dr. barry smith director national center for ontological research university at buffalo (ub) joint...
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Dr. Barry SmithDirector
National Center for Ontological ResearchUniversity at Buffalo (UB)
http://ontology.buffalo.edu/smith
Joint Doctrine Ontology
How to do biology across the genome?
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Old biology data New biology (Big, omics)
data
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The 1000 Human Genomes ProjectCancer Genome Project
1,000 Plant and Animal Reference Genomes ProjectExtreme-Environment Animal Genomes Project
International Big Cats Genome ProjectTen Thousand Microbial Genomes Project
How to link the two kinds of data?
Answer: The Gene Ontology (GO)
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A new kind of information-driven biomedical research
Uses of ‘ontology’ in PubMed abstracts
The Gene Ontology (GO) is a controlled, logically structured vocabulary to be used for consistent tagging of omics data and literature • to make these data discoverable, combinable
and analyzable with the aid of computers
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GO’s three sub-ontologies
representing types of•cellular components•molecular functions•biological processes
with logical definitions
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part_of
is_a
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Clark et al., 2005
Gene Ontology is a Living Ontology
used to tag huge amounts of data and literature (~$300 million investment)
Gene Ontology is a living ontology (editors’ version updated every night)
changes are made when gaps or errors in the GO are identified by the curators whose job is to tag data and literature with GO terms
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2004: extending GO with new ontology modules to provide representations ofproteins, species, populations, sequences, metabolism, development, diseases, symptoms, anatomy, …
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RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)Original OBO Foundry ontologies
(Gene Ontology in yellow)
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OBO Foundry grows to encompass further domains
Environments (ENVO)
Populations, Communities (PCO)
Information Artifacts (IAO)
Experiments and Investigations (OBI)
Anatomy Ontology(FMA*, CARO) Disease
Ontology (OGMS, IDO, HDO, HPO)
Information Artifact
Ontology (IAO)
Database, Document, Publication,
Citation…
Biological Process
Ontology (GO)
Ontology of Biomedical
Invesigations (OBI)
Experiment,Assay,
MeasurementProcess,
…
Cell Ontology(CL)
Subcellular Anatomy Ontology
(SAO)
Phenotypic Quality
Ontology(PATO)
Sequence Ontology
(SO)
Molecular Function Ontology
(GO)Protein Ontology(PRO)
Basic Formal Ontology (BFO)
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Joined-up biology
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Anatomy Ontology(FMA*, CARO) Disease
Ontology (OGMS, IDO, HDO, HPO)
Information Artifact
Ontology (IAO)
Database, Document, Publication,
Citation…
Biological Process
Ontology (GO)
Ontology of Biomedical
Invesigations (OBI)
Experiment,Assay,
MeasurementProcess,
…
Cell Ontology(CL)
Subcellular Anatomy Ontology
(SAO)
Phenotypic Quality
Ontology(PATO)
Sequence Ontology
(SO)
Molecular Function Ontology
(GO)Protein Ontology(PRO)
Basic Formal Ontology (BFO)
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domain neutral upper-level
ontology
domain-levelontologies
all of these ontologies are created by downward population from a common upper level ontology
http://ontology.buffalo.edu/BOBFO
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Guide to use of BFO published August 2015
John Fox, Department of Engineering Science, University of Oxford:
…As a user and teacher of ontological methods in medicine and engineering I have for years warned my students that the design of domain ontologies is a black art with no theoretical foundations and few practical principles.
…In the journey from black art to a truly scientific theory for ontology design, this book is an important milestone.
