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tomato food product
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FOODON_00001164.clj
;; dev> (run! rdf/print-doc (mop/compute-class-precedence-list :obo/FOODON_00001164))
;; -------------------------
;; :obo/FOODON_00001164
;; tomato food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00001015
;; :obo/FOODON_00001057
;; :obo/FOODON_00001163
;; :obo/FOODON_00001165
;; :obo/FOODON_00001261
;; :obo/FOODON_00002141
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/AGRO_00000154
;; crop residue
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000040
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/BFO_0000001
;; entity
;; isa?
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/BFO_0000002
;; continuant
;; isa?
;; :obo/BFO_0000001
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/BFO_0000004
;; independent continuant
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/BFO_0000024
;; fiat object part
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000040
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/BFO_0000040
;; material entity
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/ENVO_00010483
;; Everything under this parent must be a mass noun. All subclasses are to be understood as being composed primarily of the named entity, rather than restricted to that entity. For example, "ENVO:water" is to be understood as "environmental material composed primarly of some CHEBI:water". This class is currently being aligned to the Basic Formal Ontology. Following this alignment, its definition and the definitions of its subclasses will be revised.
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00001002
;; The FoodOn "food product" class is provided as a branch under which new food product categories and food products themselves can be placed. Here classes are provided to differentiate a food product by its food composition, processing and/or consumption characteristics. This avoids brand name products but it may include generic food dish categories. It has a much greater depth and polyhierarchy than other agency product type schemes have in an effort to group related products together. The upper level basis of this tree originated in the environment ontology (ENVO) and from the US Code of Federal Regulations.
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00001015
;; plant food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00001057
;; plant fruit food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00001015
;; :obo/FOODON_00001261
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00001163
;; solanaceous fruit food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00001015
;; :obo/FOODON_00001057
;; :obo/FOODON_00001165
;; :obo/FOODON_00001261
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00001165
;; solanaceous food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00001015
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00001261
;; vegetable food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00001015
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00002141
;; plant fruit as vegetable food product
;; isa?
;; :obo/AGRO_00000154
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00001015
;; :obo/FOODON_00001057
;; :obo/FOODON_00001261
;; :obo/FOODON_00002381
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :obo/PO_0025131
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00002381
;; food product by organism
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00001002
;; :obo/FOODON_00002403
;; :obo/FOODON_03400361
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_00002403
;; This class is the top of FOODON's main food product hierarchy which is described in the https://www.foodon.org website, and can be searched in lookup services like https://www.ebi.ac.uk/ols/
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/FOODON_03400361
;; This class is designed to hold 3rd party food classification schemes which are being mapped to FoodOn classes using the 'has member' relation. The two hierarchies are not melded into a subclass polyhierarchy because of possible logical inconsistencies in the agency schemes. The hierarchies of agency schemes are as true to their agency representation as possible.
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000024
;; :obo/BFO_0000040
;; :obo/ENVO_00010483
;; :obo/FOODON_00002403
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
;; -------------------------
;; :obo/PO_0025131
;; Includes both material entities such as plant structures and immaterial entities such as plant anatomical spaces. CARO:0000000 'anatomical entity' is defined as: A part of a cellular organism that is either an immaterial entity or a material entity with granularity aboove the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. Refers to BFO:0000004 'independent continuant'.
;; isa?
