TEMP
type: Ontology
auto-generated-by: OBO-Edit 2.1-beta13
date: 01:11:2011 15:47
default-namespace: Phage ontology
has_obo_format_version: 1.2
saved-by: ariane

definition
type: AnnotationProperty

term replaced by
type: AnnotationProperty

consider
type: AnnotationProperty

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

part_of
type: ObjectProperty
type: TransitiveProperty
created by: jane
creation date: 2009-04-23T02:02:33Z
has_obo_namespace: default_namespace
id: part_of

phage process
type: Class
subclass of: Restriction
  on property: part_of
  some values from: bacteriophage
definition: All processes related to the phage developmental cycles.
has_obo_namespace: Phage ontology
id: phi:0000001

Axiom
annotated source: phage process
annotated property: definition
annotated target: All processes related to the phage developmental cycles.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage infectious cycle
type: Class
subclass of: phage process
definition: The set of processes by which a bacteriophage multiplies. Upon infection of a host bacterial cell, virulent phages replicate the viral genome and assemble progeny particles. Temperate phages can either follow that same route or establish as a prophage (lysogeny). Under some circumstances the prophage can be induced and complete a lytic cycle.
database_cross_reference: GO:0019058
database_cross_reference: GO:0019067
database_cross_reference: GO:0030068
has_exact_synonym: lytic viral life cycle
has_obo_namespace: Phage ontology
has_related_synonym: viral assembly, maturation, egress, and release
has_related_synonym: viral infectious cycle
id: phi:0000002

Axiom
annotated source: phage infectious cycle
annotated property: definition
annotated target: The set of processes by which a bacteriophage multiplies. Upon infection of a host bacterial cell, virulent phages replicate the viral genome and assemble progeny particles. Temperate phages can either follow that same route or establish as a prophage (lysogeny). Under some circumstances the prophage can be induced and complete a lytic cycle.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage infectious cycle
annotated property: has_exact_synonym
annotated target: lytic viral life cycle
database_cross_reference: GO:0030068

Axiom
annotated source: phage infectious cycle
annotated property: has_related_synonym
annotated target: viral assembly, maturation, egress, and release
database_cross_reference: GO:0019067

Axiom
annotated source: phage infectious cycle
annotated property: has_related_synonym
annotated target: viral infectious cycle
database_cross_reference: GO:0019058

phage pre adsorption
type: Class
definition: Any process by which a phage loosely binds to its host surface and scans it for receptors with its fibers, spikes or a baseplate component.
has_obo_namespace: Phage ontology
id: phi:0000003
deprecated: true

Axiom
annotated source: phage pre adsorption
annotated property: definition
annotated target: Any process by which a phage loosely binds to its host surface and scans it for receptors with its fibers, spikes or a baseplate component.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage adsorption
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
subclass of: Restriction
  on property: part_of
  some values from: phage lytic cycle
definition: Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, recognizes and binds to its specific receptor on the host cell surface. This process can include enzymatic degradation of the surface polysaccharide of the bacterium.
has_obo_namespace: Phage ontology
id: phi:0000004
comment: Often defined by subtraction of the number of unadsorbed phages measured either as the number of plaque forming units (pfu) recovered following chloroform treatment of infected cells, or by co-sedimentation of pfu with cells (with or without dilution before centrifugation). These methods may give different values for the % adsorbed phage.

Axiom
annotated source: phage adsorption
annotated property: definition
annotated target: Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, recognizes and binds to its specific receptor on the host cell surface. This process can include enzymatic degradation of the surface polysaccharide of the bacterium.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage reversible adsorption
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage adsorption
definition: Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, initially recognizes and binds to its specific receptor on the host cell surface.
has_obo_namespace: Phage ontology
id: phi:0000005
comment: This process was historically defined by the release, by Waring blending or sonication, by dilution and centrifugation, or by filtration and washing, of infective virions from their complexes with cells, thus contrary to what is observed after irreversible adsorption.

