Vocabulary Knowledge

Center

Adoption Stories of the NCI Semantic Infrastructure

(and VKC Update)

Robert Freimuth, PhD

October 20, 2009

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

Vocabulary Knowledge Center

• Support for vocabulary authoring and management tools• Wiki site• Documentation and training• Community Outreach• Discussion forums• Bug reports, feature requests• Source code repository

• Supported software• LexGrid, LexBIG, LexEVS• LexWiki• NCI Protégé

• Coordinated support for NCI CBIIT tools• E.g., caCORE, caDSR

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

NCRIUK National Cancer Research Institute

•Partnership of more than 20 public and private organizations

•Goal: Promote data sharing• Data standards• Forming alliances• Developing an IT infrastructure

•Figure showing that NCRI connects to NHS, EMBL-EBI, NCIN, and caBIG. It also shows that NCRI hopes to encourage data sharing by cultural changes and by developing the ONIX informatics platform

Modified from A. Hogg, NCRI

Willingness to share

Ability to share

Cultural Change through Community Alliances

Help to build a Cancer Informatics Platform

via ONIX

NCRI ONIXOncology Information Exchange

•Released July 2009

•Adding connected resources

•Figure showing how ONIX connects to caBIG resources (data, vocabulary services), EBI resources (Elixir, data services), NCRI research capability programme (data sources), CancerGrid, and others (imaging and pathology, MRU, British library)

Modified from A. Hogg, NCRI

• Built using caBIG technology• caCORE, Introduce, caGrid, LexEVS

ONIX and Vocabularies

• ONIX uses the LexEVS 5.0 terminology server• NCI-Thesaurus• Gene Ontology

• ONIX QuickSearch• Federated queries across databases• Find and add synonyms, spelling variants, preferred terms to queries

• Working toward creation of a federated vocabulary service• Encourage publication of content

• Exploring authoring tools (e.g., LexWiki)

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

OpenPHIOpen Personalized Health Informatics

• Private bioinformatics startup

• Mission• Build a system to enhance every family's health• Reduce barriers to health databases, publications, and knowledge

• Focuses on the integration of existing tools• Open Access, Open Source, Open Data

• Products• HealthAlbum: Personal health record• HealthMining: Data mining of biomedical repositories• HealthLibrarian: Semantic search engine

OpenPHI HealthLibrarian

•Public data sets loaded into a single data warehouse

• Parsing and tagging performed by NIH/NLM Lexicon tools

• Indexing by Apache Lucene

•Data sources• Medline

• FDA

• NIH grants

• BioMed Central

• Clinical Trials

• Drugs

• Care Providers

• etc

•Figure showing how multiple data sources form the digital repository, and are mapped to terms from the NCI-Thesaurus

Modified from J. Lacal, OpenPHI

OpenPHI HealthLibrarian

•LexEVS used to serve NCI-T• Uses synonyms and term

normalization

•Cloud computing• Amazon EC2• LAMP (Linux, Apache,

MySQL, PHP & Python)

•Version 3 in development• Present information from

multiple viewpoints

•Figure showing how the HealthLibrarian provides different views: 1) community view (public health db, air quality, substance releases), 2) anatomical view (system, organ, tissue), 3) biological view (gene, protein), 4) chemical view (drug, compound). All views connect to a disease.

Modified from J. Lacal, OpenPHI

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

i2b2Informatics for Integrating Biology and the Bedside

• NIH-funded National Center for Biomedical Computing

• Building a "scalable computational framework to address the bottleneck limiting the translation of genomic findings and hypotheses in model systems or organisms relevant to human health"

• New computational paradigms and methodologies• Focus on three polygenic diseases (airway disease, hypertension, type 2 diabetes

mellitus) and one monogenic model characterized by polygenic modifiers (Huntington’s Disease)

• Cells compose the hive• Interoperable services with web interfaces• Minimal computable semantics• Deep semantics are defined by each cell and interpreted by the user

i2b2 Database

•Concept table design• Data is loaded into a static data model• Each "name" is a hierarchical string of concepts

•Figure showing the concept table design. There are 5 physical tables in the design; 4 each connect to a common central table.

Modified from R. Wynden, Ontology Mapper

Ontology Mapper

• The Ontology Mapper Cell is a general purpose instance mapper• Translates messy local data into one or more standard formats (ontologies)• Translates local semantics to standard semantics (e.g., NCI-T)

• Local instances of LexEVS• E.g., from a given cell in the hive to ISO 11179 data model

• caGrid cell exposes i2b2 resources on caGrid

• Maps are created in a Protégé Prompt plug-in and can be shared over HL7 CTS II both as open source or as commercially sold assets

• Can be loaded into caDSR

• Ontology Mapper shifts resources from IT (application building) to handling user requests for data access via dynamically constructed views of data (Data Repository Analysts)

• Mapped on demand

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

CDISCClinical Data Interchange Standards Consortium

• Global, open, multidisciplinary, non-profit organization

• Established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata

• Mission: To develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare.

