format-version: 1.2
date: 17:06:2008 17:47
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"
default-namespace: file:/Users/cjm/cvs/go/scratch/transitive_closure/z

[Term]
id: GO:0006915
name: apoptosis
namespace: biological_process
def: "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle the cell and result in cell death. Apoptosis begins internally with condensation and subsequent fragmentation of the cell nucleus (blebbing) while the plasma membrane remains intact. Other characteristics of apoptosis include DNA fragmentation and the exposure of phosphatidyl serine on the cell surface." [GOC:go_curators, ISBN:0198506732]
synonym: "apoptotic programmed cell death" EXACT []
synonym: "programmed cell death by apoptosis" EXACT []
synonym: "signaling (initiator) caspase activity" RELATED []
synonym: "type I programmed cell death" NARROW []
xref: Reactome:109581
xref: Reactome:212025
xref: Reactome:221788
xref: Reactome:230365
xref: Reactome:238478
xref: Reactome:245020
xref: Reactome:249908
xref: Reactome:252627
xref: Reactome:255810
xref: Reactome:259206
xref: Reactome:262565
xref: Reactome:265386
xref: Reactome:268517
xref: Reactome:274243
xref: Reactome:280709
xref: Reactome:286733
xref: Reactome:288390
is_a: GO:0012501 ! programmed cell death

[Term]
id: GO:0006916
name: anti-apoptosis
namespace: biological_process
def: "A process which directly inhibits any of the steps required for cell death by apoptosis." [GOC:go_curators]
synonym: "apoptosis inhibitor activity" RELATED []
is_a: GO:0043066 ! negative regulation of apoptosis

[Term]
id: GO:0008150
name: biological_process
namespace: biological_process
def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete]
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
subset: goslim_candida
subset: goslim_generic
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: goslim_yeast
subset: gosubset_prok
synonym: "biological process unknown" NARROW []
synonym: "physiological process" EXACT []

[Term]
id: GO:0008219
name: cell death
namespace: biological_process
def: "The specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:ems]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
synonym: "necrosis" RELATED []
is_a: GO:0016265 ! death
is_a: GO:0048869 ! cellular developmental process
relationship: part_of GO:0048468 ! cell development

[Term]
id: GO:0009987
name: cellular process
namespace: biological_process
def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators, GOC:isa_complete]
subset: goslim_goa
subset: goslim_pir
subset: goslim_plant
subset: gosubset_prok
synonym: "cell growth and/or maintenance" NARROW []
synonym: "cell physiology" EXACT []
synonym: "cellular physiological process" EXACT []
is_a: GO:0008150 ! biological_process
disjoint_from: GO:0032501 ! null
disjoint_from: GO:0051704 ! null

[Term]
id: GO:0012501
name: programmed cell death
namespace: biological_process
def: "Cell death resulting from activation of endogenous cellular processes." [GOC:lr]
comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'.
synonym: "necrosis" RELATED []
is_a: GO:0008219 ! cell death

[Term]
id: GO:0016265
name: death
namespace: biological_process
def: "A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism." [GOC:mah, ISBN:0877797099]
comment: See also the biological process term 'apoptosis ; GO:0006915'.
subset: goslim_generic
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0032502 ! developmental process

[Term]
id: GO:0030154
name: cell differentiation
namespace: biological_process
def: "The process whereby relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate." [ISBN:0198506732]
subset: goslim_generic
subset: goslim_goa
subset: goslim_plant
subset: gosubset_prok
is_a: GO:0048869 ! cellular developmental process

[Term]
id: GO:0032502
name: developmental process
namespace: biological_process
def: "A biological process whose specific outcome is the progression of an integrated living unit: a cell, tissue, organ, or organism over time from an initial condition to a later condition." [GOC:isa_complete]
subset: goslim_pir
subset: gosubset_prok
synonym: "development" NARROW []
is_a: GO:0008150 ! biological_process

[Term]
id: GO:0042981
name: regulation of apoptosis
namespace: biological_process
def: "Any process that modulates the occurrence or rate of cell death by apoptosis." [GOC:jl]
synonym: "apoptosis regulator activity" RELATED []
is_a: GO:0043067 ! regulation of programmed cell death
relationship: regulates GO:0006915 ! apoptosis