;; :obo/BFO_0000001
;; :obo/BFO_0000002
;; :obo/BFO_0000004
;; :obo/BFO_0000040
;; :owl/Class
;; :owl/Thing
;; :rdfs/Class
{:rdf/type :owl/Class,
:rdfs/subClassOf
[{:owl/onProperty :obo/RO_0001000,
:owl/someValuesFrom :obo/FOODON_03301453,
:rdf/type :owl/Restriction}
:obo/FOODON_00002141
:obo/FOODON_00001163],
:mop/class-direct-slots [],
:obo/IAO_0000115
#:rdf{:language "en",
:value "A food product deriving from one or more tomatoes."},
:rdfs/label #:rdf{:language "en", :value "tomato food product"},
:mop/class-direct-default-initargs {},
:mop/class-default-initargs {},
:db/ident :obo/FOODON_00001164,
:mop/class-slots
[{:db/ident :obo/APOLLO_SV_00000057,
:obo/IAO_0000115
#:rdf{:language "en",
:value
"A relation between to particulars such that aRb where b can be any kind of entity while the second is a universal. b instantiates a at some times. "},
:rdf/type
#{:owl/ObjectProperty
:owl/AsymmetricProperty
:owl/IrreflexiveProperty},
:rdfs/comment
"Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, “Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain”, O. Bodenreider, ed., Proceedings of KR-MED, 2006, 57-66. Also available online at: http://ceur-ws.org/Vol-222.",
:rdfs/domain #{:obo/BFO_0000001},
:rdfs/label #:rdf{:language "en", :value "instantiates"}}
{:db/ident :obo/IAO_0000235,
:obo/IAO_0000115
#:rdf{:language "en", :value "inverse of the relation 'denotes'"},
:obo/IAO_0000117
#:rdf{:language "en",
:value "Person: Jie Zheng, Chris Stoeckert, Mike Conlon"},
:obo/IAO_0000233
"https://github.com/information-artifact-ontology/IAO/issues/206",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000001},
:rdfs/label #:rdf{:language "en", :value "denoted by"},
:rdfs/range #{:obo/IAO_0000030}}
{:rdfs/domain
#{:obo/BFO_0000040 :obo/BFO_0000002 :obo/BFO_0000031},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002330},
:obo/IAO_0000115
"x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process",
:obo/IAO_0000114 :obo/IAO_0000125,
:rdfs/label #:rdf{:language "en", :value "expressed in"},
:obo/IAO_0000117 #:rdf{:language "en", :value "Chris Mungall"},
:db/ident :obo/RO_0002206,
:owl/inverseOf :obo/RO_0002292,
:owl/propertyChainAxiom [:obo/RO_0002206 :obo/BFO_0000050],
:obo/IAO_0000112
"'neural crest cell' SubClassOf expresses some 'Wnt1 gene'",
:rdfs/range #{:obo/CARO_0000006}}
{:db/ident :obo/OMIABIS_0000048,
:obo/IAO_0000115
#:rdf{:language "en",
:value
"a is owned by b if b has complete power over a. All rights and obligations of ownership are grounded in this (primitive) relation. The claims and obligations of ownership can be partially transferred to a third party by the owner, b."},
:obo/IAO_0000119
"Reinach, A. Sämtliche Werke. Texkritische Ausgabe, München: Philosophia Verlag, 1989, p.189-204.",
:owl/inverseOf :obo/OMIABIS_0000008,
:rdf/type #{:owl/ObjectProperty :owl/AsymmetricProperty},
:rdfs/domain [:obo/BFO_0000040 :obo/IAO_0000030],
:rdfs/label #:rdf{:language "en", :value "is owned by"},
:rdfs/range
[:obo/NCBITaxon_9606
:obo/OBI_0000245
:obo/OMRSE_00000023
:obo/OMRSE_00000033]}
{:rdfs/domain [:obo/BFO_0000031 :obo/BFO_0000040],
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002330},
:obo/IAO_0000115
"x is transcribed from y if and only if x is synthesized from template y",
:obo/IAO_0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267",
:rdfs/label "transcribed from",
:obo/IAO_0000117 "Chris Mungall",
:db/ident :obo/RO_0002510,
:owl/inverseOf :obo/RO_0002511,
:rdfs/range [:obo/BFO_0000031 :obo/BFO_0000040]}
{:rdfs/domain [:obo/BFO_0000031 :obo/BFO_0000040],
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002330},
:obo/IAO_0000115 "inverse of ribosomal translation of",
:obo/IAO_0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267",
:rdfs/label "ribosomally translates to",
