diff --git a/README.md b/README.md
index 18b4644..b3ce78c 100644
--- a/README.md
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# General Formal Ontology (GFO)
-[![Test ontology](https://github.com/Onto-Med/GFO/actions/workflows/test.yml/badge.svg)](https://github.com/Onto-Med/GFO/actions/workflows/test.yml)
+[![Test ontology](https://github.com/Onto-Med/GFO/actions/workflows/test.yml/badge.svg?branch=main)](https://github.com/Onto-Med/GFO/actions/workflows/test.yml)
[![DOI](https://zenodo.org/badge/220933953.svg)](https://zenodo.org/badge/latestdoi/220933953)
## Introduction
@@ -12,6 +12,11 @@ The General Formal Ontology is a [top-level ontology](http://en.wikipedia.org/wi
* elaborate accounts of functions and roles
* openness regarding philosophical positions such as realism, conceptualism, or nominalism by the provision of different kinds of categories as universals, concepts, or symbolic structures
+## How to Use
+The entire GFO ontology can be imported via IRI https://w3id.org/gfo. GFO is divided into modules, which are stored in separate OWL files under [modules/](modules/). Modules of interest can be imported into your ontology via their IRI (e.g., https://w3id.org/gfo/base).
+
+**GFO-light** is a simplified view of the entire GFO. It does not build on single modules but combines all basic concepts and simplified axioms of the GFO. It is primarily intended to found domain or application ontologies and can be imported via IRI https://w3id.org/gfo/light.
+
## Brief History
Work on GFO has started in 1999 in the context of the GOL project (General Ontological Language). Meanwhile, several directions of research have been recognized and divided the initial project, such that GFO is now one component of a larger framework. Work on GFO remains in progress, because the development of top-level ontologies is a long-term research effort.
@@ -19,10 +24,12 @@ Work on GFO has started in 1999 in the context of the GOL project (General Ontol
The "native" formalization language for GFO is [first-order logic (FOL)](https://en.wikipedia.org/wiki/First-order_logic). Partial axiomatizations of GFO in FOL exist in report working drafts, but are not yet available to the public.
### Release Strategy
-*gfo-basic.owl* forms the core module of GFO. We are going to continually provide further modules/extensions, dedicated to several of our research domains, like time, space, processes, etc. There may be parallel extensions for these domains, and not all extensions will be consistent with each other. All module files are provided with their own namespaces (e.g., http://purl.org/ontology/gfo-time) and can be used separately. A selection of those modules will be unified in the next version of *gfo.owl* (under the namespace http://purl.org/ontology/gfo). *gfo-light.owl* is a simplified view of the entire GFO. It does not build on single modules but combines all basic concepts and simplified axioms of the GFO. *gfo-light.owl* is primarily intended to found domain or application ontologies.
+[modules/gfo-base.owl](modules/gfo-base.owl) forms the core module of GFO. We are going to continually provide further modules/extensions, dedicated to several of our research domains, like time, space, processes, etc. There may be parallel extensions for these domains, and not all extensions will be consistent with each other. All module files are provided with their own namespaces (e.g., https://w3id.org/gfo/time) and can be used separately. A selection of those modules will be unified in the next version of [gfo.owl](gfo.owl) (under the namespace https://w3id.org/gfo).
+
+All versions of GFO and it's modules are available via `owl:versionIRI`. e.g.: https://w3id.org/gfo/release/2024-07-05
### Release History
-Work on the OWL version of GFO started in early 2006 in the context of the [GFO-Bio](http://www.onto-med.de/ontologies/gfo-bio/index.jsp) project, resulting in the 1.0 release of *gfo.owl*. The renewed release strategy in 2008 lead to *gfo-basic.owl*, a corrected and slightly simplified version.
+Work on the OWL version of GFO started in early 2006 in the context of the [GFO-Bio](http://www.onto-med.de/ontologies/gfo-bio/index.jsp) project, resulting in the 1.0 release of [gfo.owl](gfo.owl).
## Documentation and Publications
### Onto-Med Report Series on GFO
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> **Heller B, Herre H**. Formal Ontology and Principles of GOL. Onto-Med Report Nr. 1. Research Group Ontologies in Medicine (Onto-Med), University of Leipzig.
### Further Documentation
-Apart from the GFO reports, we have not yet completed the work on more introductory or tutorial material. This is going to happen in the nearer future. Currently, the easiest way to access the basic categories of GFO is to view the file *gfo-basic.owl* in an ontology editor (e.g. [OwlSight](https://www.w3.org/2001/sw/wiki/OWLSight) or [Protégé](https://protege.stanford.edu)). In particular, that file provides short descriptions for each category.
+Apart from the GFO reports, we have not yet completed the work on more introductory or tutorial material. This is going to happen in the nearer future. Currently, the easiest way to access the basic categories of GFO is to view the file [gfo-light.owl] in an ontology editor (e.g. [Protégé](https://protege.stanford.edu)). In particular, that file provides short descriptions for each category.
diff --git a/gfo-basic.owl b/gfo-basic.owl
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- Copyright (c) 2006-2008, Regents of the Research Group Ontologies in Medicine (Onto-Med), University of Leipzig, Germany.
- All rights reserved.
-
- Redistribution and use in source and binary forms, with or without modification,
- are permitted provided that the following conditions are met:
-
- 1. Redistributions of source code must retain the above copyright notice, this list
- of conditions and the following disclaimer.
