1. Joint Doctrine Ontology
Dr. Barry Smith
Director
National Center for Ontological Research
University at Buffalo (UB)

2. How to do biology across the genome?
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sequence of X chromosome in baker’s yeast

3. Old biology data New biology (Big, omics) data
The 1000 Human Genomes Project
Cancer Genome Project
1,000 Plant and Animal Reference Genomes Project
Extreme-Environment Animal Genomes Project
International Big Cats Genome Project
Ten Thousand Microbial Genomes Project
The sequencing floor in BGI Hong Kong, showing the Illumina Hiseq 2000 sequencers

4. How to link the two kinds of data?
Answer: The Gene Ontology (GO)

5. A new kind of information-driven biomedical research
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
Uses of ‘ontology’ in PubMed abstracts

6. GO’s three sub-ontologies
representing types of
cellular components
molecular functions
biological processes
with logical definitions

7. part_of
is_a
The gene ontology consortium develops ontologies and makes annotation of gene products to those ontologies. The ontologies are databases containing sets of biological processes, molecular functions, and cellular components and the relationships between them. Annotators within the consortium use these ontologies to categorise gene products. During my talk today I’m going to explain about the uses of GO and give a more detailed explanation of the ontolgoies and of the system of annotation. Then Harold Drabkin is going to talk in more detail about annotation and about how you can submit annotations of your own gene products of interest.
Clark et al., 2005

8. 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

9. 2004: extending GO with new ontology modules to provide representations of
proteins, species, populations, sequences, metabolism, development, diseases, symptoms, anatomy, …

10. Original OBO Foundry ontologies
RELATION
TO TIME
GRANULARITY
CONTINUANT
OCCURRENT
INDEPENDENT
DEPENDENT
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
Anatomical Entity
(FMA, CARO)
Organ
Function
(FMP, CPRO)
Phenotypic Quality (PaTO)
Biological Process
(GO)
CELL AND CELLULAR COMPONENT
Cell
(CL)
Cellular Component
(FMA, GO)
Cellular Function
MOLECULE
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
Molecular Process
Original OBO Foundry ontologies
(Gene Ontology in yellow)

11. OBO Foundry grows to encompass further domains
Environments (ENVO)
Populations, Communities (PCO)
Information Artifacts (IAO)
Experiments and Investigations (OBI)

12. Basic Formal Ontology (BFO)
Joined-up biology
Basic Formal Ontology (BFO)
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,
Measurement
Process,
Cell Ontology
(CL)
Subcellular Anatomy Ontology (SAO)
Phenotypic Quality
Ontology (PATO)
Sequence Ontology
(SO)
Molecular Function Ontology
(GO)
Protein Ontology
(PRO)
* = dedicated NIH funding

14. Basic Formal Ontology (BFO)
all of these ontologies are created by downward population from a common upper level ontology
Basic Formal Ontology (BFO)
domain neutral upper-level
ontology
domain-level
ontologies
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,
Measurement
Process,
Cell Ontology
(CL)
Subcellular Anatomy Ontology (SAO)
Phenotypic Quality
Ontology (PATO)
Sequence Ontology
(SO)
Molecular Function Ontology
(GO)
Protein Ontology
(PRO)
* = dedicated NIH funding

15. Guide to use of BFO published August 2015

16. 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.

17. BFO now being used in many other areas to ensure interoperability by providing common domain neutral starting point for distributed ontology creation
NIF Standard
Neuroscience Information Framework
eagle-I ontologies
Integrated Semantic Framework / CTSA Connect
cROP / Planteome
Common Reference Ontologies for Plants
UNEP Ontology Framework
United Nations Environment Programme
USGS National Map
United States Geological Survey
TRIP Ontologies
Federal Highway Administration (FHWA) Transportation Research Informatics Platform (TRIP)
Common Core Ontologies (CCO)
US Army / I2WD and ARL, IARPA, JIDO, ONR, AFRL

18. 158 ontologies reusing BFO: http://ifomis.uni-saarland.de/bfo/users

19. BFO

20. BFO implementations BFO 2.0 OWL (W3C Web Ontology Language 2)
BFO 2.0 CLIF (draft) (Common Logic (CL) standard ISO 24707)
See:

