IAO-Core Towards a General-Purpose, Top-Level Information Artifact Ontology Barry Smith University at Buffalo USA Tatiana Malyuta New York City College of Technology USA

Outline Background Objectives Basics of the Approach – Representative dimensions of Information Artifacts – Non-representative dimensions of Information Artifacts BFO Foundation – Information Artifacts and Copyability – Generic dependence and concretization Foundational Information Entities 2

Information Artifact Ontology (IAO) IAO was created by ontologists working in biomedicine artifact-ontology/ artifact-ontology/ Terms of the ontology were reused in multiple ontologies (the following slide). IAO is, after the Basic Formal Ontology (BFO) [1] (and before the Gene Ontology) the most often re-used ontology among all ontologies in the NCBO Bioportal. 3

Ontologies Using IAO Adverse Event Reporting Ontology (AERO) Bioinformatics Web Service Ontology (OBIWS) Biological Collections Ontology Chemical Methods Ontology (CHMO) Cognitive Paradigm Ontology (COGPO) Comparative Data Analysis Ontology (CDAO) Computational Neuroscience Ontology (CNO) Core Clinical Protocol Ontology (C2PO) Document Act Ontology Eagle-I Research Resource Ontology (ERO) Emotion Ontology (MFOEM) Experimental Factor Ontology (EFO) Financial Report Ontology Infectious Disease Ontology (IDO) Influenza Research Database (IRD) Information Entity Ontology Mental Functioning Ontology (MF) Neural ElectroMagnetic Ontologies (NEMO) Ontology for Biomedical Investigations (OBI) Ontology for Drug Discovery Investigations (DDI) Ontology for General Medical Science (OGMS) Ontology for Newborn Screening Follow-up and Translational Research (ONSTR) Ontology of Clinical Research (OCRE) Ontology of Data Mining (OntoDM) Ontology of General Purpose Datatypes (ONTODT) Ontology of Medically Related Social Entities (OMRSE) Ontology of Vaccine Adverse Events (OVAE) Oral Health and Disease Ontology (OHDO) Population and Community Ontology (PCO) Proper Name Ontology Semanticscience Integrated Ontology (SIO) Software Ontology (SWO) Translational Medicine Ontology (TMO) Vaccine Ontology (VO) 4

Objective of the Effort To propose [2] an ontology that is close to being a small subset of IAO – most of the terms in IAO Core are already present in IAO itself – which is designed to be used as a starting point for downward population by those working in fields outside biological science. Our specific focus grows out of the need for an ontology of information artifacts in different areas, e.g. military and intelligence, to be applied to diverse data such as for example sensor, image, and signals data. 5

Objective of the Effort (cont.) IAO needs to provide a consistent ontological framework which will support – Consistent expansion of the IAO reference ontologies – Building application-specific IAO extensions to allow To explicate terms used in various domain-specific standard taxonomies of information artifacts (e.g. in military and intelligence domains) To annotate the corresponding instance-level information for purposes of retrieval and analysis 6

IAO Core The suggested IAO Core contains a small number of foundational information entities that represent various aspects or dimensions of what we are used to call ‘information artifacts’ and which will lay a foundation for building consistent information artifact ontologies. 7

Aboutness IAO Core will follow the IAO in taking the idea of aboutness as central to its definition of information artifacts. Information artifacts are about – they are representations of (or support human beings in forming representations of) – some entity. For example, a note that says ‘IAO Workshop takes place on 09/22/2014 in Brazil’ is about the current workshop. 8

Representations A representation is for example an image or description of any other kind which refers to (is of or about), or is intended to refer to, some entity or entities external to the representation (even though it may leave out many aspects of its target). Some representations can be compositions of other representations, for example a map of state (is about the state) is composed of the maps of the state counties (is about the counties). 9

Representative Dimension When we talk about an information artifact, we mean a representation that is fixed in some medium in such a way that it can serve to make the cognitive representations existing in the minds of separate subjects publicly accessible in some enduring fashion. 10

Non-representative Dimensions Sometimes when we discuss an information artifact we refer to its aspects other than aboutness For example, we may be interested in the way the representation is organized (structured), e.g. as a spreadsheet. – To take care of such cases IAO will need to include terms for these structural aspects of information artifacts. Examples are single characters (such as the letter ‘a’), spaces and punctuation marks; a line of space inserted between two lines of text on a screen; an cell in a spreadsheet. – These figure as parts of representations. 11

Non-representative Dimensions (cont.) We will need also terms designating patterns of qualities in the physical things which bear information – for example the pattern formed by the ink marks arranged on this piece of paper. And finally, we will need these physical entities themselves that have been deliberately created to serve as bearers of such patterns of qualities (for example a hard drive on which some database is stored). 12

Types and Relations of BFO 13 Generically Dependent Continuant (GDC) Independent Continuant (IC) Specifically Dependent Continuant (SDC) Is concretized inGenerically depends on Generic dependency: If a is a GDC and b is an IC, to say that a generically depends on b means: a requires either b to serve as its carrier or some other entity c which is of the same type as b. Concretization: If b is a SDC, c is a GDC, and d is an IC, to say that b concretizes c at t means: b s-depends_on d at t and c g-depends on d at t; if c migrates from one bearer d to another bearer e than a copy of b will be created in e.