:obo/IAO_0000117 "Chris Mungall",
:db/ident :obo/RO_0002513,
:rdfs/range [:obo/BFO_0000031 :obo/BFO_0000040]}
{:rdfs/domain [:obo/BFO_0000031 :obo/BFO_0000040],
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002330},
:obo/IAO_0000115
"x is the ribosomal translation of y if and only if a ribosome reads x through a series of triplet codon-amino acid adaptor activities (GO:0030533) and produces y",
:obo/IAO_0000119 "http://www.ncbi.nlm.nih.gov/pubmed/20226267",
:rdfs/label "ribosomal translation of",
:obo/IAO_0000117 "Chris Mungall",
:db/ident :obo/RO_0002512,
:owl/inverseOf :obo/RO_0002513,
:rdfs/range [:obo/BFO_0000031 :obo/BFO_0000040]}
{:rdfs/domain
#{:obo/BFO_0000040 :obo/BFO_0000004 :obo/BFO_0000031},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000116
"We would like to be able to express the rule: if t transcribed from g, and t is a noncoding RNA and has an evolved function, then t has gene product g.",
:rdfs/subPropertyOf #{:obo/RO_0002330},
:obo/IAO_0000115
"definition \"x has gene product of y if and only if y is a gene (SO:0000704) that participates in some gene expression process (GO:0010467) where the output of that process is either y or something that is ribosomally translated from x\"",
:obo/IAO_0000114 :obo/IAO_0000125,
:rdfs/label #:rdf{:language "en", :value "gene product of"},
:obo/IAO_0000117 #:rdf{:language "en", :value "Chris Mungall"},
:db/ident :obo/RO_0002204,
:owl/inverseOf :obo/RO_0002205,
:owl/propertyChainAxiom [:obo/RO_0002512 :obo/RO_0002510],
:rdfs/range #{:obo/BFO_0000040 :obo/BFO_0000002 :obo/BFO_0000031}}
{:db/ident :obo/RO_0002506,
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040 :obo/BFO_0000002},
:rdfs/label "causal relation between entities",
:rdfs/range #{:obo/BFO_0000040 :obo/BFO_0000002},
:rdfs/subPropertyOf #{:obo/RO_0002410}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type
#{:owl/ObjectProperty
:owl/InverseFunctionalProperty
:owl/FunctionalProperty},
:obo/IAO_0000412 "http://purl.obolibrary.org/obo/bfo.owl",
:obo/BFO_0000180 "hasHistory",
:rdfs/subPropertyOf #{:obo/BFO_0000166 :obo/BFO_0000067},
:obo/IAO_0000115
#:rdf{:language "en",
:value "b has_history c iff c history_of b [XXX-001"},
:rdfs/isDefinedBy "http://purl.obolibrary.org/obo/bfo.owl",
:rdfs/label #:rdf{:language "en", :value "has history"},
:obo/BFO_0000179 "has-history",
:db/ident :obo/BFO_0000185,
:obo/IAO_0000600
"[copied from inverse property 'history of'] b history_of c if c is a material entity or site and b is a history that is the unique history of cAxiom: if b history_of c and b history_of d then c=d [XXX-001",
:rdfs/range #{:obo/BFO_0000015}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/SymmetricProperty :owl/ObjectProperty},
:obo/IAO_0000111 "has disposition to bind",
:obo/IAO_0000116
"This is a shortcut relation, and should expand to say that the two material entities have dispositions, point to the process in which they from a complex that realizes those dispositions, and points to the complex in which the two entities are 'bound to' each other",
:obo/IAO_0000115
"A relationship between two material entitites that each have disposition to form a complex with the other. ",
:obo/IAO_0000114 :obo/IAO_0000123,
:obo/IAO_0000119 "IEDB",
:rdfs/label "has disposition to bind",
:db/ident :obo/OBI_0001637,
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/RO_0011008,
:obo/IAO_0000115
"The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "increases by expression quantity of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0011024}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000111 #:rdf{:language "en", :value "contained in"},
:obo/IAO_0000116
["Containment is location not involving parthood, and arises only where some immaterial continuant is involved."