21. 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

22. Civil Military Operations Village Target Database

23. IAO: Information Artifact IAO: Information Artifact
BFO: Spatial Region
IAO: Information Artifact
BFO:
Material
Entity
BFO: Site

24. Ontology Support of MAMA Mission Assurance through Mission Awareness
Ron Rudnicki
CUBRC Ontology Lead
Ontology Support of MAMA Mission Assurance through Mission Awareness

25. 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

26. JS J7 LtCol James McArthur

27.
Ontology work for
NextGen (Next Generation) Air Transportation System
National Nuclear Security Administration, DoE
Joint-Forces Command Joint Warfighting Center
Army Net-Centric Data Strategy Center of Excellence
Army Intelligence and Information Warfare Directorate (I2WD)
and for many national and international biomedical research and healthcare agencies

28. 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

29. 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.

30. integration

31. defense message system

32. department of defense civilian

33. inactive duty training (JP1)

34. all of JP1

35. 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?

36. 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

37. 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

38. 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.

39. Plans as Documents

40. Joint Document Hierarchy

41. Joint Electronic Library

42. Joint Electronic Library

43. Joint Electronic Library

46. From plan as document artifact to plan as smart grid artifact
The “Living Plan”
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

47. The “Living Doctrine”
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 webpage
Revise doctrine not document by document but term by term

48. Military Doctrine feeds into Military Planning
Doctrine provides an authoritative body of consistent* statements on
how military forces conduct (joint) operations
how military plans are to be constructed
provides a common lexicon
which must be used by military planners and leaders
which will be what those charged with execution of military plans will anticipate and understand
will allow ingestion and consistent aggregation of data concerning lessons learned
*ideally

49. Common lexicon For people (people need to understand each other)
Training (Developing doctrine, …)
Planning (Joint operations, SOPs, …)
Executing (C2, …)
Reporting, Outcomes evaluation, lessons learned
For machines
Compiling data (e.g. results of testing …)
Sharing of data (Compiling lessons learned …)
Collective inferencing

51. Plan Specification Elements
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

52. Joint Planning Ontology (JP 5-0)
together with needed elements of CCO
will provide the framework for understanding how these elements hang together

53. Plan Ontology (fragment)
Draft of

60. What is the living plan?
Plan creation and maintenance system Living plan Tactical (…) plan outputs for execution

61. Compare
Language creation and maintenance system (schools, …) The English language Utterances, written linguistic outputs

62. Compare
Price maintenance and creation system Prices (of 1 Euro, of a beer in a Paris bar …) Individual acts of exchange

63. Compare
The law creation and maintenance system (the legislature, local courts…) The body of law Individual legal and police actions

64. What is the living plan?
The plan creation and maintenance system The living plan (analogue of the body of law) Tactical (…) plan outputs for execution (analogues of utterances, of speakers of a language, of judges …)

65. Joint Doctrine Ontology initial modules
Scope
Pub
Project
Mission Ontology (Capstone)
JP 1
MAMA
Civil Operations
JP 3-57
JSOU
Space Operations
JP 3-14
Air Mobility Operations
JP 3-17
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

66. Werner SNOMED work

67. Basic Formal Ontology (BFO)
Common Core Ontologies (CCO)
Joint Publication (JP)

68. Basic Formal Ontology (BFO) Common Core Ontologies (CCO)
BFO:Continuant
BFO:Specifically Dependent Continuant
BFO:Realizable Entity
BFO:Disposition
JP 1: Accountability
JP 1:Authority
JP 1: Administrative Control
JP 1: Command(1)
JP 1:Combant Command
JP 1:Functional Component Command
JP 1:Unified Action
JP 1:Command Authority
JP 1:Control(1)
JP 1:Coordinating Authority
JP 1:Direct Liaison Authorized
JP 1:Directive Authority for Logistics
JP 1:Operational 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)

69. JP 3-0:Operation(2) Basic Formal Ontology (BFO)
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 Warfighting
JP 1: Integration(1)
JP 1:Act of Joint Force
Basic Formal Ontology (BFO)
Common Core Ontologies (CCO)
Joint Publication (JP)