[Term]
id: GO:0043066
name: negative regulation of apoptosis
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of cell death by apoptosis." [GOC:jl]
synonym: "down regulation of apoptosis" EXACT []
synonym: "down-regulation of apoptosis" EXACT []
synonym: "downregulation of apoptosis" EXACT []
synonym: "inhibition of apoptosis" NARROW []
is_a: GO:0042981 ! regulation of apoptosis
is_a: GO:0043069 ! negative regulation of programmed cell death
relationship: negatively_regulates GO:0006915 ! apoptosis

[Term]
id: GO:0043067
name: regulation of programmed cell death
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl]
is_a: GO:0050793 ! regulation of developmental process
is_a: GO:0050794 ! regulation of cellular process
relationship: regulates GO:0012501 ! programmed cell death

[Term]
id: GO:0043069
name: negative regulation of programmed cell death
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl]
synonym: "down regulation of programmed cell death" EXACT []
synonym: "down-regulation of programmed cell death" EXACT []
synonym: "downregulation of programmed cell death" EXACT []
synonym: "inhibition of programmed cell death" NARROW []
is_a: GO:0043067 ! regulation of programmed cell death
is_a: GO:0048523 ! negative regulation of cellular process
is_a: GO:0051093 ! negative regulation of developmental process
relationship: negatively_regulates GO:0012501 ! programmed cell death

[Term]
id: GO:0045767
name: regulation of anti-apoptosis
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of anti-apoptosis." [GOC:go_curators]
is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0006916 ! anti-apoptosis

[Term]
id: GO:0045768
name: positive regulation of anti-apoptosis
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of anti-apoptosis." [GOC:go_curators]
synonym: "activation of anti-apoptosis" NARROW []
synonym: "stimulation of anti-apoptosis" NARROW []
synonym: "up regulation of anti-apoptosis" EXACT []
synonym: "up-regulation of anti-apoptosis" EXACT []
synonym: "upregulation of anti-apoptosis" EXACT []
is_a: GO:0045767 ! regulation of anti-apoptosis
is_a: GO:0048518 ! positive regulation of biological process
relationship: positively_regulates GO:0006916 ! anti-apoptosis

[Term]
id: GO:0048468
name: cell development
namespace: biological_process
def: "The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." [GOC:go_curators]
subset: goslim_candida
subset: gosubset_prok
is_a: GO:0009987 ! cellular process
relationship: part_of GO:0030154 ! cell differentiation

[Term]
id: GO:0048518
name: positive regulation of biological process
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jic]
subset: gosubset_prok
synonym: "activation of biological process" NARROW []
synonym: "positive regulation of physiological process" EXACT []
synonym: "stimulation of biological process" NARROW []
synonym: "up regulation of biological process" EXACT []
synonym: "up-regulation of biological process" EXACT []
synonym: "upregulation of biological process" EXACT []
is_a: GO:0050789 ! regulation of biological process
relationship: positively_regulates GO:0008150 ! biological_process

[Term]
id: GO:0048519
name: negative regulation of biological process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jic]
subset: gosubset_prok
synonym: "down regulation of biological process" EXACT []
synonym: "down-regulation of biological process" EXACT []
synonym: "downregulation of biological process" EXACT []
synonym: "inhibition of biological process" NARROW []
synonym: "negative regulation of physiological process" EXACT []
is_a: GO:0050789 ! regulation of biological process
relationship: negatively_regulates GO:0008150 ! biological_process

[Term]
id: GO:0048523
name: negative regulation of cellular process
namespace: biological_process
def: "Any process that stops, prevents or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:jic]
subset: gosubset_prok
synonym: "down regulation of cellular process" EXACT []
synonym: "down-regulation of cellular process" EXACT []
synonym: "downregulation of cellular process" EXACT []
synonym: "inhibition of cellular process" NARROW []
synonym: "negative regulation of cellular physiological process" EXACT []
is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0050794 ! regulation of cellular process
relationship: negatively_regulates GO:0009987 ! cellular process

[Term]
id: GO:0048869
name: cellular developmental process
namespace: biological_process
def: "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." [GOC:isa_complete]
subset: gosubset_prok
is_a: GO:0009987 ! cellular process
is_a: GO:0032502 ! developmental process

[Term]
id: GO:0050789
name: regulation of biological process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators]
subset: goslim_generic
subset: goslim_goa
subset: gosubset_prok
synonym: "regulation of physiological process" EXACT []
is_a: GO:0065007 ! biological regulation
relationship: regulates GO:0008150 ! biological_process