-
- 2. Redistributions in binary form must reproduce the above copyright notice, this list
- of conditions and the following disclaimer in the documentation and/or other
- materials provided with the distribution.
-
- 3. Neither the name of the Research Group Ontologies in Medicine (Onto-Med), University
- of Leipzig nor the names of its contributors may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS
- OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
- AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
- CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
- IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- Version 1.0 ($Revision: 1.13 $)
- This file belongs to the OWL distribution of GFO, cf. http://www.onto-med.de/ontologies/gfo.
------------------
-
-It comprises a set of selected major and rather stable GFO categories, with the intention to serve as a comprehensible starting point which
-
-1. should be useful for immediate modeling purposes,
-2. covers GFO's areas and exhibits outstanding GFO features
-3. omits categories of more theoretical character or those which are easily definable
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-Categories of the third kind will be provided in separate extensions.
-
------------------
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-In some comments, references to documents are used. These refer to several versions of the following report:
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-Herre, H.; Heller, B.; Burek, P.; Hoehndorf, R.; Loebe, F. & Michalek, H.. General Formal Ontology (GFO): A Foundational Ontology Integrating Objects and Processes. Part I: Basic Principles. Research Group Ontologies in Medicine (Onto-Med), University of Leipzig.
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-[herre-h-2006--a]: Version 1.0, Onto-Med Report Nr. 8, 01.07.2006
-[part1-v1.0.1] Version 1.0.1., Draft, 14.02.2007
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- Abstract has-part is the inverse of the abstract part-of relationship.
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- abstract part-of
- The abstract part-of relation is denoted by p(x,y); the argument-types of this relation are not specified, i.e. we allow arbitrary entities to be arguments. We assume that p(x,y) satisfies the condition of a partial ordering, .i.e. the following axioms: reflexivity, antisymmetry and transitivity.
-[RH, 2006 based on herre-h-2006--a, p.44]
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- "Boundary of" connects boundaries to the entities which they bind.
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- coincides with
- Coincidence is a relationship between space boundaries or time boundaries, respectively. Intuitively, two such boundaries are coincident if and only if they occupy “the same” space, or point in time, but they are still different entities.
-[herre-h-2006--a, p.46]
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- depends on
- This relation captures the notion of existential dependence.
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- exhibits
- In the GFO-account of persistence, perpetuants exhibit presentials, i.e., the former ``exist through'' the latter at the time where the presential exists. With respect to persistants, presentials instantiate persistants.
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- Presentials exist at a single time boundary.
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- A presential is framed by a spatial region if the location which the presential occupies is a spatial part of that region.
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- A spatial region frames a presential if the location which the presential occupies is a spatial part of that region.
-[FL, 2008-02-27, based on herre-h-2006--a, p. 21]
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- The has-boundary relation connects entities with their boundaries, e.g. chronoids to time boundaries, topoids to surfaces, etc.
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- Temporal regions have exactly one extremal left time boundary.
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- has-part
- The inverse of part-of.
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- has participant
- Temporally extended entities have participants.
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- has proper part
- The inverse of proper part-of.
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- has property
- Entities can have properties. In GFO, properties are individualized, and "has property" links an entity to its particular property.
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- has right time boundary
- Temporal regions have exactly one extremal right time boundary.
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- has role
- The inverse of role of.
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- has spatial boundary
- Space entities may have spatial boundaries.
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- has temporal part
- The inverse of temporal part-of.
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- has time boundary
- Temporal regions have temporal boundaries.
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- has token
- The specific relation from a symbol structure (a category in GFO) to an entity seen as an occurrence of that symbol structure, as a token of it.
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- instance of
- The instantiation relation holds between an entity and a category. Put differently, the category is predicated of that entity, the entity is the instance of that category. Entities of all kinds can be instances, which results in categories which have individuals as instances or categories which may have categories as instances, such as "species".
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- instantiated by
- Inverse of instance of.
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- left boundary of
- Left boundary of a temporal region.
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- necessary for
- An entity is necessary for another one if the latter is required for the former to exist.
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- occupied by
- Presentials exist in space, and the space entity occupied by a presential is uniquely determined (where a fixed granularity is assumed).
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- occupies
- Presentials exist in space, and the space entity occupied by a presential is uniquely determined (where a fixed granularity is assumed).
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- part of
- The relation between parts and wholes.
-The union of several domain-specific part-of relationships not contained explicitly in gfo-basic, like spatial part-of or part-of among material structures.
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- participates in
- Intuitively, objects participate in processes, for instance. In GFO, participation accommodates the GFO approach to persistence, i.e., at least presentials can participate in processes. Moreover, it is useful to extend the notion of participation also to other temporally extended entities.
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- played by
- The inverse of plays-role.
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- plays role
- Entities can play roles with respect to some other entity which provides a context for that role. The plays-role relationship links an entity with its role.
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- projection of
- If, for instance, a process happens during a certain time, i.e., some temporal region, that region is the projection of that process (to time).
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- projects to
- Links an entity to its temporal extension.
-Entities which are in time are related to the corresponding temporal regions by projects to. Moreover, entities related to others which are in time may likewise project to temporal regions.
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- proper part of
- The irreflexive variant of part-of.
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- property of
- Links properties to their bearers.
