LexBIG Release Overview Aug 21, 2008

LexBIG Context Project Goals for Sept –Incremental point release of LexBIG infrastructure to support EVS activities –caGrid deployment of LexEVS services and submission for Silver Certification review –Transition ownership of EVS code 3-4 month development cycle Support/Bug Fixes/GForge backlog Select new features

LexEVS Grid Services EVS Services (e.g. Distributed LexBIG) LexBIG Java API LexBIG Context LexGrid Model & Storage Browsers and Applications

Conceptual Overview LexBIG Java API LexGrid Model & Storage

API/Runtime GForge #15015: Fix to correctly match the special case 'conceptCode' property when mixed with other property names in a single restriction.GForge #15015 GForge #15071: Make copyright information accessible without requiring EVS secure login.GForge #15071 Misc fixes: e.g. Fix hierarchy path to root convenience method to ensure the resolve flag is recognized when populating concept details. Model support: Internal refactoring of database and index code to support changes to LexGrid and LexBIG models. changes MultiDatabase support: Fixed cursor problem when running against Oracle. BioPortal Support: Fix to ResourceManager mapping of code system name and version identifiers in order to prevent errors disambiguating coding schemes that carry the same name but different version identifiers.Fix Added resolve methods to CodedNodeSet allowing option to return results without fully resolving concept references, thereby eliminating database access (resolves from Lucene indexes only).

Information Model, Load, Export GForge #8670 : Add support to import Standardized MedDRA Query (SMQ) attributes as association qualifiers.GForge #8670 GForge #8671 : Recognize additional complex properties, represented as embedded XML fragments, during import of NCI OWL sources.GForge #8671 GForge #12357: Provide externally configurable preferences for loaders accepting optional parameters, either as a program generated object or XML file capable of validation against a formal schema (XSD).GForge #12357 GForge #12997: Fix to remove extraneous addition of 'is_a' as source on load of OWL sources.GForge #12997 GForge #13175: Fix to propertyLink creation on UMLS load to honor representational form on import of AUI text.GForge #13175 GForge #13193: Allow optional specification of a manifest file (xml) on all loaders (other than native LexGrid XML) to allow customization of coding scheme metadata. Manifests can be applied at time of load as part of a post- load process.GForge #13193

Manifest Example

Information Model, Load, Export GForge #13501: New loader for direct import from HL7 RIM database.GForge #13501 GForge #13565: Utilize MRRANK RRF file during load of LOINC (and potentially other) UMLS sources.GForge #13565 GForge #13954: Fix to populate SupportedProperty mapping on UMLS load.GForge #13954 GForge #14252: Add ability to load and query NCI Metathesaurus history.GForge #14252 GForge #14483: Fix to populate SupportedHierarchy mapping on UMLS load.GForge #14483 GForge #14485: Add support on load of the UMLS Semantic Network toGForge #14485 optionally import inferred relationships, defined through inheritance. GForge #14767: Import all synonyms on OBO load.GForge #14767 BioPortal Support: Various fixes to OBO export; e.g. fixed OBO parsing to correctly extract properties based on source and subref information. Research Activity: Deliver prototype of new ‘generic’ OWL loader based on Protégé (provided in for evaluation purposes), for non-NCI OWL sources. Incorporate model changes as introduced for ongoing support, silver submission, and prototype OWL functionality.model changes

HL7 Import

GUI and Command Line Tools GForge #12572: Enhance ProfileScheme program example.GForge #12572 GForge #12995: Add database information to the GUI display.GForge #12995 Provide GUI options and command scripts to support the new HL7 RIM and prototype OWL loaders. Allow options (on both GUI and command scripts) for loaders to accept an optional manifest file to be applied during the load. Also provide GUI option and administrative script to apply a manifest to an already loaded vocabulary. Allow options (on both GUI and command scripts) for loaders to accept preferences where applicable.

Build & Test GForge #16155: Create manifest XML for NCI test sources based on changes to the manifest XSD schema.GForge #16155 Provide simplified packaging and distribution of LexBIG 1st party code as a single jar file. Enhance JUnit tests for new functions and improved coverage of previous functions (e.g. hierarchy API). Update example and test files (e.g. Automobiles.xml) as required to reflect model changes. Refreshed 3rd party jar files as required for currency.