Axiom
annotated source: phage reversible adsorption
annotated property: definition
annotated target: Process by which a bacteriophage, using its tail fibers, spikes or a baseplate component, initially recognizes and binds to its specific receptor on the host cell surface.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage irreversible adsorption
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage adsorption
definition: The process by which conformational changes of virion proteins or injection of virion proteins into the infected cell initially commit infection. Disruption of the phage:cell complex at this step results in the loss of infective phage virions.
has_obo_namespace: Phage ontology
id: phi:0000006

Axiom
annotated source: phage irreversible adsorption
annotated property: definition
annotated target: The process by which conformational changes of virion proteins or injection of virion proteins into the infected cell initially commit infection. Disruption of the phage:cell complex at this step results in the loss of infective phage virions.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage lysogeny
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage infectious cycle
definition: A set of processes by which temperate bacteriophages establish as a prophage either integrated in the host genome at a more or less specific or random location or as a linear or as a circular plasmid in the host cytoplasm. The lytic functions are repressed by a phage encoded lysogeny repressor. The lysogenic bacterium is immune to superinfection by phages related to the prophage and susceptible to that same repressor. Phages that are insensitive to that repressor are called heteroimmune.
has_broad_synonym: establishment of viral latency
database_cross_reference: GO:001904
has_obo_namespace: Phage ontology
id: phi:0000007

Axiom
annotated source: phage lysogeny
annotated property: definition
annotated target: A set of processes by which temperate bacteriophages establish as a prophage either integrated in the host genome at a more or less specific or random location or as a linear or as a circular plasmid in the host cytoplasm. The lytic functions are repressed by a phage encoded lysogeny repressor. The lysogenic bacterium is immune to superinfection by phages related to the prophage and susceptible to that same repressor. Phages that are insensitive to that repressor are called heteroimmune.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage lysogeny
annotated property: has_broad_synonym
annotated target: establishment of viral latency
database_cross_reference: GO:001904

phage DNA translocation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
subclass of: Restriction
  on property: part_of
  some values from: phage lytic cycle
definition: Process by which a bacteriophage transfers its DNA in the host cell.
has_broad_synonym: viral genome transport in host cell
database_cross_reference: GO:0046796
has_obo_namespace: Phage ontology
id: phi:0000008
comment: Formerly Ejection/injection.

Axiom
annotated source: phage DNA translocation
annotated property: definition
annotated target: Process by which a bacteriophage transfers its DNA in the host cell.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage DNA translocation
annotated property: has_broad_synonym
annotated target: viral genome transport in host cell
database_cross_reference: GO:0046796

phage assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lytic cycle
definition: Processes leading to the building of a mature phage particle.
has_exact_synonym: phage morphogenesis
has_obo_namespace: Phage ontology
id: phi:0000009
comment: GO:0042963 definition is not appropriate: A late phase of bacteriophage replication during which all the components necessary for the formation of a mature virion collect at a particular site in the bacterial cell and the basic structure of the virus particle is formed.

Axiom
annotated source: phage assembly
annotated property: definition
annotated target: Processes leading to the building of a mature phage particle.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage assembly
annotated property: has_exact_synonym
annotated target: phage morphogenesis
database_cross_reference: PHI:AT

phage head/capsid assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage assembly
definition: Process by which phage heads/capsids are assembled.
has_broad_synonym: viral capsid assembly
database_cross_reference: GO:0019069
has_obo_namespace: Phage ontology
id: phi:0000010

Axiom
annotated source: phage head/capsid assembly
annotated property: definition
annotated target: Process by which phage heads/capsids are assembled.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage head/capsid assembly
annotated property: has_broad_synonym
annotated target: viral capsid assembly
database_cross_reference: GO:0019069

phage tail fiber assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage assembly
definition: Process by which phage tail fibers are assembled.
has_obo_namespace: Phage ontology
id: phi:0000011

Axiom
annotated source: phage tail fiber assembly
annotated property: definition
annotated target: Process by which phage tail fibers are assembled.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage head tail joining
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage assembly
definition: Process by which tailed phage heads and tails are put together.
has_obo_namespace: Phage ontology
id: phi:0000012