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- right boundary of
- Right boundary of a temporal region.
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- role of
- The relationship between a role and its context. Typically, the nature of the context determines that of the roles, which are in some sense a part of that context. E.g., processes form the context for certain roles (processual roles), such that the latter are recognizable as processes.
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- spatial boundary of
- Spatial boundaries may bound spatial entities.
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- temporal part-of
- A part-of relationship between two time entities. Time-boundaries cannot have parts.
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- time boundary of
- Time boundaries bound temporal regions.
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- token of
- Inverse of the has token relations.
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- Abstract
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- Abstract individuals are independent from time and space (they are not in time and space).
-Examples: the number "2" or pi.
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- Amount of substrate
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- An amount of substrate is a presential, namely the matter of some material object. Amounts of substrate follow different identity criteria than material objects, i.e., they instantiate different persistants.
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-Appropriate connotations of "amount of substrate" are "stuff" (in the common understanding) or "mass term" (in linguistics).
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- Category
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- Categories satisfy the following conditions: (1) Categories can be instantiated; (2) Categories can be predicated of other entities.
-Categories are defined intensional-with-an-s. They are, therefore, closely related to language.
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- Change
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- A change refers to a structure centered around two presentials, which are boundaries of one and the same process. If they exist at coinciding time boundaries, the change comes close to notions in the literature like "punctual" or "instantaneous event" as well as "moment" (in a temporal reading). Alternatively, the presentials may be boundaries at the opposite ends of a process of arbitrary extension.
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-Either notion of change is relative to contradictory conditions between which a transition takes place. These conditions refer to some collection of pairwise disjoint subcategories of one category.
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- Chronoid
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-Every chronoid has exactly two extremal and
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- Concept
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- Concepts are categories that are expressed by linguistic signs and are present in someone’s mind.
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- Concrete
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- Concrete individuals have a relation to time or space (they are in time and space).
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- Continuous change
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- A continuous change is a change such that
-(1) its process boundaries exist at non-coincident time-boundaries,
-(2) any two non-coincident process boundaries of its process are distinguished with respect to the reference category and
-(3) any two coincident process boundaries exhibit no such distinction, i.e., no discrete changes of the same reference category.
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- Continuous process
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- A process is a continuous process if it can be partitioned such that the partition contains only states or processes within a continuous change. Those states and changes must be based on the same reference category.
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- Discrete change
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- A discrete change is a change at coincident time boundaries, for which a recognizable difference exists. That means, there is a category with two disjoint sub-categories such that each of these is instantiated by exactly one of the process boundaries in the change.
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- Discrete processes have a partitioning into an alteration of discrete changes and states.
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- Entity
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- Everything is an entity, i.e., entity is the category which everything instantiates.
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- We use the term entity for everything that exists where existence is understood in the broadest sense.
-[part1-v1.0.1, p.5]
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- Event
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- Events are processual structures comprising a process, and one of its extremal process boundaries. The latter must further satisfy a condition which differs from the condition applicable to all other boundaries of the process. I.e., the extremal boundary instantiates a sub-category of the event's reference category which is disjoint with that category instantiated by the remaining process boundaries. [FL, 2008-03-13]
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- Individual
- Individuals are entities that are not instantiable.
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- A material entity which depends on a material object and occupies a spatial boundary.
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- Material object
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- A material structure is an individual which satisfies the following conditions:
-it is a presential, it occupies space, it is a bearer of qualities, but other entities cannot have
-it as quality, and it consists of an amount of substrate, and it instantiates a persistant ("has identity").
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- Occurrent
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- The category of occurrents comprises several categories that can be derived from processes.
-[FL, 2008-03-06 based on part1-v.1.0.1, p.30]
- NOTE: In earlier versions, "Occurrent" denoted the category named "Processual Structure" herein.
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- Perpetuant
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- A perpetuant is a concrete individual which persists through time and exhibits presentials.
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- Point
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- Presential
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- A presential exists wholly at exactly one time boundary.
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- Process
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- Processes are directly in time, they develop over and unfold in time. Processes have characteristics which cannot be captured by a collection of time boundaries. In particular, processes exhibit internal coherence.
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- Processual Structure
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- The category of processual structures centers around the more intuitive notion of processes. It captures processes themselves and occurrents, i.e., primarily structures of several other kinds that can be derived from processes.
-[FL, 2008-03-13 based on part1-v1.0.1, p.30]
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- Processual role
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- Processual roles are roles with a process as context, and they are dependent processes.
-[FL, 2008-02-27]
- A processual role corresponds to the manner in which a single participant behaves in some process.
-[herre-h-2006--a, p.38]
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- Property
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- A property is a dependent entity which another entities has, i.e., that entity exhibits its property. Other common terms for property in natural language are characteristic, feature, quality, etc.
-[FL, 2008-02-27]
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- Relational role
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-
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- A relational role corresponds to the way in which an argument participates in some relation.
-[herre-h-2006--a, p.38]
-
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- Relator
-
- A relator mediates between or connects entities. It is a dependent entity which depends on those entities connected.
-[FL, 2008-03-13]
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- Right time boundary
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- see time boundary description
-[FL, 2008-02-27]
-
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- Role
-
- A role corresponds to the involvement of some entity (the player of the role) within another entity (the context of the role).
-Examples of role terms: student, patient, runner, reader, factor.
