Terminology Tooling - Mayo Clinic Informatics

Report
CIMI “Terminology” Meeting
Agenda
• Terminology Tooling Proposal
• Information modelling tooling (requirements,
options and selection process) (if time)
• Tooling framework and other tooling
requirements (if time)
Terminology Tooling
Terminology Tooling Puzzle
Query and Browsing
Programmatic API
Collaborative Authoring
Issue Tracking
Terminology Tooling Puzzle
Query and Browsing
– Concepts, Value Sets, Maps, etc.
Web Browser
Snow OWL Lite
CTS2 Clients and Widgets
itServer (?)
(other)
Web Protege
Terminology Tooling Puzzle
Programmatic API (REST or SOAP?)
• Snow OWL Server
• Ocean’s terminology server
• Apelon DTS
• CTS2
• SPARQL
• SQL
• (other?)
• (SNOMED Query Specification)
Terminology Tooling Puzzle
Collaborative Authoring
• IHTSDO Workbench / Kaiser Extensions
– (hosting?)
– SVN
• Snow Owl
Refset Creation
• Snow OWL
• IHTSDO refset creation tool (for SNOMED refsets)
• IHTSDO Workbench / Kaiser Extensions
• (others)
Remembering our Vision…
Application
Interface
Service
Data
...
What Is Needed to Create a New Paradigm?
• Standard set of detailed clinical data
models coupled with…
• Standard coded terminology
• Standard API’s (Application Programmer
Interfaces) for healthcare related services
• Open sharing of models, coded terms,
and API’s
• Sharing of decision logic and applications
Information Model Ideas
CEMs
DCMs
CDA
Templates
Repository
of Shared
Models in
a Single
Formalism
openEHR
Archetypes
CEN
Archetypes
# 10
LRA
Models
V2 “|”
CEM
Standard
LRA
Terminologies
V2 XML
HTML
V3 XML
V3 Next
Realm
Realm
Specific
UML
Realm
Translators
Specific
Specializations
Realm
Specific
Specializations
Realm
Specific
Specializations
Specific
Specializations
Specializations
CMETs, HMDs
RMIMs
Initial Loading of Repository
Translators
Translators
ADL
CDA
OWL
SOA
CDISC
SHARE CEN Payload
Archetype
Information Model Ideas
CEMs
DCMs
CDA
Templates
Repository
of Shared
Models in
a Single
Formalism
openEHR
Archetypes
CEN
Archetypes
# 11
LRA
Models
V2 “|”
CEM
Standard
LRA
Terminologies
V2 XML
HTML
V3 XML
V3 Next
Realm
Realm
Specific
UML
Realm
Translators
Specific
Specializations
Realm
Specific
Specializations
Realm
Specific
Specializations
Specific
Specializations
Specializations
CMETs, HMDs
RMIMs
Initial Loading of Repository
Translators
Translators
ADL
CDA
OWL
SOA
CDISC
SHARE CEN Payload
Archetype
Proposal
Core RF2 Tables
RF2
Tables
Proposal
Add Refset Editor Extensions
RF2
Tables
Refset
Editor
Extension
Workflow management extensions installed via editor
Proposal
Add CIMI Specific Extensions
RF2
Tables
Refset
Editor
Extension
CIMI
Specific
Extensions
Where possible, would be RF2 Refset Format
Would include non-SCT value sets and content links
Proposal
Host on internet service
RF2
Tables
Refset
Editor
Extension
CIMI
Specific
Extensions
Could be hosting organization, Amazon Cloud, Mayo (via Amazon Cloud)
Basic security and backup
Mirrors would be possible (or even desirable?)
Refset Editor
RefsetEditor
RefsetEditor
RefsetEditor
RF2
Table
s
Refs
et
Edit
or
Exte
nsio
n
CIMI
Specif
ic
Exten
sions
Issues: RefsetEditor doesn’t actually (directly) create RF2 Content!
RefsetEditor takes RF2 Tables as input
Still a tad on the buggy side but…
(Both issues are fixable but will take time)
Terminology Services
CTS2 Server
RF2
Table
s
Refs
et
Edit
or
Exte
nsio
n
CIMI
Specif
ic
Exten
sions
CTS2 Server
Other Server
MySQL Client
Servers could be:
• centrally hosted
• client based
Authoring Tools
IHTSDO
Workbench
IHTSDO
Workbench
Snow Owl
WB
Backing
Store
RF2
Table
s
Refs
et
Edit
or
Exte
nsio
n
QA
Subsumption
, Tooling
CIMI
Specif
ic
Exten
sions
Mechanisms of Interchange
• Direct SQL Queries
• CTS2 or other API’s
• Delta import and export
• Complete file import and export
IM Tooling
Proposal
(Shorter Term)
• Terminology “model” and backing store is
enhanced RF2
• Exchange can be one of:
– Direct update to RF2 data base (trusted apps)
– RF2 Delta Imports (and Exports)
– CTS2 Update Packages
• Multiple authoring tools can be used depending
on environment
• Authoring tools are responsible for
synchronization w/ backing store
– May involve scripting and work in some cases
Proposal
(Shorter Term)
• Clients may
– Access SQL tables directly
• We may augment with Lucene and other helpers
– Use CTS2 API
– Use any other API that works against backing store
Possible Enhancement?
Triple
Store
RF2
Tables
Refset
Editor
Extension
CIMI
Specific
Extensions
Snow Owl
• B2i could provide:
– Terminology server to meet the REST and web
browsing requirement and export CIMI data
– Second server to support collaborative authoring
& issue tracking
– Snow Owl authoring license restricted to CIMI’s
namespace, and
– Support and maintenance for the above.
Topic 2
Information Modeling
• Logical Model Designer (Snow Owl) and/or
– Subset of AOM (LOM) w/ additional constructs
– Serialization Ecore Classes (LOM XMI file)
• Need LOM transformation tools
• MDHT UML tooling and/or
– Needs significant work to produce ADL 1.5
• Ocean ADL workbench and/or
– Needs significant work to edit ADL 1.5
• Excel + duct-tape and/or
• Mindmaps + duct-tape and/or
• Others?
• Set of “big ticket” (must have) requirements
for modeling tools in order to get started
• Separate the capabilities of the tools from the
underlying storage formats
Topic 2
Information Modeling
• Question: Can we take an approach similar to
that proposed for Terminology?
Information Model Ideas
CEMs
DCMs
CDA
Templates
Repository
of Shared
Models in
a Single
Formalism
openEHR
Archetypes
CEN
Archetypes
# 26
LRA
Models
V2 “|”
CEM
Standard
LRA
Terminologies
V2 XML
HTML
V3 XML
V3 Next
Realm
Realm
Specific
UML
Realm
Translators
Specific
Specializations
Realm
Specific
Specializations
Realm
Specific
Specializations
Specific
Specializations
Specializations
CMETs, HMDs
RMIMs
Initial Loading of Repository
Translators
Translators
ADL
CDA
OWL
SOA
CDISC
SHARE CEN Payload
Archetype
Information Modeling
• What would be the “store” and medium of
interchange?

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