#:rdf{:language "en",
:value
"Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):"}
#:rdf{:language "en",
:value
"Intended meaning:\ndomain: material entity\nrange: spatial region or site (immaterial continuant)\n "}],
:obo/RO_0001900 :obo/RO_0001901,
:rdfs/label #:rdf{:language "en", :value "contained in"},
:oboInOwl/inSubset :subsets/ro-eco,
:db/ident :obo/RO_0001018,
:owl/inverseOf :obo/RO_0001019,
:owl/propertyChainAxiom [:obo/RO_0001025 :obo/BFO_0000050],
:obo/IAO_0000118 #:rdf{:language "en", :value "contained_in"},
:rdfs/range #{:obo/BFO_0000004}}
{:db/ident :obo/RO_0002595,
:obo/IAO_0000115
"A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label
"causal relation between material entity and a process",
:rdfs/range #{:obo/BFO_0000015},
:rdfs/subPropertyOf #{:obo/RO_0002410}}
{:db/ident :obo/RO_0001020,
:obo/IAO_0000112
"penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)",
:obo/IAO_0000115
"A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.",
:owl/inverseOf :obo/RO_0001022,
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label
#:rdf{:language "en", :value "is allergic trigger for"},
:rdfs/subPropertyOf #{:obo/RO_0003302}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/seeAlso
["https://github.com/obophenotype/uberon/issues/170"
"http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png"],
:rdfs/subPropertyOf #{:obo/RO_0002323},
:obo/IAO_0000115
"A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network.",
:obo/IAO_0000114 :obo/IAO_0000428,
:rdfs/label
#:rdf{:language "en", :value "in branching relationship with"},
:obo/IAO_0000117 "Chris Mungall",
:obo/RO_0004036 :obo/BFO_0000050,
:db/ident :obo/RO_0002375,
:obo/IAO_0000232
["This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)"
"Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships"],
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/RO_0003001,
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty :owl/IrreflexiveProperty},
:obo/IAO_0000115
#:rdf{:language "en",
:value
"\"immersed in\" is a relation between a (physical) entity and a fluid substance in which the entity is wholely or substantially surrounded by the substance."},
:obo/IAO_0000114 :obo/IAO_0000428,
:rdfs/label #:rdf{:language "en", :value "immersed in"},
:obo/IAO_0000117 "Damion Dooley",
:db/ident :obo/RO_0009003,
:obo/IAO_0000112
#:rdf{:language "en",
:value "sardines 'immersed in' some 'oil and mustard'"},
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/RO_0003002,
:obo/IAO_0000115
"Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "represses expression of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0002449}}
{:db/ident :obo/RO_0011007,
:obo/IAO_0000115
"The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B.\n\nFor example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "decreases by repression quantity of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0011023}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000111
#:rdf{:language "en", :value "is_manufactured_by"},
:obo/IAO_0000115
#:rdf{:language "en",
:value
"c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the \"Manufacturer Role\", and those people/and or machines were members or of directed by the organization to do this."},
:obo/IAO_0000114 :obo/IAO_0000123,
:rdfs/label #:rdf{:language "en", :value "is_manufactured_by"},
:obo/IAO_0000117
[#:rdf{:language "en", :value "Alan Ruttenberg"}
#:rdf{:language "en", :value "Liju Fan"}],
:db/ident :obo/OBI_0000304,
:obo/IAO_0000112
#:rdf{:language "en",
:value
"http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)"},
:obo/IAO_0000118
[#:rdf{:language "en", :value "has_manufacturer"}
#:rdf{:language "en", :value "has_make"}],
:rdfs/range [:obo/NCBITaxon_9606 :obo/OBI_0000245]}
{:db/ident :obo/RO_0011003,
:obo/IAO_0000115
"The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "regulates quantity of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0002566}}
{:db/ident :obo/RO_0002434,
:obo/IAO_0000115