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BFO now being used in many other areas to ensure interoperability by providing common domain neutral starting point for distributed ontology creationNIF Standard Neuroscience Information Framework eagle-I ontologies Integrated Semantic Framework / CTSA
ConnectcROP / Planteome Common Reference Ontologies for PlantsUNEP Ontology Framework
United Nations Environment Programme
USGS National Map United States Geological SurveyTRIP Ontologies Federal Highway Administration (FHWA)
Transportation Research Informatics Platform (TRIP)
Common Core Ontologies (CCO)
US Army / I2WD and ARL, IARPA, JIDO, ONR, AFRL
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158 ontologies reusing BFO: http://ifomis.uni-saarland.de/bfo/users
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BFO
BFO implementations
BFO 2.0 OWL (W3C Web Ontology Language 2)
BFO 2.0 CLIF (draft) (Common Logic (CL) standard ISO 24707)
See: https://github.com/BFO-ontology/BFO
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What makes BFO unique
very large user base of ontology experts
used in a wide variety of ontology projects as a starting point for domain ontology development
very small, and correspondingly easy to learn and easy to use
can be applied in the same way to many different kinds of problem case
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Civil Military Operations Village Target Database
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IAO: Information Artifact
BFO: Spatial Region
BFO: SiteIAO: Information Artifact
BFO: Material
Entity
Ontology Support of MAMAMission Assurance through
Mission Awareness
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Ron RudnickiCUBRC Ontology Lead
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Implement BFO-based ontologies
• support Securboration in the creation of a set of ontologies in the domains of TRANSCOM and JSpOC missions
• enhance the TRANSCOM and JSpOC mission ontologies by aligning them to the doctrinal ontology modules
• create an Ontological Representation of Joint Doctrine, based on interaction with J7 Doctrine staff
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JS J7 LtCol James McArthur
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http://goo.gl/Kgm4an
Ontology work for
NextGen (Next Generation) Air Transportation SystemNational Nuclear Security Administration, DoEJoint-Forces Command Joint Warfighting CenterArmy Net-Centric Data Strategy Center of ExcellenceArmy Intelligence and Information Warfare Directorate (I2WD)
and for many national and international biomedical research and healthcare agencies
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Potential Benefits of Joint Doctrine Ontology to Doctrine Authors
- enabling the creation of flexible visualizations of how different parts of doctrine interact
- allowing a tracing of dependences between definitions that can help to ensure that changes in definitions cascade appropriately through all dependent definitions when revisions are made
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tactical control (JP1)
= def. The authority over forces that is limited to the detailed direction and control of movements or maneuvers within the operational area necessary to accomplish missions or tasks assigned.
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integration
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defense message system
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department of defense civilian
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inactive duty training (JP1)
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all of JP1
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Enable identification of logical issues in JP definitions
Component =def.• 1. One of the subordinate organizations that
constitute a joint force. (JP1)How do these subordinate organizations relate to organizations that exist also outside the joint force?
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Potential Benefits of Joint Doctrine Ontology to Doctrine Users
- enabling more effective discovery of doctrinal knowledge in forms useful for computational reasoning
- providing for each term in the DoD Dictionary its own web page, serving as a repository of usage and of revision history
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Allowing new uses for the content of doctrine
- allowing the DoD Dictionary to serve as entry point for web-based searches across multiple repositories of authoritative data (net-centricity)
- facilitating greater coordination of training and operations particularly as these involve IT systems working alongside human beings
- increasing automation of processes such as plan specification, ops assessment, BlueForce Status, and scenario development
- allowing new sorts of assessment processes, for example based on measures of adherence to doctrine, processes which may in turn give rise to new ways of computationally identifying areas where changes in doctrine may be needed
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Ontology is no longer a black art
The Joint Doctrine Ontology will enable doctrine to serve as a new source of ground truth for ontologists across DoD and IC that will help to identify gaps and errors in existing military ontologies. It will thereby support consistent agile ontology development of a sort that will counteract current tendencies towards silo-formation and failure of interoperation.
Plans as Documents
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of FILL-IN
Joint Document Hierarchy
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Joint Electronic Library http://www.dtic.mil/doctrine/i
of FILL-IN42
Joint Electronic Library http://www.dtic.mil/doctrine/i
of FILL-IN43
Joint Electronic Library http://www.dtic.mil/doctrine/i
of FILL-IN44
of FILL-IN45
of FILL-IN
is continuously and increasingly maintained in a state of satisfactory Coherence and Relevance in response to significant changes in the actual or anticipated execution environment.