-[FL, 2008-02-27]
-
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-
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- Social role
-
- A social role corresponds to the involvement of a social object within some society.
-[herre-h-2006--a, p.38]
-
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- Space entity
-
-
- Spatial entities in GFO are analyzed according to the ideas of Franz Brentano. Starting from connected three-dimensional entitites (topoids), related spatial entities can be distinguished.
-[FL, 2008-02-27]
- [herre-h-2006--a, sect. 5.2]
-
-
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- Space time entity
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- A space-time-entity is something in which concrete entities can be located.
-[FL, 2008-02-27]
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- Spatial boundary
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- Boundaries of regions are surfaces, boundaries of
-surfaces are lines, and boundaries of lines are
-points. As in the case of time-boundaries, spatial
-boundaries have no independent existence, i.e. they depend on the
-spatial entity of which they are boundaries.
-
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- Spatial region
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- Space regions are mereological sums of topoids.
-
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- State
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- [part1-v1.0.1, p.34]
- A process is a state with respect to a category iff every of its process boundaries instantiates that category.
-[FL, 2008-03-13]
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-[FL, 2008-02-27]
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- Symbol structure
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- Symbolic structures are signs or texts that may be instantiated by tokens.
-[herre-h-2006--a, p.6]
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- Temporal region
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- Time Regions are defined as the mereological sum of chronoids,
-i.e. time regions may consist of non-connected intervals of time.
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- Time entity
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- The time model of GFO is based on Brentano and the glass continuum of Allen&Hayes.
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- Time boundary
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- Time boundaries depend on a chronoids and can coincide.
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-Left time boundaries, if viewed from the perspective of bounding a specific chronoid, are those which are earlier than any inner or right time boundary of that chronoid. On the other hand, within a pair of coincident time boundaries, a left time boundary is later than the right time boundary in that pair.
-
-[FL, 2008-02-27]
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- Topoid
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- Topoids are connected compact regions of space. They have spatial boundaries.
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- Universal
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- Universals are immanent categories. They exist in re.
-[FL, 2008-02-27]
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diff --git a/gfo-light.owl b/gfo-light.owl
index 7d2676f..5424858 100644
--- a/gfo-light.owl
+++ b/gfo-light.owl
@@ -1,14 +1,28 @@
-
-
-
- 2023-06-23T12:00
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:vann="http://purl.org/vocab/vann/"
+ xmlns:foaf="http://xmlns.com/foaf/0.1/"
+ xmlns:doap="http://usefulinc.com/ns/doap#"
+ xmlns:bibo="http://purl.org/ontology/bibo/">
+
+ 2024-07-05
+ 2024-07-05
+
+ General Formal Ontology Light (GFO-light)
+ General Formal Ontology Light (GFO-light)
+ 2006-08-28
+ https://w3id.org/gfo/light/
+ gfo-light
+ https://github.com/Onto-Med/GFO
+
+
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The instantiation relation holds between a category and an item. It is not a relation between categories and individuals due to higher order categories such as "species".
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Left boundary of a chronoid.
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Right boundary of a chronoid.
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Abstract individuals are independent of space and time, for example the number number '2' or pi.
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Individuals that are related to other individuals by some kind of dependency relation are called attributives.
@@ -523,78 +537,78 @@
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The notion of category covers all abstract entities that can be instantiated by or are predicated of other entities.
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Chronoids may be understood as closely similar to real-valued intervals with endpoints.
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Complex individuals are composed of elementary ones or components.
Complex individuals are constituents of situations (with a high degree of independence).
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Concrete individuals have an immediate relation to time or to time and space.
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Continuants persist through time and are wholly present at every time point of their lifetime.
@@ -602,39 +616,39 @@
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Everything which exists is called an entity.
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Material facts are composed of a relator and material objects playing the corresponding roles. Material facts are continuants.
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The notion of function is built upon that of role: we introduce a function as a category that captures a role played by some entity in the context of a goal achievement (GA), where the GA provides a teleological specification of transitioning to something that is intended to be achieved.
@@ -642,83 +656,83 @@
-
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Individuals are entities which cannot be further instantiated.
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Every material object consists of an amount of stuff.
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Presentials exhibited by material objects are called material structures.
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Object situations consist of material objects and relations between them.
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A presential is wholly present at exactly one time point.
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A presentic situation is a snapshot of an object situation.
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Processes are a special kind of processual complexes. Processes are directly in time, they have characteristics which cannot be captured by a collection of time boundaries.
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Processual complexes are concrete individuals that have a temporal extension.
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Processual roles corresponds to the manner in which a single participant behaves in some process.
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Qualities are attributives and, typically, a quality inheres in its bearer.
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Relational role corresponds to the way in which an argument participates in some relation.
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Relators connects entities (role players) via roles (they depend on more than one player via their roles).
@@ -930,14 +944,14 @@
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A role individual is defined as a relational entity that links any entity, called the role player (or filler), with some context, in which the entity plays that role.
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Material situations are parts of the material world (at the macroscopic level) that can be consistently comprehended as a whole.
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A situoid (or processual situation) is a part of the spatiotemporal world that arises from an object situation if all objects are replaced by the corresponding processes.
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Social role corresponds to the involvement of a social object within some society.
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phenomenal space
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While every space region has an extension, there is an idealization of a greatest space region, containing any space region as part.