"A relationship that holds between two entities in which the processes executed by the two entities are causally connected.",
:oboInOwl/hasExactSynonym "in pairwise interaction with",
:rdf/type #{:owl/SymmetricProperty :owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "interacts with",
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty :owl/IrreflexiveProperty},
:obo/IAO_0000116
#:rdf{:language "en",
:value
"The relation X 'has substance added' some Y doesn't imply that X still has Y in any detectable fashion subsequent to the addition. Water in dehydrated food or ice cubes are examples, as is food that undergoes chemical transformation. This definition should encompass recipe ingredients."},
:obo/IAO_0000115
#:rdf{:language "en",
:value
"\"has substance added\" is a relation existing between a (physical) entity and a substance in which the entity has had the substance added to it at some point in time."},
:obo/IAO_0000114 :obo/IAO_0000428,
:rdfs/label #:rdf{:language "en", :value "has substance added"},
:obo/IAO_0000117 "Damion Dooley",
:db/ident :obo/RO_0009001,
:obo/IAO_0000112
#:rdf{:language "en",
:value "muffin 'has substance added' some 'baking soda'"},
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000115
#:rdf{:language "en",
:value
"'has consumer' is a relation between a material entity and an organism in which the former can normally be digested or otherwise absorbed by the latter without immediate or persistent ill effect."},
:obo/IAO_0000114 :obo/IAO_0000428,
:rdfs/label #:rdf{:language "en", :value "has consumer"},
:obo/IAO_0000117 "Damion Dooley",
:db/ident :obo/RO_0009004,
:obo/IAO_0000112
#:rdf{:language "en",
:value "sardine has consumer some homo sapiens"},
:rdfs/range #{:obo/CARO_0001010}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0011004},
:obo/IAO_0000115
"The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.",
:rdfs/label "indirectly positively regulates activity of",
:obo/IAO_0000117 "Vasundra Touré",
:db/ident :obo/RO_0011013,
:obo/IAO_0000118 "indirectly activates",
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/RO_0003000,
:owl/inverseOf :obo/RO_0003001,
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:oboInOwl/hasRelatedSynonym
"has active pharmaceutical ingredient",
:rdfs/subPropertyOf #{:obo/BFO_0000051},
:obo/IAO_0000115
"A relationship that holds between a substance and a chemical entity, if the chemical entity is part of the substance, and the chemical entity forms the biologically active component of the substance.",
:rdfs/label "has active ingredient",
:oboInOwl/hasExactSynonym "has active substance",
:db/ident :obo/RO_0002248,
:owl/inverseOf :obo/RO_0002249,
:obo/IAO_0000112
"Any portion of roundup 'has active ingredient' some glyphosate",
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty :owl/IrreflexiveProperty},
:obo/IAO_0000115
#:rdf{:language "en",
:value
"\"has substance removed\" is a relation existing between two physical entities in which the first entity has had the second entity (a substance) removed from it at some point in time."},
:obo/IAO_0000114 :obo/IAO_0000428,
:rdfs/label #:rdf{:language "en", :value "has substance removed"},
:obo/IAO_0000117 #:rdf{:language "en", :value "Damion Dooley"},
:db/ident :obo/RO_0009002,
:obo/IAO_0000112
#:rdf{:language "en",
:value
"'egg white' 'has substance removed' some 'egg yolk'"},
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf
#{:obo/RO_0002436 :obo/RO_0011002 :obo/RO_0002566},
:obo/IAO_0000115
"The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.",
:rdfs/label "directly regulates activity of",
:oboInOwl/hasExactSynonym "molecularly controls",
:db/ident :obo/RO_0002448,
:owl/propertyChainAxiom
[:obo/RO_0002327 :obo/RO_0002211 :obo/RO_0002333],
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/RO_0011002,
:obo/IAO_0000115
"The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "regulates activity of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0002566}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002131},
:obo/IAO_0000115