From plan as document artifact to plan as smart grid artifact
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The “Living Plan”
of FILL-IN
is continuously and increasingly maintained in a state of satisfactory Coherence and Relevance in response to significant changes in the actual or anticipated execution environment (= the entire galaxy)
Give each term in JP 1-02 its own URL and its own webpageRevise doctrine not document by document but term by term
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The “Living Doctrine”
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of FILL-IN
Plan Specification Elements
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Locator: PlanSpec-ID, Times (creation, approval, validity …)Specifications of • Owner• Contributors• Approver• References (= links) to
• contained plans• to containing plans• to complementary component plans• parent(s) in doctrinal hierarchy• children in doctrinal hierarchy
• Mission value• Goal state • Predicted outcomes• Execution condition• Completion condition• Assumed world statesAssets• Actions• Dissemination
Joint Planning Ontology (JP 5-0)
• together with needed elements of CCO• will provide the framework for understanding
how these elements hang together
Plan Ontology (fragment)
Draft of 09-14-2014
Joint Doctrine Ontology initial modules
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Scope Pub ProjectMission Ontology (Capstone) JP 1 MAMA
Civil Operations JP 3-57 JSOU
Space Operations JP 3-14 MAMA
Air Mobility Operations JP 3-17 MAMA
Logistics (Sustainment) JP 4-0 AFRL Wright Patterson
Transport JP 4-01 MAMA / Securboration
Planning JP 5-0 Living Plan
Air Force Planning Annex 3-0 Living Plan
Werner SNOMED work
Basic Formal Ontology (BFO)Common Core Ontologies (CCO)Joint Publication (JP)
BFO:Continuant
BFO:Specifically Dependent Continuant
BFO:Realizable Entity
BFO:Disposition
JP 1: Accountab
ility
JP 1:Authorit
y
JP 1: Ad
ministrative
Control
JP 1: Co
mmand(1)
JP 1:Comban
t Co
mmand
JP 1:Functional
Compone
nt Comman
d
JP 1:Unified Action
JP 1:Command Authori
ty
JP 1:Control(1)
JP 1:Coordinating
Authority
JP 1:Direct
Liaison
Authorize
d
JP 1:Directive
Authority for
Logistics
JP 1:Operation
al Control
JP 1:Tactical
Control
JP 1:Training and Readiness Oversight
JP 1:Command Relationship
JP 1:Function
JP 1:National
Security
JP 1:Operational Readiness
JP 1:Task
JP 3-0:Mission(1)
JP 1:Unity of Effort
Basic Formal Ontology (BFO)Common Core Ontologies (CCO)Joint Publication (JP)
BFO:Occurrent
BFO:Process
CCO:Act
CCO:Intentional Act
CCO:Act of Artifact Processing
JP 1: Integration(3)
JP 1:Act of Delegating Authority
JP 1:Act of Exercise of Authority
JP 1:Act of Command and Control
CCO:Act of Military Force
JP 3-0:Operation(2)
JP 1:Contingency Operation
CCO:Act of Protection Warfightin
g
JP 1: Integration(1)
JP 1:Act of
Joint Forc
e
Basic Formal Ontology (BFO)Common Core Ontologies (CCO)Joint Publication (JP)
An Overview of the Common Core Ontologies (CCO)
August 26, 2015
Ron Rudnicki
716-204-5208
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CCO-related projects
• IARPA Knowledge, Discovery and Dissemination (KDD)
• Intelligence and Information Warfare Directorate (I2WD)
• JIDA Cognitive Counter – Improvised Explosive Device Signature System (C2IS2)
• ONR Tactical Cloud Reference Implementation (TCRI)• Army Research Laboratory (ARL) Controlled English
for Agile Ontology Development• Federal Highway Administration (FHWA) The
Development of a Transportation Research Informatics Platform (TRIP)
• ONR Readiness through Orchestration and Analytics in Distributed Systems (ROADS)
• Produce ontologies into which any data source can be translated– Facilitate query and analytics across data
sources
• Data sets will cover a wide variety of domains, some unexpected– Ontologies must adapt to change and
extension
• No single privileged view of the data– Ontologies must serve the needs of users
having diverse interests
Objective and Challenges
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Use of a Proven Methodology
• The Open Biological and Biomedical Ontologies (OBO) Foundry– Consortium of groups pursuing a strategy
to overcome the “siloing” of data– Lessons learned from over $100M of
investment in ontology development– Affiliations include:
• Gene Ontology• Biomedical Informatics Research Network• National Center for Biomedical Ontology• Clinical and Translational Science Awards
The Realist Methodology
Uses a Proxy of the Original Source as the Common Standard
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Prima facie choice for a common standard
Provides an objective means for settling disputes