Axiom
annotated source: phage head tail joining
annotated property: definition
annotated target: Process by which tailed phage heads and tails are put together.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage release by lysis
type: Class
subclass of: phage release
definition: Process of dissolution of cells by the action of specific phage encoded enzymes that causes cell rupture and release of the phage progeny.
has_broad_synonym: lytic viral release
database_cross_reference: GO:0019077
has_obo_namespace: Phage ontology
id: phi:0000013

Axiom
annotated source: phage release by lysis
annotated property: definition
annotated target: Process of dissolution of cells by the action of specific phage encoded enzymes that causes cell rupture and release of the phage progeny.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage release by lysis
annotated property: has_broad_synonym
annotated target: lytic viral release
database_cross_reference: GO:0019077

phage release
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lytic cycle
definition: Process of releasing mature phage particles from the host cell.
has_broad_synonym: release of virus from host
database_cross_reference: GO:0019076
has_obo_namespace: Phage ontology
id: phi:0000014

Axiom
annotated source: phage release
annotated property: definition
annotated target: Process of releasing mature phage particles from the host cell.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage release
annotated property: has_broad_synonym
annotated target: release of virus from host
database_cross_reference: GO:0019076

phage tail assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage assembly
definition: Process by which tailed phage tails are assembled.
has_obo_namespace: Phage ontology
id: phi:0000015

Axiom
annotated source: phage tail assembly
annotated property: definition
annotated target: Process by which tailed phage tails are assembled.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

cell wall synthesis inhibition
type: Class
subclass of: phage release
definition: Process used by some phages as part_of the host cell lysis process.
has_obo_namespace: Phage ontology
id: phi:0000016

Axiom
annotated source: cell wall synthesis inhibition
annotated property: definition
annotated target: Process used by some phages as part_of the host cell lysis process.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage prohead/capsid assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage head/capsid assembly
definition: Process of building the precursor of the phage head/capsid, which shall later encapsidate the viral genome.
has_obo_namespace: Phage ontology
id: phi:0000017

Axiom
annotated source: phage prohead/capsid assembly
annotated property: definition
annotated target: Process of building the precursor of the phage head/capsid, which shall later encapsidate the viral genome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage genome packaging
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage head/capsid assembly
definition: Process of incorporation of the phage genome into the phage head/capsid.
has_broad_synonym: viral DNA genome packaging
has_broad_synonym: viral genome packaging
database_cross_reference: GO:0019072
database_cross_reference: GO:0019073
has_obo_namespace: Phage ontology
id: phi:0000018

Axiom
annotated source: phage genome packaging
annotated property: definition
annotated target: Process of incorporation of the phage genome into the phage head/capsid.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage genome packaging
annotated property: has_broad_synonym
annotated target: viral DNA genome packaging
database_cross_reference: GO:0019072

Axiom
annotated source: phage genome packaging
annotated property: has_broad_synonym
annotated target: viral genome packaging
database_cross_reference: GO:0019073

phage DNA maturation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage genome packaging
definition: Processing of replicated DNA into a packageable structure, often a linear concatemer.
has_broad_synonym: viral DNA cleavage
has_broad_synonym: viral genome maturation
database_cross_reference: GO:0019070
database_cross_reference: GO:0019071
has_obo_namespace: Phage ontology
id: phi:0000019

Axiom
annotated source: phage DNA maturation
annotated property: definition
annotated target: Processing of replicated DNA into a packageable structure, often a linear concatemer.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage DNA maturation
annotated property: has_broad_synonym
annotated target: viral DNA cleavage
database_cross_reference: GO:0019070

Axiom
annotated source: phage DNA maturation
annotated property: has_broad_synonym
annotated target: viral genome maturation
database_cross_reference: GO:0019071

phage headful packaging
type: Class
subclass of: phage DNA maturation
definition: Mode of packaging of double stranded DNA phage genomes with terminally redundant and possibly circularly permuted ends. These are generated by the activity of the phage-encoded terminase, which as part_of the phage head specifically binds the pac site on tandem arrays of phage DNA copies and is triggered to cut the DNA when the phage head is full.
has_obo_namespace: Phage ontology
id: phi:0000020
comment: Generalized transducing phages usually use this mode of packaging. The prohead terminase binds pac-like sites on the host chromosome and processes it as if it was phage DNA.