[Term]
id: GO:0050793
name: regulation of developmental process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators]
subset: gosubset_prok
is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0032502 ! developmental process

[Term]
id: GO:0050794
name: regulation of cellular process
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [GOC:go_curators]
subset: gosubset_prok
synonym: "regulation of cellular physiological process" EXACT []
is_a: GO:0050789 ! regulation of biological process
relationship: regulates GO:0009987 ! cellular process

[Term]
id: GO:0051093
name: negative regulation of developmental process
namespace: biological_process
def: "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai]
subset: gosubset_prok
synonym: "down regulation of developmental process" EXACT []
synonym: "down-regulation of developmental process" EXACT []
synonym: "downregulation of developmental process" EXACT []
synonym: "inhibition of developmental process" NARROW []
is_a: GO:0048519 ! negative regulation of biological process
is_a: GO:0050793 ! regulation of developmental process
relationship: negatively_regulates GO:0032502 ! developmental process

[Term]
id: GO:0065007
name: biological regulation
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of any biological process, quality or function." [GOC:isa_complete]
subset: goslim_pir
subset: gosubset_prok
synonym: "regulation" BROAD []
is_a: GO:0008150 ! biological_process

[Term]
id: MGI:MGI:88139
name: Bcl2l1
namespace: feature
synonym: "Bcl(X)L"   []
synonym: "Bcl-XL"   []
synonym: "Bcl-Xs"   []
synonym: "BclX"   []
synonym: "bcl-x"   []
is_a: gene 
!relationship: OBD:in_organism NCBITaxon:10090
relationship: has_function_in GO:0045768

[Term]
id: RGD:RGD:2138
name: Apoe
namespace: feature
is_a: gene 
!relationship: OBD:in_organism NCBITaxon:10116
relationship: has_function_in GO:0006916

[Typedef]
id: negatively_regulates
name: negatively_regulates
namespace: gene_ontology
is_a: regulates ! regulates
transitive_over: part_of

[Typedef]
id: part_of
name: part_of
namespace: gene_ontology
xref: OBO_REL:part_of
is_transitive: true

[Typedef]
id: positively_regulates
name: positively_regulates
namespace: gene_ontology
is_a: regulates ! regulates
transitive_over: part_of

[Typedef]
id: regulates
name: regulates
namespace: gene_ontology
transitive_over: part_of

[Typedef]
id: indirectly_regulates
name: indirectly_regulates
namespace: gene_ontology
holds_over_chain: regulates regulates
is_transitive: true

[Typedef]
id: indirectly_positively_regulates
name: indirectly_positively_regulates
is_a: indirectly_regulates
namespace: gene_ontology
holds_over_chain: positively_regulates positively_regulates
holds_over_chain: negatively_regulates negatively_regulates
is_transitive: true

[Typedef]
id: indirectly_negatively_regulates
name: indirectly_negatively_regulates
is_a: indirectly_regulates
namespace: gene_ontology
holds_over_chain: positively_regulates negatively_regulates
holds_over_chain: negatively_regulates positively_regulates 

[Typedef]
id: regulator_of
name: regulator_of
namespace: relation
comment: 
domain: IndependentContinuant 
range: Process 
holds_over_chain: has_function_in regulates  ! regulates

[Typedef]
id: indirect_regulator_of
name: indirect_regulator_of
namespace: relation
comment: 
domain: IndependentContinuant 
range: Process 
holds_over_chain: has_function_in indirectly_regulates

[Typedef]
id: indirect_positive_regulator_of
namespace: relation
comment: 
domain: IndependentContinuant 
range: Process 
holds_over_chain: has_function_in indirectly_positively_regulates

[Typedef]
id: indirect_negative_regulator_of
namespace: relation
comment: 
domain: IndependentContinuant 
range: Process 
holds_over_chain: has_function_in indirectly_negatively_regulates

[Typedef]
id: positive_regulator_of
name: positive_regulator_of
namespace: relation
comment: 
is_a: regulator_of 
domain: IndependentContinuant 
range: Process 
holds_over_chain: has_function_in positively_regulates  ! positively_regulates

[Typedef]
id: negative_regulator_of
name: negative_regulator_of
namespace: relation
comment: 
is_a: regulator_of 
domain: IndependentContinuant 
range: Process 
holds_over_chain: has_function_in negatively_regulates  ! negatively_regulates

[Typedef]
id: has_function_in
name: has_function_in