Adds the constraint that every assertion within an ontology must be true
Modular Architecture Limits Ontologies to Workable Sizes
One Axis of Modularization is Level of Generality
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Content and structure is inherited from higher levels
Upper OntologiesDescribe the Structure
of the World
Mid-Level OntologiesAdd General Content
to the Structure
Domain Level Ontologies
Add Content Relevant to a Community
Upper and mid-level ontologies are stable and of manageable scale
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An Informal View the BFO Classifications of Entities
Attribute
Process
SiteTemporal Region
Physical Object
has
participates in
occurs atoccurs on
Site
contained in
Second Axis of Modularization is Content
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The Design of the Common Core Ontologies
• BFO = domain-neutral categories of objects and processes
• CCOs: a set of vocabulary modules that can describe objects and processes that are common to many domains of interest, defined ontologically through downward-population from BFO
• Domain Ontologies• Doctrine Ontologies
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The Common Core and Domain Ontologies
Basic Formal Ontology (BFO)
Extended Relation Ontology
Time Ontology
Quality Ontology
Information Entity
Ontology
Geospatial Ontology
Event Ontology Artifact
OntologyAgent
Ontology
Emotion Ontology
Ethnicity Ontology
Occupation Ontology
Hydrographic Feature
Ontology
Physiographic Feature
Ontology Currency Unit
OntologyUnits of Measure Ontology
Curriculum Ontology
Citizenship Ontology
Upper Ontology:
Common Core Ontology:
Domain Ontology:
Watercraft Ontology
Sensor Ontology Agent
Information Ontology
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Tests to Ensure Conformance of Domain Ontologies
• Inconsistency – A class is identified as being uninstantiable
• Semantic Smuggling – A class or property is reused with changed content
• Multiple Inheritance – A class or property is asserted to be a subclass of more than one superclass
• Taxonomy Overloading – A class or property is related to its parent by a relationship other than subclass
• Containment – A class or property is not a child of any class or property of the imported ontologies
• Conflation – A class or property includes information model assertions that are not true of the domain
• Logic of Terms – A class or property is a set-theoretic combination of other classes or properties
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Unity of Effort, a Common Picture of Situation, and Accomplishing the
Enterprise’s Mission – Not Just Program or Unit Missions
F:\Marketing\US Army\ASA-ALT - COE\ASA ALT-021 Edwards Elephant.ppt
August 24, 2015
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“There is still a tendency in each separate unit…to be a one-handed puncher. By that I mean that the rifleman wants to shoot, the tanker to charge, the artilleryman to fire…That is not the way to win battles. If the band played a piece first with the piccolo, then with the brass horn, then with the clarinet, and then with the trumpet, there would be a hell of a lot of noise but no music. To get the harmony in music each instrument must support the others. To get harmony in battle, each weapon must support the other. Team play wins. You musicians of Mars must not wait for the band leader to signal you…You must each of your own volition see to it that you come into this concert at the proper place and at the proper time…”
General George S. Patton, Jr., 8 July1941, address to the men of the 2nd
Armored Division, The PattonPapers, Vol. II, 1974
Opening Quotation in Chapter 1, “Synchronization”,Field Manual (FM) 3-09.31 /
Marine Corps Reference Publication (MCRP)3-16C, Tactics, Techniques, and Procedures
For Fire Support for the Combine Arms Commander,
General George Patton
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Insights into Data and Information Interoperability –From Indian Folklore
Joint Doctrine
JIE
GFM-DI
NIEM
Ontology is the consistent representation of reality across fields of endeavor, organizations, and IT systems. Ontology includes concepts and methods for developing such
representations. Today, DoD is participating in multiple efforts, some of which are represented above as blind men feeling portions of the DoD information elephant. Each effort is seeking to
produce consistent representations of reality with its individual concepts and methods. This produces inconsistent representations of reality. Better to coordinate early than reconcile
later.
DoDAF