Axiom
annotated source: phage headful packaging
annotated property: definition
annotated target: Mode of packaging of double stranded DNA phage genomes with terminally redundant and possibly circularly permuted ends. These are generated by the activity of the phage-encoded terminase, which as part_of the phage head specifically binds the pac site on tandem arrays of phage DNA copies and is triggered to cut the DNA when the phage head is full.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage 3'extended cos packaging
type: Class
subclass of: phage DNA maturation
definition: Mode of packaging of double stranded DNA phage genomes with 3' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 3' protruding 'sticky' ends.
has_obo_namespace: Phage ontology
id: phi:0000021

Axiom
annotated source: phage 3'extended cos packaging
annotated property: definition
annotated target: Mode of packaging of double stranded DNA phage genomes with 3' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 3' protruding 'sticky' ends.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage 5'extended cos packaging
type: Class
subclass of: phage DNA maturation
definition: Mode of packaging of double stranded DNA phage genomes with 5' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 5' protruding 'sticky' ends.
has_obo_namespace: Phage ontology
id: phi:0000022

Axiom
annotated source: phage 5'extended cos packaging
annotated property: definition
annotated target: Mode of packaging of double stranded DNA phage genomes with 5' protruding ends. These are generated by the activity of the phage encoded terminase, which, when bound to the phage prohead, specifically binds the cos sites on tandem arrays of phage DNA copies and introduces staggered nicks to generate the 5' protruding 'sticky' ends.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage budding
type: Class
subclass of: phage release
definition: Process of releasing mature enveloped phage particles (Plasmaviridae phages) by formation of a bulge.
database_cross_reference: GO:0019078
has_obo_namespace: Phage ontology
has_related_synonym: lytic viral budding
id: phi:0000023

Axiom
annotated source: phage budding
annotated property: definition
annotated target: Process of releasing mature enveloped phage particles (Plasmaviridae phages) by formation of a bulge.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage budding
annotated property: has_related_synonym
annotated target: lytic viral budding
database_cross_reference: GO:0019078

phage genome replication
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage assembly
definition: Process of replicating the phage genome.
has_broad_synonym: viral genome replication
database_cross_reference: GO:0019079
has_obo_namespace: Phage ontology
id: phi:0000024

Axiom
annotated source: phage genome replication
annotated property: definition
annotated target: Process of replicating the phage genome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage genome replication
annotated property: has_broad_synonym
annotated target: viral genome replication
database_cross_reference: GO:0019079

phage RNA replication
type: Class
subclass of: phage genome replication
definition: Process of replicating a phage RNA genome.
has_obo_namespace: Phage ontology
id: phi:0000025

Axiom
annotated source: phage RNA replication
annotated property: definition
annotated target: Process of replicating a phage RNA genome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage DNA replication
type: Class
subclass of: phage genome replication
definition: Process of replicating a phage DNA genome.
has_obo_namespace: Phage ontology
id: phi:0000026

Axiom
annotated source: phage DNA replication
annotated property: definition
annotated target: Process of replicating a phage DNA genome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

regulation of phage replication
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage genome replication
definition: Any process that modulates the frequency, rate or extent of the phage genome replication.
database_cross_reference: GO:0045069
has_exact_synonym: regulation of viral genome replication
has_obo_namespace: Phage ontology
id: phi:0000027