• >230 Members

• Need to harmonize data elements across organizations• Genzyme, GSK, Eli Lilly, Mayo Clinic, MD Anderson

CSHARECDISC Shared Health and Research Electronic Library

• Based on LexWiki• Collaborative terminology authoring platform based on Semantic MediaWiki

• Enables harmonization of data elements• Different sources• Different terminologies

• Features• Categorize, browse, and search data elements• Group related data elements• Propose harmonized data elements

• More to come!• Metadata registries: Thursday Oct 22, 11:15-12:15 (G. Jiang)• Live demonstration by the Vocabulary Knowledge Center (TBD)

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

Upcoming Presentations

• International Semantic Web Conference• A RDF-base Normalized Model for Biomedical Lexical Grid (C.Tao, et al)• LexRDF Model: An RDF-based Unified Model for Heterogeneous Biomedical

Ontologies (C.Tao, et al)

• AMIA Annual Symposium• caBIG® Vocabulary Knowledge Center (R. Freimuth, et al)• Comparing and Evaluating Terminology Services APIs: RxNav, UMLSKS, and

LexBIG (J. Pathak, et al)• Measuring Semantic Richness of Biomedical Ontologies Using OWL Constructs

(G.Jiang, et al)• An Approach for Representing Ontologies Modeled in LexGrid in OWL (C.Tao, et

al)• The Enterprise Data Trust at Mayo Clinic: A semantically integrated warehouse of

biomedical data (C.Chute, et al)

Tool ReleasesNCI Protégé 1.4

• Release scheduled for October 2009• Last major release of the NCIEditTab Protégé plug-in

• Enhancements• Refactoring for maintenance and performance• Added ability to use negation ("NOT") in queries• Added Lucene Match, Property Present, and Property Absent search types

• Significantly extended flexibility of lexical queries• Export to spreadsheet includes super classes

Tool ReleasesLexEVS 5.1

• Release scheduled for December 2009

• Enhancements• Support for content in RRF (e.g., NCI Meta-Thesauraus)• Value domain support (pick lists)• Query performance and behavior enhancements• Improved loader framework (modularity)• BDA (Build and Deployment Automation) support for deployment to remote servers

LexEVS 5.0 Boot Camp

• November 17-19, 2009

• NCI CBIIT Training Facility (Rockville, MD)

• Target audience• Intermediate to advanced LexEVS users• Users migrating from EVS 3.x or LexEVS 4.x

• Goals• Understand new components of the LexGrid model• Utilize the API in local, distributed, and grid environments• Install and configure LexEVS 5.0 (all 3 environments)• Learn about the extensions, loaders, and convenience methods• Learn how to use the GUI

• See the VKC wiki for more information

LexAjax

• Develop an Ajax interface for LexEVS

• Project goals• Develop an Ajax based service based on the LexEVS API and LexGrid data model

that can support a variety of web based auto completion, dropdown forms, etc.• Develop a basic set of graphics widgets.• Integrate the graphics widget into LexWiki to provide a set of tools that can be used

with Semantic Forms and other wiki based terminology access tools.

• Benefits include• Further integration of semantic infrastructure• Enhanced capability to serve terminology content to web applications

• Release scheduled for December 2009

Special Projects

• Terminology Index• Expanding the list of terminologies• Soliciting use cases and experiences

• Standards Organizations• Coordinating with VCDE effort• Terminology focus (e.g., HL7 CTS2)

• NCI Semantic Infrastructure• Requirements• Support for the Concept of Operations

Agenda

• Introduction

• NCRI ONIX

• OpenPHI

• CTSA Ontology Mapper

• CSHARE

• VKC Activities and Projects

• Discussion

Feedback and Requests

• We want your feedback to guide our future activities!• Do you want the VKC to provide specific products or resources? Tell us!

• Figure showing the location of the "feedback" link on the Vocabulary Knowledge Center web page (in the navigational bar under "vocabkc contents")

Contact theVocabulary Knowledge Center

•Visit our web site online• https://cabig-kc.nci.nih.gov/Vocab/

KC

•Post a question to the discussion forums

• https://cabig-kc.nci.nih.gov/Vocab/forums

•Send us an e-mail• vocabkc@mayo.edu

•Figure: Screen shot of the Vocabulary Knowledge Center home page (for visual interest only)

Materials are available at the registration table