format-version: 1.0
date: 28:06:2006 13:57
saved-by: easr
auto-generated-by: easr
default-namespace: apo
remark: <p>This file holds the Upper Level Ontology in APO.</p>

[Term]
id: APO:U0000000
name: cell-cycle entity
def: "A process or continuant." [APO:ea]
synonym: "cell cycle entity" EXACT [APO:ea]

[Term]
id: APO:U0000001
name: continuant
def: "Entities which endure, or continue to exist, through time while undergoing different sort of changes, including changes of place." [PMID:15892874]
synonym: "endurant" EXACT [PMID:15892874]
synonym: "thing" BROAD [PMID:15892874]
disjoint_from: APO:U0000002 ! process
is_a: APO:U0000000 ! cell-cycle entity

[Term]
id: APO:U0000002
name: process
def: "Entities that unfold themselves in successive temporal phases." [PMID:15892874]
synonym: "perdurant" EXACT [PMID:15892874]
synonym: "ocurrent" BROAD [PMID:15892874]
disjoint_from: APO:U0000001 ! continuant
is_a: APO:U0000000 ! cell-cycle entity

[Term]
id: APO:U0000003
name: biopolymer
def: "A polymer, such as a protein, nucleic acid, or transcript, ocurring in, or formed by, living systems." [APO:ea]
synonym: "bio-polymer" EXACT [APO:ea]
is_a: APO:U0000001 ! continuant

[Term]
id: APO:U0000004
name: gene
def: "A locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions." [SO:0000704]
xref: SO:0000704
disjoint_from: APO:U0000005 ! protein
is_a: APO:U0000003 ! biopolymer

[Term]
id: APO:U0000005
name: protein
def: "One or more polypeptides which may, or may not, be covalently bonded, and which assume a native secondary and tertiary structure." [SO:0000358]
xref: SO:0000358
disjoint_from: APO:U0000004 ! gene
is_a: APO:U0000003 ! biopolymer

[Term]
id: APO:U0000006
name: transcript
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:0000673]
xref: SO:0000673
is_a: APO:U0000003 ! biopolymer

[Term]
id: APO:U0000007
name: interaction
def: "Any reciprocal or mutual action or effect between two continuants." [APO:ea]
is_a: APO:U0000002 ! process

[Term]
id: APO:U0000008
name: pathway
def: "A chain of interactions undergone by a given biopolymer or molecular entity in a particular organism." [APO:ea]
is_a: APO:U0000002 ! process

[Term]
id: APO:U0000009
name: small molecule
def: "A small structural unit of matter consisting of one or more atoms." [APO:ea]
is_a: APO:U0000001 ! continuant

[Term]
id: APO:U0000010
name: complex
def: "Any distinct chemical species in which two or more identical or nonidentical chemical species are associated." [APO:ea]
is_a: APO:U0000001 ! continuant

[Typedef]
id: is_a
name: is_a
builtin: true
def: "For continuants: C is_a C' if and only if: given any c that instantiates C at a time t, c instantiates C' at t. For processes: P is_a P' if and only if: that given any p that instantiates P, then p instantiates P'." [PMID:15892874]
comment: The is_a relationship is considered axiomatic by the obo file format specification, and by OWL
exact_synonym: "is_subtype_of" []
xref_analog: owl:subClassOf
is_reflexive: true
is_anti_symmetric: true
is_transitive: true