From 75150fa50599eb9b231c79085fd510d37988eeea Mon Sep 17 00:00:00 2001 From: Chris Mungall Date: Thu, 13 Jul 2017 07:33:01 -0700 Subject: [PATCH] actual fix for #233 --- src/envo/Makefile | 2 +- src/envo/imports/bfo_import.owl | 150 ++++++++++++++++++++++++++++++++++------ 2 files changed, 131 insertions(+), 21 deletions(-) diff --git a/src/envo/Makefile b/src/envo/Makefile index 77e3db6..2b6e449 100644 --- a/src/envo/Makefile +++ b/src/envo/Makefile @@ -184,7 +184,7 @@ mirror/ro-classes.owl: envo-edit.owl owltools $(OBO)/ro.owl --merge-imports-closure --make-subset-by-properties -f // --remove-external-classes -k RO --remove-annotation-assertions -l -s -d -o $@ mirror/bfo.owl: envo-edit.owl - owltools $(OBO)/ro.owl --merge-imports-closure --make-subset-by-properties -f // --remove-external-classes BFO --remove-annotation-assertions -l -s -d --remove-dangling --set-ontology-id $(OBO)/bfo.owl -o $@ + owltools $(OBO)/bfo.owl --merge-imports-closure --make-subset-by-properties -f // --remove-external-classes BFO --remove-annotation-assertions -l -s -d --remove-dangling --set-ontology-id $(OBO)/bfo.owl -o $@ .PRECIOUS: mirror/%.owl mirror/uberon.owl: envo-edit.owl diff --git a/src/envo/imports/bfo_import.owl b/src/envo/imports/bfo_import.owl index f602346..1b99e4f 100644 --- a/src/envo/imports/bfo_import.owl +++ b/src/envo/imports/bfo_import.owl @@ -3,13 +3,11 @@ xml:base="http://purl.obolibrary.org/obo/envo/imports/bfo_import.owl" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:obo="http://purl.obolibrary.org/obo/" - xmlns:dc="http://purl.org/dc/elements/1.1/"> - - - + xmlns:obo="http://purl.obolibrary.org/obo/"> + @@ -30,6 +28,12 @@ + + + + + + + + + entity + + + + - continuant + - An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. + continuant @@ -54,8 +66,8 @@ + occurrent - An entity that has temporal parts and that happens, unfolds or develops through time. @@ -63,10 +75,26 @@ - independent continuant - A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + independent continuant + + + + + b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) + + + + + + + + + + + spatial region @@ -74,19 +102,25 @@ - process - An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + process + + + + p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) + + - disposition + disposition @@ -94,9 +128,18 @@ + + realizable entity + + + + + + + - A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. + quality @@ -104,19 +147,42 @@ - specifically dependent continuant - A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + specifically dependent continuant + + + + b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) + + - role - A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + role + + + + + + + + + fiat object part + + + + + + + + + function @@ -124,13 +190,57 @@ + + material entity + + + + + + + + + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + continuant fiat boundary + + + + + b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) + + + + + + + + - An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. + immaterial entity + + + + + + + + + + one-dimensional continuant fiat boundary + + + + + + + + + two-dimensional continuant fiat boundary - +