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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

3/

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

rudnicki@cubrc.org

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