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homogeneous four-dimensional space-time continuum
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The concept of stuff has instances that are amounts of stuff. Accordingly,“Gold is a stuff”, for example, is read as “Every amount of gold is an amount of stuff”.
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The time model of GFO is based on Brentano and the glass continuum of Allen&Hayes.
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diff --git a/gfo.owl b/gfo.owl
index c809e9b..a940462 100644
--- a/gfo.owl
+++ b/gfo.owl
@@ -1,21 +1,18 @@
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-]>
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- Copyright (c) 2006, Regents of the Research Group Ontologies in Medicine (Onto-Med), University of Leipzig, Germany.
+
+
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+ Copyright (c) 2006, Regents of the Research Group Ontologies in Medicine (Onto-Med), University of Leipzig, Germany.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
@@ -40,1189 +37,18 @@
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- Version 1.0 ($Revision: 1.9 $)
-
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- Abstract individuals are independent from time and space (they are not in time and space).
-Examples: the number "2" or pi.
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- Actions are occurents which are caused by some presential (the agent) at every (inner and outer) time-boundary of the chronoid framing the occurent.
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-Categories are defined intensional-with-an-s. They are, therefore, closely related to language.
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- A change in the technical sense refers to a pair of process
-boundaries. Either at coinciding boundaries (then it comes close to
-notions like ``punctual'' or ``instantaneous event'' as well as
-``moment'' -- in a temporal reading), or at boundaries at the opposite
-ends of a process of arbitrary extension.
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-The notion of change is relative to contradictory conditions
-between which a transition takes place. These contradictions refer to
-some collection of pairwise disjoint universals.
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-equivalently called time-points.
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- Concrete individuals have a relation to time or space (they are in time and space).
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- We consider a collection of presential facts which exist at the same time-boundary. Such collections may be considered themselves as presentials, and we call them configurations.
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-It is further required that configurations contain at least one material object.
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- Processes where all non-coinciding internal boundaries are intrinsic changes.
-These turn out as purely continuous processes, described e.g.
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- A function F is a universal (conceptual structure) defined in purely teleological terms with respect to a given goal G which commonly is ascribed by means of has-function relation to entities that are the realizations of the function F, execute such a realization or are intended to do it.
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- Histories consist of a number of process boundaries.
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-We assume that any history can be embedded into a process, which then
-forms a foundation of the history. If it were not for this foundation,
-one would face the problem of singling out the right boundaries in
-order to get a natural history: It is not sensible to measure the
-temperature of a patient first, then determine his weight, followed by
-measuring his blood pressure and to consider these strangely arbitrary
-process boundaries as a history of the patient's body data.
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- Instantanuous changes are represented by change(e1,e2, u1, u2, u), where e1 and e2 are a pair of coincident process boundaries, and u1 and u2 are disjoint sub-universals of u. Instantanuous changes are therefore changes of properties on two coinciding time boundaries.
-
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- Deprecated.
-For the purpose of formalizing intrinsic changes, a minimal chronoid universal D(c) is employed in order to capture the idea of observable differences during certain chronoids, whereas the change itself does not allow the observation of a difference. The predicate change(e1,e2, u1, u2, u, D(c)) is intended to formalize this approach.
-
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- An item is everything which is not a set. Also called ur-element.
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- A material structure is an individual which satisfies the following conditions:
-it is a presential, it occupies space, it is a bearer of qualities, but other entities cannot have
-it as quality, and it consists of an amount of substrate, and it instantiates a persistant ("has identity").
-
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- 1
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- Material persistants are particular universals whose instances are
-material structures; they are related to those entities which are called
-sometimes continuants or objects, as apples, cars or houses.
-Material persistants capture the phenomenon of persistance through time of a material
-object. A material persistant P satisfies a number of neccessary conditions. For every
-material persistant P there exists a process P such that
-the set of instances of P coincides with the set of process-boundaries
-of P. This implies the existence of a chronoid c
-such that for every time-point t of c there exists exactly
-one instance of P at time point t.
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-These levels can be further refined.
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- In accordance with the work of R. Poli, we divide the
-psychological/mental stratum into the layer of
-awareness and the layer of
-personality. Awareness comprises most
-of what is studied by cognitive science (perception, memory,
-reasoning, etc). Personality on the other hand concerns the phenomenon
-of will and the way in which someone reacts to her experiences.
-
-
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- Occurents have temporal parts and thus cannot be present at a time-boundary. Time
-belongs to them, because they happen in time and the time of the occurent
-is built into it. The relation between an occurent and a chronoid is
-determined by the projection relation.
-
-Occurents are also called generalized processes in the GFO.
-
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- Ontological_layer, all of its subconcepts and the properties layer_of and on_layer are work in progress in a premature beta state.
- a collective term for gfo:stratum and gfo:level
-
- Beta
-
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- Persistants are GFO's way to capture identity over time.
-
-GFO pursues an approach which
-accounts for persistence by means of a suitable
-universal whose instances are presentials. Such universals are called
-persistants. These do not change and they can be used to
-explain how presentials which have different properties at different
-times can nevertheless be the same.
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- A presential exists wholly at exactly one time boundary.
-
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-
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-
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-
-
- 1
-
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-
-
- Processes are a special kind of occurent. Processes are directly in time, they have characteristics which cannot be captured by a collection of time boundaries.
-
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-
-
- Processual roles are dependent processes. They are roles with a process as context.
