format-version: 1.4
date: 09:02:2007 13:57
saved-by: vlmir
auto-generated-by: ONTO-PERL 1.29
default-namespace: test_ontology
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_pir "PIR GO slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
subsetdef: PSI-MI_slim "Subset of PSI-MI"

[Term]
id: GRAO:0000000
name: biological entity
def: "A biological process or continuant." [GRAO:vm]
synonym: "biological-entity" EXACT [GRAO:vm]

[Term]
id: GRAO:0000001
name: biological continuant
def: "Biological entities which endure, or continue to exist, through time while undergoing different sort of changes, including changes of place." [PMID:15892874, GRAO:vm]
synonym: "biological endurant" EXACT [PMID:15892874]
synonym: "biological thing" BROAD [PMID:15892874]
is_a: GRAO:0000000 ! biological entity

[Term]
id: GRAO:0000002
name: biological process
def: "Biological entities that unfold themselves in successive temporal phases." [PMID:15892874, GRAO:vm]
synonym: "biological ocurrent" BROAD [PMID:15892874]
synonym: "biological perdurant" EXACT [PMID:15892874]
is_a: GRAO:0000000 ! biological entity
disjoint_from: GRAO:0000001 ! biological continuant

[Term]
id: GRAO:0000003
name: gene
def: "Each of the units of heredity which (except for polygenes) may be regarded as the controlling agents in the expression of single phenotypic characters and are usually segments of a chromosome at fixed positions relative to each other." [http://www.oed.com, GRAO:ea]
is_a: GRAO:0000001 ! biological continuant

[Term]
id: GRAO:0000004
name: gene product
def: "A gene product, such as a protein, or transcript, ocurring in, or formed by, living systems." [GRAO:vm]
is_a: GRAO:0000001 ! biological continuant

[Term]
id: GRAO:0000005
name: protein
def: "Proteins are polymeric macromolecules composed of one or more long chains of amino acids linked by peptide bonds, usually coiled and folded into complex globular or fibrous structures." [http://www.oed.com, GRAO:ea]
is_a: GRAO:0000004 ! gene product

[Term]
id: GRAO:0000006
name: modified protein
def: "A protein which underwent any sort of post-tranlational modification (e.g. phosphorylation)" [GRAO:vm]
is_a: GRAO:0000005 ! protein

[Term]
id: GRAO:0000007
name: kegg_cluster
def: "A cluster of ortholgous genes/proteins." [GRAO:vm]
is_a: GRAO:0000001 ! biological continuant

[Term]
id: GRAO:0000008
name: kegg_pathway
def: "A biochemical pathway." [GRAO:vm]
is_a: GRAO:0000001 ! biological continuant

[Term]
id: NCBI:9606
name: Homo sapiens
is_a: GRAO:0000001 ! biological continuant

[Term]
id: NCBI:10090
name: Mus musculus
is_a: GRAO:0000001 ! biological continuant

[Term]
id: NCBI:10116
name: Rattus norvegicus
is_a: GRAO:0000001 ! biological continuant

[Term]
id: NCBI:4896
name: Schizosaccharomyces pombe
is_a: GRAO:0000001 ! biological continuant

[Term]
id: UniProtKB:O14460
is_a: GRAO:0000005 ! protein
relationship: has_source NCBI:4896 ! Schizosaccharomyces pombe

[Term]
id: GO:0033217
name: regulation of transcription from RNA polymerase II promoter in response to iron ion starvation
namespace: biological_process
def: "Modulation of the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of a stimulus indicating the organism is deprived of iron ions." [GOC:mah]
synonym: "regulation of transcription from RNA polymerase II promoter in response to iron deficiency" EXACT []
is_a: GRAO:0000002 ! biological process

[Term]
id: GO:0005783
name: endoplasmic reticulum
namespace: cellular_component
def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]
subset: goslim_candida
subset: goslim_generic
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
synonym: "ER" EXACT []
xref: NIF_Subcellular:sao1036339110
xref: Wikipedia:Endoplasmic_reticulum
is_a: GRAO:0000001 ! biological continuant

[Term]
id: GO:0005789
name: endoplasmic reticulum membrane
namespace: cellular_component
def: "The lipid bilayer surrounding the endoplasmic reticulum." [GOC:mah]
synonym: "ER membrane" EXACT []
is_a: GRAO:0000001 ! biological continuant