Generic Dependency and Concretization Thus GDCs can migrate, for example through the process of exact copying which allows the very same information content to be saved to multiple storage devices (IC). For example, the chessboard pattern, the Coca Cola logo, a traffic sign. Such migration is possible if a GDC is concretized in a counterpart SDC. For example, the pattern of black and white squares on this wooden chessboard here; the pattern of red and white swirls on the label of this Coca Cola bottle; the pattern of paint on this traffic signboard. 14

Types of Information Artifacts When we talk about an ‘information artifact’, we refer to both: – (IA1) the continuant physical artifacts, such as hard drives and paper documents, which are the bearers of information, – (IA2) the continuant information entities, which these physical artifacts carry, including those that are about something. 15

IAO Core and BFO The information artifacts identified under IA1 are independent continuants (IC). Those identified under IA2 are generically dependent continuants (GDCs). This means that they are entities – such as an intelligence report – which can be copied from one physical bearer to another. These copies are specifically dependent continuants (SDC) and are called ‘concretizations’ of the GDC. More precisely, each GDC is concretized by a pattern, a specific quality inhering for example in the tiny piles of ink on the piece of paper in your pocket or in differentially excited pixels on your screen. When the GDC is copied, then a qualitatively identical pattern (i.e. SDC) is created on a new physical information bearer. 16

Examples You may concretize a poem (GDC) as a pattern of traces (SDC) on a magnetic tape(IC). You may concretize a piece of software (GDC) by installing it (creating a SDC) in your computer (IC). You may concretize a recipe (GDC) that you find in a cookbook (IC) by turning it into a plan which exists as a realizable dependent continuant (SDC) in your head (IC). 17

Foundational Information Entities Now we can introduce the foundational information entities that form the basis of the IAO Core and correspond to the discussed dimensions of information artifacts 18

Information Content Entity In accordance with our approach that assumes the primary role of aboutness, we first introduce the Information Content Entity (ICE) as a GDC that is about something (for example, a description of Lake Titicaca, a description of the qualities of igneous rock). The target of aboutness is a portion of reality, either an instance or a type. 19

Information Structure Entity We then introduce an Information Structure Entity (ISE) that is a GDC that is not an ICE but which is complemented or complementable by one or more ICEs to create another ICE (for example, a cell in a spreadsheet, hard line break, space between words, semi-colon). 20

Information Quality Entity An Information Quality Entity (IQE) is a quality that concretizes some ICE or ISE. Typically an IQE will be a complex pattern made up of multiple qualities joined together spatially, for example, the quality of light patterns on this screen before you now. 21

Information Artifact And finally, we will introduce the formal definition of the Information Artifact (IA). Before that, we define an Artifact as a Material Entity that was created or modified or selected by some Agent to realize a certain function or to fulfill a certain role (for example, a screwdriver, a hard drive, a traffic sign). Then, an IA is an artifact whose function is to bear an IQE (for example, a hard drive, a blank sheet of paper, a passport, a currency note). 22

Foundational Information Entities and BFO 23 Generically Dependent Continuant (GDC) Independent Continuant (IC) Specifically Dependent Continuant (SDC) Information Content Entity (ICE) Information Artifact (IA) Information Quality Entity (IQE) Information Structure Entity (ISE)

Examples ICE: report, assessment ISE: comma, table, column of a table IQE: the quality of light patterns on this screen before you now IA: hard drive, paper, dollar bill, passport 24

Examples of Using IAO Core in Annotations 25 Modified Combined Obstacle Overlay

Examples of Using IAO Core in Annotations (cont.) ICE: MCOO IA: Acetate Sheet Aboutness: Avenue of Approach, Strategic Defense Belt, Amphibious Operations, Objective of an operation Other attributes of the IA: – uses-symbology MIL-STD-2525C – authored-by person #4644 – part-of plan IA#2 26

IA Types Singular IA.A singular IA x is an IA the purpose of which is not realized in a copy (Comment: a copy of an IA x is an IA y that has the same ICE or ISE as x), for example, a dollar bill. Repeatable IA. A repeatable IA is an IA a copy of which serves the same purpose as the original, for example,a newspaper, a scientific publication. Replaceable IA. A replaceable IA is a repeatable IA which is such that a copy can serve the same purpose as the original only if the original is not able to be used, for example, a passport. 27

Reference and Application-Specific IAO In [3] we introduced the idea of reference and application-specific ontologies. ‘Reference ontology’, is an ontology that captures generic content and is designed for aggressive reuse in multiple different types of context. Our assumption is that most reference ontologies will be created manually on the basis of explicit assertion of the taxonomical and other relations between their terms. ‘Application ontology’, is an ontology that is tied to specific local applications. 28

Methodology of Ontology Development In the era of the Big Data ontology development will inevitably be distributed. To ensure consistency and interoperability of the resulting ontologies, they have to be based in respective reference ontologies. The goal of the IAO Core is to serve as a basis of the Reference IAO, which in turn will serve as a basis of application-specific IAO dealing with diverse in many ways information artifacts. 29

References 1.Barry Smith, “Basic Formal Ontology 2.0. Draft Specificaitons and User’s Guide”. reference/BFO2-Reference.docx. reference/BFO2-Reference.docx 2.Barry Smith, Tatiana Malyuta, Ron Rudnicku, William S. Mandrick, David Salmen, Peter Morosoff, Danielle Duff, James Schoening, Kesny Parent, “IAO-Intel. An Ontology of Information Artifacts in the Intelligence Domain”, Proceedings of STIDS Conference, Barry Smith, Tatiana Malyuta, William S. Mandrick, Chia Fu, Kesny Parent, Milan Patel, “Horizontal integration of warfighter intelligence data. A shared semantic resource for the Intelligence Community”, Proceedings of STIDS Conference, 2012 (CEUR 996), pp. 112–