"x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x.",
:obo/IAO_0000119 "UBERON:cjm",
:rdfs/label "conduit for",
:obo/IAO_0000117 "Chris Mungall",
:oboInOwl/inSubset :subsets/ro-eco,
:db/ident :obo/RO_0002570,
:obo/IAO_0000232
"This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through.",
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000111 "bound_to",
:obo/IAO_0000116
"The definition of this term is modeled after the Chebi:50967 and GO:0005488 terms. Further alignment of the logical definitions with those ontologies will require agreement on the placement of GO:molecular function in BFO among other things. OBI will retire this term once such an alignment is achieved as 'bound to' is not in the primary OBI scope.",
:obo/IAO_0000115
"A relationship between two material entities that form a complex based on a selective, non-covalent interaction.",
:obo/IAO_0000114 :obo/IAO_0000123,
:rdfs/label "bound_to",
:db/ident :obo/OBI_1110119,
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain [:obo/BFO_0000029 :obo/BFO_0000040],
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000412 "http://purl.obolibrary.org/obo/bfo.owl",
:obo/BFO_0000180 "containsProcess",
:obo/IAO_0000115
"[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t [XXX-001",
:rdfs/isDefinedBy "http://purl.obolibrary.org/obo/bfo.owl",
:rdfs/label #:rdf{:language "en", :value "contains process"},
:obo/BFO_0000179 "contains-process",
:db/ident :obo/BFO_0000067,
:rdfs/range [:obo/BFO_0000015 :obo/BFO_0000035]}
{:db/ident :obo/RO_0003003,
:obo/IAO_0000115
"Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "increases expression of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0002450}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002448},
:obo/IAO_0000115
"The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.",
:rdfs/label "directly positively regulates activity of",
:oboInOwl/hasExactSynonym "molecularly increases activity of",
:db/ident :obo/RO_0002450,
:owl/propertyChainAxiom
[:obo/RO_0002327 :obo/RO_0002629 :obo/RO_0002333],
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0011009},
:obo/IAO_0000115
"An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.",
:rdfs/label "stabilizes quantity of",
:obo/IAO_0000117 "Vasundra Touré",
:db/ident :obo/RO_0011015,
:obo/IAO_0000112
"AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)",
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000111 "has_supplier",
:obo/IAO_0000115
"A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.",
:obo/IAO_0000114 :obo/IAO_0000120,
:rdfs/label "has_supplier",
:obo/IAO_0000117
["PERSON: Frank Gibson"
"PERSON: Alan Rutternberg"
"PERSON: Melanie Courtot"
"PERSON: Cristian Cocos"],
:db/ident :obo/OBI_0000647,
:rdfs/range [:obo/NCBITaxon_9606 :obo/OBI_0000245]}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002448},
:obo/IAO_0000115
"The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.",
:rdfs/label "directly negatively regulates activity of",
:oboInOwl/hasExactSynonym "molecularly decreases activity of",
:db/ident :obo/RO_0002449,
:owl/propertyChainAxiom
[:obo/RO_0002327 :obo/RO_0002630 :obo/RO_0002333],
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/COB_0000801,
:rdf/type #{:owl/DatatypeProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label
#:rdf{:language "en", :value "has number of atomic nuclei"},
:rdfs/range #{:xsd/nonNegativeInteger}}
{:db/ident :obo/RO_0001021,
:obo/IAO_0000115
"A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.",
:owl/inverseOf :obo/RO_0001023,
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label
#:rdf{:language "en", :value "is autoimmune trigger for"},
:rdfs/subPropertyOf #{:obo/RO_0003302}}
{:db/ident :obo/RO_0011010,
:obo/IAO_0000115
"The entity A has an activity that directly negatively regulates the quantity of B.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "directly negatively regulates quantity of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0011021}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/SymmetricProperty :owl/ObjectProperty},