[Term]
id: GO:0016020
name: membrane
namespace: cellular_component
def: "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:mah, ISBN:0815316194]
subset: goslim_candida
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
xref: Wikipedia:Biological_membrane
is_a: GRAO:0000001 ! biological continuant

[Term]
id: GO:0016021
name: integral to membrane
namespace: cellular_component
def: "Penetrating at least one phospholipid bilayer of a membrane. May also refer to the state of being buried in the bilayer with no exposure outside the bilayer. When used to describe a protein, indicates that all or part of the peptide sequence is embedded in the membrane." [GOC:go_curators]
subset: gosubset_prok
synonym: "transmembrane" RELATED [GOC:mah]
xref: Wikipedia:Transmembrane_protein
is_a: GRAO:0000001 ! biological continuant

[Term]
id: MI:0407
name: direct interaction
def: "Interaction that is proven to involve only its interactors." [PMID:14755292]
subset: PSI-MI_slim
is_a: MI:0915 ! physical association

[Term]
id: MI:0914
name: association
def: "Molecules that are experimentally shown to be associated potentially by sharing just one interactor. Often associated molecules are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule." [PMID:14755292]
subset: PSI-MI_slim
is_a: GRAO:0000002 ! biological process

[Term]
id: MI:0915
name: physical association
def: "Molecules that are experimentally shown to belong to the same functional or structural complex." [PMID:14755292]
subset: PSI-MI_slim
is_a: MI:0914 ! association

[Term]
id: MOD:00000
name: protein modification
is_a: ULO:0000001 ! biological material entity
relationship: part_of SO:0000104 ! protein

[Typedef]
id: is_a
name: is a

[Typedef]
id: codes_for
name: codes for
def: "g encodes for p where g a Gene and p is a Protein." [CCO:ea]
synonym: "encodes" EXACT [CCO:ea]
xref: CCO_REL:codes_for

[Typedef]
id: encoded_by
name: is encoded by
def: "p is encoded by g where p is a Protein and g a Gene." [CCO:ea]
synonym: "is coded by" EXACT [CCO:ea]
synonym: "is produced by" EXACT [CCO:ea]
xref: CCO_REL:encoded_by

[Typedef]
id: has_source
name: has source
def: "o has_source O where o is a gene or gene product and O an organism." [CCO:ea]
xref: CCO_REL:has_source

[Typedef]
id: has_ortholog
name: has ortholog

[Typedef]
id: has_coortholog
name: has coortholog

[Typedef]
id: has_inparalog
name: has inparalog

[Typedef]
id: has_function
name: has function
def: "Relation between an independent continuant and a function." [GOC:cjm]
comment: heart has_function to-pump-blood
is_a: bearer_of ! is bearer of
inverse_of: function_of ! is function of

[Typedef]
id: has_participant
name: has participant
def: "P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t" [PMID:15892874]
comment: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
inverse_of: participates_in ! participates in

[Typedef]
id: located_in
name: is located in
def: "C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)" [PMID:15892874]
comment: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1.    Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
is_reflexive: true
is_transitive: true
is_a: overlapped_by ! is overlapped by
holds_over_chain: contained_in located_in
holds_over_chain: located_in contained_in
holds_over_chain: located_in part_of
holds_over_chain: part_of located_in

[Typedef]
id: participates_in
name: participates in
inverse_of: has_participant ! has participant
holds_over_chain: participates_in part_of

[Typedef]
id: transformation_of
name: is transformation of
def: "Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2." [PMID:15892874]
comment: When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
is_transitive: true
inverse_of: transforms_into ! transforms into

[Typedef]
id: transforms_into
name: transforms into
xref: CCO_REL:transforms_into
inverse_of: transformation_of ! is transformation of

[Typedef]
id: part_of_cluster
name: part of cluster

[Typedef]
id: participates_in_pathway
name: participates in pathway

[Typedef]
id: part_of
name: part of

[Typedef]
id: function_of
name: function of

[Typedef]
id: bearer_of
name: bearer of

[Typedef]
id: contained_in
name: contained in

[Typedef]
id: overlapped_by
name: overlapped by