-
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- The concept of a property value reflects a relationship between the property of x and the same property as exhibited by another entity y.
-
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- Set is a category pertaining to the individuals in the ZFC set theory.
-
-
-
-
-
- A situation is a special configuration which can be comprehended as a whole and satisfies certain conditions of unity, which are imposed by relations and categories associated with the situation. Herein, we consider situations to be the most complex kind of presentials.
-
-
-
-
- Situoids are processes whose boundaries are situations and which satisfy certain principles of coherence, comprehensibility, and continuity. They are regarded as the most complex integrated wholes of the world. A situoid is, intuitively, a part of the
-world which is a coherent and comprehensible whole and does not need other entities in order to exist. Every situoid has a temporal extent and is framed by a topoid.
-
-
-
-
-
-
-
-
-
-
-
- On the one hand, the social stratum is
-divided into Agents and
-Institutions. Agents are the bearers of the social
-roles that humans play. Institutions are defined as systems of
-interrelated social components. On the other hand, a social system can
-be seen as a network in which businesses, politics, art, language (and
-many other facets) both present their own features and
-influence each other.
-
-
-
-
- GFO uses Brentano space.
-
-
-
-
-
-
-
-
-
-
-
- Boundaries of regions are surfaces, boundaries of
-surfaces are lines, and boundaries of lines are
-points. As in the case of time-boundaries, spatial
-boundaries have no independent existence, i.e. they depend on the
-spatial entity of which they are boundaries.
-
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- Space regions are mereological sums of topoids.
-
-
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-
-
- A process without an instantanuous change at any of its inner time boundaries is called a state.
-
-
-
-
- According to (Poli, 2001, 2002) (based
-on the philosopher Hartmann) we distinguish at least three ontological
-strata of the world: the material stratum, the
-mental/psychological stratum, and the
-social stratum stratum.
-
-Every entity of the world participates in certain
-strata and levels. We take the position that the layers are
-characterized by integrated systems of categories. Hence, a layer can
-be understood as a meta-category whose instances are categories of
-certain kinds. Among these levels specific forms of categorial and
-existential dependencies hold. For example, a mental entity requires
-an animate material object as its existential bearer.
-
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- Time Regions are defined as the mereological sum of chronoids,
-i.e. time regions may consist of non-connected intervals of time.
-
-
-
-
-
- The time model of GFO is based on Brentano and the glass continuum of Allen&Hayes.
-
-
-
-
-
- Time boundaries depend on a chronoids (i.e. they have no independent
-existence) and can coincide.
-
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- Topoids are connected compact regions of space. They have spatial boundaries.
-
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- Universals are immanent universals. They exist in re.
-
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-
-
- Property values usually appear in groups which are called value structures, value spaces or measurement systems.
-Each of these structures corresponds to some property. More intuitively, one could say that the property may be measured with respect to some measurement system.
-For instance, sizes may be measured with the values ``small'' ``big'' or ``very big'', which are the elements of one value structure.
-
-The notion of a value structure of a property is similar to a quality dimension in (Gardenfors, 2000).
-
-Further, value structures are related to quality spaces in DOLCE (Masolo, 2003}. A quality space consists of all ``quales'' (our property values) of some ``quality'' (our property).
-
-Often it seems to be the case that a notion of distance can be defined, and that certain layers of value structures are isomorphic to some subset of real numbers, which allows for a mapping of values to pairs of a real number and a unit, as in the case of ``10 kg''.
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- The abstract part-of relation is denoted by p(x,y);
-the argument-types of this relation are not specified, i.e. we allow
-arbitrary entities to be arguments. We assume that p(x,y) satisfies
-the condition of a partial ordering, .i.e. the following axioms: reflexivity, antisymmetry and transitivity.
-
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- This relation captures the notion of existential dependence.
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- "goal" here refers to "final state" in (Burek, 2006).
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- The instantiation relation holds between a category and an item. It is not a relation between categories and individuals due to higher order categories such as "species".
-
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- Left boundary of a chronoid.
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- "requirement" here refers to "initial state" in (Burek, 2006).
-
-
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- Right boundary of a chronoid.
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-
-
+ 2024-07-05
+ 2024-07-05
+
+
+
+ General Formal Ontology (GFO)
+ General Formal Ontology (GFO)
+ 2006-08-28
+ https://w3id.org/gfo/
+ gfo
+ https://github.com/Onto-Med/GFO
+
+
+
diff --git a/modules/gfo-base.owl b/modules/gfo-base.owl
new file mode 100644
index 0000000..d6d8e4b
--- /dev/null
+++ b/modules/gfo-base.owl
@@ -0,0 +1,1236 @@
+
+
+
+
+
+ Copyright (c) 2006, Regents of the Research Group Ontologies in Medicine (Onto-Med), University of Leipzig, Germany.
+ All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+
+ 1. Redistributions of source code must retain the above copyright notice, this list
+ of conditions and the following disclaimer.
+
+ 2. Redistributions in binary form must reproduce the above copyright notice, this list
+ of conditions and the following disclaimer in the documentation and/or other
+ materials provided with the distribution.