73. An Overview of the Common Core Ontologies (CCO)
August 26, 2015
Ron Rudnicki

74. 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)

75. Objective and Challenges
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

76. Design Choices - Linked Data
Every Data Source is Linked to Every Other
Expensive to build
and maintain
Locating information
is difficult
Queries and analytics are run on ad hoc vocabularies

77. Design Choices - Mapping to a Standard
Every Data Source is Linked through a Common Standard
Greatly reduces the number of mappings
Queries and analytics are operating on vocabularies having same structure
Common Standard Vocabulary
Standard lacks objective justification
The common standard becomes large and monolithic

78. 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

79. The Realist Methodology
Uses a Proxy of the Original Source as the Common Standard
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

80. Ground Truth Based on Standards
Partial List of Doctrine and Standards Used
Basic Formal Ontology (BFO)
DOD Dictionary of Military and Associated Terms (JP 1-02)
Operations (FM 3-0)
Multinational Operations (JP 3-16)
Counterinsurgency (FM 3-24)
International Standard Industrial Classification of all Economic Activities Rev.4 (ISIC4)
Universal Joint Task List (CJSCM C)
Weapon Technical Intelligence (WTI) Improvised Explosive Device IED Lexicon
JC3IEDM
Information Artifact Ontology (IAO)
Phenotype and Trait Ontology (PATO)
Foundational Model of Anatomy (FMA)
Regional Connection Calculus (RCC-8)
Allen Time Calculus
Wikipedia

81. Modular Architecture Limits Ontologies to Workable Sizes
One Axis of Modularization is Level of Generality
Upper Ontologies
Describe the Structure of the World
Upper and mid-level ontologies are stable and of manageable scale
Content and structure is inherited from higher levels
Mid-Level Ontologies
Add General Content to the Structure
Domain Level Ontologies
Add Content Relevant to a Community

82. An Informal View the BFO Classifications of Entities
Second Axis of Modularization is Content
Process
participates in
Physical Object
occurs on
occurs at
contained in
Temporal Region
Site
has
Site
Attribute

83. 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

84. The Common Core and Domain Ontologies
Basic Formal Ontology (BFO)
Upper Ontology:
Common Core Ontology:
Extended Relation Ontology
Domain Ontology:
Event Ontology
Agent Ontology
Quality Ontology
Artifact Ontology
Geospatial Ontology
Time Ontology
Ethnicity Ontology
Hydrographic Feature Ontology
Information Entity Ontology
Curriculum Ontology
Occupation Ontology
Physiographic Feature Ontology
Currency Unit Ontology
Citizenship Ontology
Units of Measure Ontology
Emotion Ontology
Sensor Ontology
Watercraft Ontology
Agent Information Ontology

86. The Common Core Ontology Development Methodology
The Common Core Ontologies contain content to translate a significant portion of application data sources. For the remainder, ontologies that extend from the Common Core are developed. As additional application data sources are introduced the existing extension ontologies are reused whenever possible creating an ever diminishing need for new ontology content.

87. Planned Evolution of Ontologies
A limited number of upper and mid-level ontologies are carefully managed
Domain ontologies are developed by subject matter experts and tested by automated procedures
Content is pushed from domain ontologies to mid-level ontologies as usage levels warrant

88. 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

89. Unity of Effort, a Common Picture of Situation, and Accomplishing the Enterprise’s Mission – Not Just Program or Unit Missions
August 24, 2015
F:\Marketing\US Army\ASA-ALT - COE\ASA ALT-021 Edwards Elephant.ppt

90. General George Patton
“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 July
1941, address to the men of the 2nd
Armored Division, The Patton
Papers, Vol. II, 1974
Opening Quotation in Chapter 1, “Synchronization”,
Field Manual (FM) /
Marine Corps Reference Publication (MCRP)
3-16C, Tactics, Techniques, and Procedures
For Fire Support for the Combine Arms Commander,

91. Insights into Data and Information Interoperability –
From Indian Folklore
Joint Doctrine
GFM-DI
JIE
NIEM
DoDAF
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.