:rdfs/seeAlso
["http://dx.doi.org/10.1016/j.ecoinf.2014.08.005"
"http://eol.org/schema/terms/interactsWith"],
:rdfs/subPropertyOf #{:obo/RO_0002321 :obo/RO_0002434},
:obo/IAO_0000115
"An interaction relationship in which at least one of the partners is an organism and the other is either an organism or an abiotic entity with which the organism interacts.",
:rdfs/label "biotically interacts with",
:obo/IAO_0000117 "Chris Mungall",
:oboInOwl/inSubset :subsets/ro-eco,
:db/ident :obo/RO_0002437,
:obo/IAO_0000118 "interacts with on organism level",
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/VO_0005242,
:obo/IAO_0000115
"An object property that represents a relation between a material entity and biological process",
:obo/IAO_0000117 "Anthony Huffman, Oliver He",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label
#:rdf{:language "en",
:value "up-expressed as immune signature of"},
:rdfs/range #{:obo/BFO_0000015}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0011010},
:obo/IAO_0000115
"An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.",
:rdfs/label "destabilizes quantity of",
:obo/IAO_0000117 "Vasundra Touré",
:db/ident :obo/RO_0011014,
:obo/IAO_0000112
"AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)",
:rdfs/range #{:obo/BFO_0000040}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:rdfs/subPropertyOf #{:obo/RO_0002323},
:obo/IAO_0000115
"a colocalizes_with b if and only if a is transiently or peripherally associated with b[GO].",
:dcterms/creator "Gene Ontology Consortium",
:rdfs/label #:rdf{:language "en", :value "colocalizes with"},
:obo/IAO_0000117 "Chris Mungall",
:oboInOwl/inSubset :obo/valid_for_go_gp2term,
:db/ident :obo/RO_0002325,
:obo/IAO_0000232
"In the context of the Gene Ontology, colocalizes_with may be used for annotating to cellular component terms[GO]",
:obo/IAO_0000112
"Clp1p relocalizes from the nucleolus to the spindle and site of cell division; i.e. it is associated transiently with the spindle pole body and the contractile ring (evidence from GFP fusion). Clp1p colocalizes_with spindle pole body (GO:0005816) and contractile ring (GO:0005826)",
:rdfs/range #{:obo/BFO_0000040}}
{:db/ident :obo/RO_0011004,
:obo/IAO_0000115
"The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label
#:rdf{:language "en", :value "indirectly regulates activity of"},
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0011002}}
{:db/ident :obo/RO_0011009,
:obo/IAO_0000115
"The entity A has an activity that directly positively regulates the quantity of B.",
:obo/IAO_0000117 "Vasundra Touré",
:rdf/type #{:owl/ObjectProperty},
:rdfs/domain #{:obo/BFO_0000040},
:rdfs/label "directly positively regulates quantity of",
:rdfs/range #{:obo/BFO_0000040},
:rdfs/subPropertyOf #{:obo/RO_0011021}}
{:rdfs/domain #{:obo/BFO_0000040},
:rdf/type #{:owl/ObjectProperty},
:obo/IAO_0000116
[#:rdf{:language "en",
:value
"Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."}
#:rdf{:language "en",
:value
"A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."}],
:obo/IAO_0000115
#:rdf{:language "en",
:value
"a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"},
:obo/RO_0001900 :obo/RO_0001901,
:rdfs/label #:rdf{:language "en", :value "has 2D boundary"},
:db/ident :obo/RO_0002002,
:obo/IAO_0000112
#:rdf{:language "en",
:value "my body has 2D boundary the surface of my skin"},
:obo/IAO_0000118
[#:rdf{:language "en", :value "has boundary"}
#:rdf{:language "en", :value "has_2D_boundary"}],
:rdfs/range #{:obo/BFO_0000141}}],
:mop/class-precedence-list
[:obo/FOODON_00001164
:obo/AGRO_00000154
:obo/BFO_0000001
:obo/BFO_0000002
:obo/BFO_0000004
:obo/BFO_0000024
:obo/BFO_0000040
:obo/ENVO_00010483
:obo/FOODON_00001002
:obo/FOODON_00001015
:obo/FOODON_00001057
:obo/FOODON_00001163
:obo/FOODON_00001165
:obo/FOODON_00001261
:obo/FOODON_00002141
:obo/FOODON_00002381
:obo/FOODON_00002403
:obo/FOODON_03400361
:obo/PO_0025131
:owl/Class
:owl/Thing
:rdfs/Class]}
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