+
+ 3. Neither the name of the Research Group Ontologies in Medicine (Onto-Med), University
+ of Leipzig nor the names of its contributors may be used to endorse or promote products
+ derived from this software without specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS
+ OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
+ AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
+ IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+ OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ 2024-07-05
+ 2024-07-05
+
+ General Formal Ontology Base (GFO-base)
+ General Formal Ontology Base (GFO-base)
+ 2006-08-28
+ https://w3id.org/gfo/base/
+ gfo-base
+ https://github.com/Onto-Med/GFO
+
+
+
+
+
+
+ Abstract individuals are independent from time and space (they are not in time and space).
+Examples: the number "2" or pi.
+
+
+
+
+
+
+ Actions are occurents which are caused by some presential (the agent) at every (inner and outer) time-boundary of the chronoid framing the occurent.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Categories satisfy the following conditions: (1) Categories can be instantiated; (2) Categories can be predicated of other entities.
+Categories are defined intensional-with-an-s. They are, therefore, closely related to language.
+
+
+
+
+
+ A change in the technical sense refers to a pair of process
+boundaries. Either at coinciding boundaries (then it comes close to
+notions like ``punctual'' or ``instantaneous event'' as well as
+``moment'' -- in a temporal reading), or at boundaries at the opposite
+ends of a process of arbitrary extension.
+
+The notion of change is relative to contradictory conditions
+between which a transition takes place. These contradictions refer to
+some collection of pairwise disjoint universals.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Chronoids are entities sui generis.
+
+Every chronoid has exactly two extremal and
+infinitely many inner time boundaries which are
+equivalently called time-points.
+
+
+
+
+
+
+
+
+
+
+ Concrete individuals have a relation to time or space (they are in time and space).
+
+
+
+
+
+
+ We consider a collection of presential facts which exist at the same time-boundary. Such collections may be considered themselves as presentials, and we call them configurations.
+
+It is further required that configurations contain at least one material object.
+
+
+
+
+
+
+ Configuroids are, in the simplest case, integrated wholes made up of material structure processes and property processes.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ For the purpose of formalizing continuous changes, a minimal chronoid universal D(c) is employed in order to capture the idea of observable differences during certain chronoids, whereas the change itself does not allow the observation of a difference. The predicate change(e1,e2, u1, u2, u, D(c)) is intended to formalize this approach. Continous changes occur over time (a chronoid).
+
+
+
+
+
+ Processes where all non-coinciding internal boundaries are intrinsic changes.
+These turn out as purely continuous processes, described e.g.
+in physics by differential equations.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Discrete processes are made up of alterations of extrinsic changes and states.
+
+
+
+
+
+
+ Everything which exists is called an entity.
+
+
+
+
+
+
+
+ Deprecated. Extrinsic changes are represented by change(e1,e2, u1, u2, u), where e1 and e2 are a pair of coincident process boundaries, and u1 and u2 are disjoint sub-universals of u.
+
+
+
+
+
+ A function F is a universal (conceptual structure) defined in purely teleological terms with respect to a given goal G which commonly is ascribed by means of has-function relation to entities that are the realizations of the function F, execute such a realization or are intended to do it.
+
+
+
+
+ Histories consist of a number of process boundaries.
+
+We assume that any history can be embedded into a process, which then
+forms a foundation of the history. If it were not for this foundation,
+one would face the problem of singling out the right boundaries in
+order to get a natural history: It is not sensible to measure the
+temperature of a patient first, then determine his weight, followed by
+measuring his blood pressure and to consider these strangely arbitrary
+process boundaries as a history of the patient's body data.
+
+
+
+
+
+
+
+
+
+
+
+ Individuals are entities which cannot be further instantiated.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Instantanuous changes are represented by change(e1,e2, u1, u2, u), where e1 and e2 are a pair of coincident process boundaries, and u1 and u2 are disjoint sub-universals of u. Instantanuous changes are therefore changes of properties on two coinciding time boundaries.
+
+
+
+
+
+ Deprecated.
+For the purpose of formalizing intrinsic changes, a minimal chronoid universal D(c) is employed in order to capture the idea of observable differences during certain chronoids, whereas the change itself does not allow the observation of a difference. The predicate change(e1,e2, u1, u2, u, D(c)) is intended to formalize this approach.
+
+
+
+
+
+ An item is everything which is not a set. Also called ur-element.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ An ontological level, which is sth. more restricted and "part of" some gfo:Stratum.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A material structure is an individual which satisfies the following conditions:
+it is a presential, it occupies space, it is a bearer of qualities, but other entities cannot have
+it as quality, and it consists of an amount of substrate, and it instantiates a persistant ("has identity").
+
+
+
+ 1
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Material persistants are particular universals whose instances are
+material structures; they are related to those entities which are called
+sometimes continuants or objects, as apples, cars or houses.
+Material persistants capture the phenomenon of persistance through time of a material
+object. A material persistant P satisfies a number of neccessary conditions. For every
+material persistant P there exists a process P such that
+the set of instances of P coincides with the set of process-boundaries
+of P. This implies the existence of a chronoid c
+such that for every time-point t of c there exists exactly
+one instance of P at time point t.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ According to (Poli,2001), the basic structure of the material stratum is a distinction of physical, chemical and biological levels.
+These levels can be further refined.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ In accordance with the work of R. Poli, we divide the
+psychological/mental stratum into the layer of
+awareness and the layer of
+personality. Awareness comprises most
+of what is studied by cognitive science (perception, memory,
+reasoning, etc). Personality on the other hand concerns the phenomenon
+of will and the way in which someone reacts to her experiences.
