 
...
  •  the 
...
  •  LexGrid 
...
  •  model. 
...
  •  If 
...
  •  'association' 
...
  •  is 
...
  •  specified, 
...
  •  each 
...
  •  data 
...
  •  type 
...
  •  property 
...
  •  is 
...
  •  recorded 
...
  •  in 
...
  •  LexGrid 
...
  •  as 
...
  •  an 
...
  •  entity-to-entity 
...
  •  relationship. 
...
  •  If 
...
  •  'conceptProperty' 
...
  •  is 
...
  •  specified, 
...
  •  traditional 
...
  •  LexGrid 
...
  •  properties 
...
  •  are 
...
  •  created 
...
  •  and 
...
  •  assigned 
...
  •  directly 
...
  •  to 
...
  •  new 
...
  •  entities. 
...
  •  If 
...
  •  'both' 
...
  •  is 
...
  •  specified, 
...
  •  both 
...
  •  entity 
...
  •  relationships 
...
  •  and 
...
  •  standard 
...
  •  LexGrid 
...
  •  entity 
...
  •  properties 
...
  •  are 
...
  •  generated. 
...
  •  The 
...
  •  default 
...
  •  is 
...
  •  'both'.
...
  • Namespace 
...
  •  prefixes 
...
  •  from 
...
  •  the 
...
  •  owl 
...
  •  source 
...
  •  will 
...
  •  be 
...
  •  registered 
...
  •  as 
...
  •  supportedNamespace 
...
  •  instead 
...
  •  of 
...
  •  supportedCodingScheme.
...
  • Copyright 
...
  •  information 
...
  •  is 
...
  •  no 
...
  •  more 
...
  •  hardcoded 
...
  •  into 
...
  •  the 
...
  •  loader. 
...
  •  The 
...
  •  copyright 
...
  •  should 
...
  •  be 
...
  •  specified 
...
  •  in 
...
  •  the 
...
  •  manifest.
...
  • The 
...
  •  Loader 
...
  •  will 
...
  •  not 
...
  •  hardcode 
...
  •  the 
...
  •  codingschemeName 
...
  •  as 
...
  •  NCI_Thesaurus. 
...
  •  Manifest 
...
  •  option 
...
  •  has 
...
  •  to 
...
  •  be 
...
  •  used 
...
  •  to 
...
  •  change 
...
  •  it.
...
  • Associations 
...
  •  have 
...
  •  been 
...
  •  distributed 
...
  •  among 
...
  •  two 
...
  •  containers 
...
  •  (association 
...
  •  and 
...
  •  roles)
...
  • Concepts 
...
  •  will 
...
  •  not 
...
  •  have 
...
  •  properties 
...
  •  "NCI-preferred-term" 
...
  •  and 
...
  •  "CONCEPT-NAME". 
...
  •  How 
...
  •  ever, 
...
  •  required 
...
  •  properties 
...
  •  can 
...
  •  be 
...
  •  introduced 
...
  •  by 
...
  •  using 
...
  •  preferences 
...
  •  option 
...
  •  "PrioritizedPresentationNames", 
...
  •  "PrioritizedDefinitionNames" 
...
  •  and 
...
  •  "PrioritizedCommentNames".
...
  • Complex 
...
  •  properties 
...
  •  are 
...
  •  not 
...
  •  handled 
...
  •  by 
...
  •  default 
...
  •  by 
...
  •  the 
...
  •  owl 
...
  •  loader. 
...
  •  Use 
...
  •  preference 
...
  •  option 
...
  •  "ProcessComplexProps" 
...
  •  to 
...
  •  enable 
...
  •  it.
...
  • The 
...
  •  restrictions 
...
  •  an 
...
  •  equivalent 
...
  •  class 
...
  •  are 
...
  •  connected 
...
  •  to 
...
  •  the 
...
  •  parent 
...
  •  concept 
...
  •  as 
...
  •  it 
...
  •  was 
...
  •  done 
...
  •  in 
...
  •  NCI-OWL 
...
  •  loader. 
...
  •  However, 
...
  •  if 
...
  •  strict 
...
  •  owl 
...
  •  implementation 
...
  •  is 
...
  •  required 
...
  •  (restrictions 
...
  •  an 
...
  •  equivalent 
...
  •  class 
...
  •  not 
...
  •  connected 
...
  •  to 
...
  •  the 
...
  •  parent 
...
  •  concept) 
...
  •  , 
...
  •  use 
...
  •  the 
...
  •  preference 
...
  •  option 
...
  •  "StrictOWLImplementation"
...
  • Deprecated 
...
  •  concepts 
...
  •  issue 
...
  •  has 
...
  •  been 
...
  •  resolved 
...
  •  by 
...
  •  comparing 
...
  •  "rdfResource.getRDFType().getName()" 
...
  •  with 
...
  •  the 
...
  •  literal.
...
  • Root 
...
  •  node 
...
  •  identification: 
...
  •  If 
...
  •  the 
...
  •  preference 
...
  •  option 
...
  •  "MatchRootName" 
...
  •  is 
...
  •  specified, 
...
  •  the 
...
  •  root 
...
  •  nodes 
...
  •  are 
...
  •  identified 
...
  •  from 
...
  •  it. 
...
  •  Otherwise 
...
  •  root 
...
  •  node 
...
  •  is 
...
  •  identified 
...
  •  from 
...
  •  the 
...
  •  protege 
...
  •  owl 
...
  •  api.
...
  • The 
...
  •  associations 
...
  •  "hasInstance", 
...
  •  "hasDomain", 
...
  •  "hasRange", 
...
  •  "hasDatatype" 
...
  •  and 
...
  •  "hasDatatypeValue" 
...
  •  has 
...
  •  been 
...
  •  renamed 
...
  •  to 
...
  •  "instance", 
...
  •  "domain", 
...
  •  "range", 
...
  •  "datatype", 
...
  •  "datatypevalue" 
...
  •  respectively.
...
  • LexGrid 
...
  •  data 
...
  •  streaming 
...
  •  options 
...
  •  have 
...
  •  been 
...
  •  introduced 
...
  •  for 
...
  •  effective 
...
  •  memory 
...
  •  utilizations. 
...
  •  Users 
...
  •  can 
...
  •  choose 
...
  •  the 
...
  •  memory 
...
  •  safe 
...
  •  modes 
...
  •  based 
...
  •  on 
...
  •  the 
...
  •  requirements.
...
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