+
+
+
+
+ Occurents have temporal parts and thus cannot be present at a time-boundary. Time
+belongs to them, because they happen in time and the time of the occurent
+is built into it. The relation between an occurent and a chronoid is
+determined by the projection relation.
+
+Occurents are also called generalized processes in the GFO.
+
+
+
+
+
+ Ontological_layer, all of its subconcepts and the properties layer_of and on_layer are work in progress in a premature beta state.
+ a collective term for gfo:stratum and gfo:level
+
+ Beta
+
+
+
+ Persistants are GFO's way to capture identity over time.
+
+GFO pursues an approach which
+accounts for persistence by means of a suitable
+universal whose instances are presentials. Such universals are called
+persistants. These do not change and they can be used to
+explain how presentials which have different properties at different
+times can nevertheless be the same.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ A presential exists wholly at exactly one time boundary.
+
+
+
+
+
+
+
+
+
+
+ 1
+
+
+
+
+
+
+
+ Processes are a special kind of occurent. Processes are directly in time, they have characteristics which cannot be captured by a collection of time boundaries.
+
+
+
+
+
+
+ Processual roles are dependent processes. They are roles with a process as context.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The concept of a property value reflects a relationship between the property of x and the same property as exhibited by another entity y.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Set is a category pertaining to the individuals in the ZFC set theory.
+
+
+
+
+
+ A situation is a special configuration which can be comprehended as a whole and satisfies certain conditions of unity, which are imposed by relations and categories associated with the situation. Herein, we consider situations to be the most complex kind of presentials.
+
+
+
+
+ Situoids are processes whose boundaries are situations and which satisfy certain principles of coherence, comprehensibility, and continuity. They are regarded as the most complex integrated wholes of the world. A situoid is, intuitively, a part of the
+world which is a coherent and comprehensible whole and does not need other entities in order to exist. Every situoid has a temporal extent and is framed by a topoid.
+
+
+
+
+
+
+
+
+
+
+
+ On the one hand, the social stratum is
+divided into Agents and
+Institutions. Agents are the bearers of the social
+roles that humans play. Institutions are defined as systems of
+interrelated social components. On the other hand, a social system can
+be seen as a network in which businesses, politics, art, language (and
+many other facets) both present their own features and
+influence each other.
+
+
+
+
+ GFO uses Brentano space.
+
+
+
+
+
+
+
+
+
+
+
+ Boundaries of regions are surfaces, boundaries of
+surfaces are lines, and boundaries of lines are
+points. As in the case of time-boundaries, spatial
+boundaries have no independent existence, i.e. they depend on the
+spatial entity of which they are boundaries.
+
+
+
+
+
+
+
+
+
+
+
+ Space regions are mereological sums of topoids.
+
+
+
+
+
+ A process without an instantanuous change at any of its inner time boundaries is called a state.
+
+
+
+
+ According to (Poli, 2001, 2002) (based
+on the philosopher Hartmann) we distinguish at least three ontological
+strata of the world: the material stratum, the
+mental/psychological stratum, and the
+social stratum stratum.
+
+Every entity of the world participates in certain
+strata and levels. We take the position that the layers are
+characterized by integrated systems of categories. Hence, a layer can
+be understood as a meta-category whose instances are categories of
+certain kinds. Among these levels specific forms of categorial and
+existential dependencies hold. For example, a mental entity requires
+an animate material object as its existential bearer.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Time Regions are defined as the mereological sum of chronoids,
+i.e. time regions may consist of non-connected intervals of time.
+
+
+
+
+
+ The time model of GFO is based on Brentano and the glass continuum of Allen&Hayes.
+
+
+
+
+
+ Time boundaries depend on a chronoids (i.e. they have no independent
+existence) and can coincide.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Topoids are connected compact regions of space. They have spatial boundaries.
+
+
+
+
+ Universals are immanent universals. They exist in re.
+
+
+
+
+
+
+
+
+
+
+
+
+ Property values usually appear in groups which are called value structures, value spaces or measurement systems.
+Each of these structures corresponds to some property. More intuitively, one could say that the property may be measured with respect to some measurement system.
+For instance, sizes may be measured with the values ``small'' ``big'' or ``very big'', which are the elements of one value structure.
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+The notion of a value structure of a property is similar to a quality dimension in (Gardenfors, 2000).
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+Further, value structures are related to quality spaces in DOLCE (Masolo, 2003}. A quality space consists of all ``quales'' (our property values) of some ``quality'' (our property).
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+Often it seems to be the case that a notion of distance can be defined, and that certain layers of value structures are isomorphic to some subset of real numbers, which allows for a mapping of values to pairs of a real number and a unit, as in the case of ``10 kg''.
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+ The abstract part-of relation is denoted by p(x,y);
+the argument-types of this relation are not specified, i.e. we allow
+arbitrary entities to be arguments. We assume that p(x,y) satisfies
+the condition of a partial ordering, .i.e. the following axioms: reflexivity, antisymmetry and transitivity.
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+ This relation captures the notion of existential dependence.
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+ "goal" here refers to "final state" in (Burek, 2006).
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+ The instantiation relation holds between a category and an item. It is not a relation between categories and individuals due to higher order categories such as "species".
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+ Left boundary of a chronoid.
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+ "requirement" here refers to "initial state" in (Burek, 2006).
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