Axiom
annotated source: regulation of phage replication
annotated property: definition
annotated target: Any process that modulates the frequency, rate or extent of the phage genome replication.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: regulation of phage replication
annotated property: has_exact_synonym
annotated target: regulation of viral genome replication
database_cross_reference: GO:0045069

protein primed DNA replication
type: Class
subclass of: phage DNA replication
definition: Process of DNA-dependent DNA replication primed by a phage encoded protein bound at the ends of its linear genome to produce two linear daughter DNA molecules.
has_obo_namespace: Phage ontology
id: phi:0000028

Axiom
annotated source: protein primed DNA replication
annotated property: definition
annotated target: Process of DNA-dependent DNA replication primed by a phage encoded protein bound at the ends of its linear genome to produce two linear daughter DNA molecules.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

sigma DNA replication
type: Class
subclass of: phage DNA replication
definition: Process of DNA-dependent DNA replication proceeding by the rolling circle mode, i.e. on a circular DNA molecule to produce a concatemer.
database_cross_reference: GO:0008167
has_exact_synonym: sigma virus replication
has_obo_namespace: Phage ontology
id: phi:0000029

Axiom
annotated source: sigma DNA replication
annotated property: definition
annotated target: Process of DNA-dependent DNA replication proceeding by the rolling circle mode, i.e. on a circular DNA molecule to produce a concatemer.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: sigma DNA replication
annotated property: has_exact_synonym
annotated target: sigma virus replication
database_cross_reference: GO:0008167

theta DNA replication
type: Class
subclass of: phage DNA replication
definition: Process of DNA replication proceeding uni or bidirectionally on a circular DNA template to produce two daughter circular DNA molecules .
has_obo_namespace: Phage ontology
id: phi:0000030

Axiom
annotated source: theta DNA replication
annotated property: definition
annotated target: Process of DNA replication proceeding uni or bidirectionally on a circular DNA template to produce two daughter circular DNA molecules .
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

transpositional DNA replication
type: Class
subclass of: phage DNA replication
definition: Process of DNA-dependent DNA replication proceeding by successive rounds of replicative transposition.
has_obo_namespace: Phage ontology
id: phi:0000031
comment: This mode of replication is used by the transposable phages.

Axiom
annotated source: transpositional DNA replication
annotated property: definition
annotated target: Process of DNA-dependent DNA replication proceeding by successive rounds of replicative transposition.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

recombination directed DNA replication
type: Class
subclass of: phage DNA replication
definition: Process of DNA-dependent DNA replication intiated by homologous recombination.
has_obo_namespace: Phage ontology
id: phi:0000032
comment: Typically used by phages of the T4 family.

Axiom
annotated source: recombination directed DNA replication
annotated property: definition
annotated target: Process of DNA-dependent DNA replication intiated by homologous recombination.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
subclass of: Restriction
  on property: part_of
  some values from: phage lytic cycle
definition: Cascade of transcription and translation of the phage genes.
has_broad_synonym: viral genome expression
database_cross_reference: GO:0019080
has_obo_namespace: Phage ontology
id: phi:0000033

Axiom
annotated source: phage gene expression
annotated property: definition
annotated target: Cascade of transcription and translation of the phage genes.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage gene expression
annotated property: has_broad_synonym
annotated target: viral genome expression
database_cross_reference: GO:0019080

phage gene transcription
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage gene expression
definition: Cascade of transcription of the phage genes.
has_obo_namespace: Phage ontology
id: phi:0000034

Axiom
annotated source: phage gene transcription
annotated property: definition
annotated target: Cascade of transcription of the phage genes.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage class I gene transcription
type: Class
subclass of: phage gene transcription
definition: The transcriptional period of the earliest expressed viral genes mainly encoding transcriptional regulators.
database_cross_reference: GO:0019085
has_exact_synonym: immediate early viral mRNA transcription
has_obo_namespace: Phage ontology
has_related_synonym: phage early transcription
id: phi:0000035

Axiom
annotated source: phage class I gene transcription
annotated property: definition
annotated target: The transcriptional period of the earliest expressed viral genes mainly encoding transcriptional regulators.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage class I gene transcription
annotated property: has_exact_synonym
annotated target: immediate early viral mRNA transcription
database_cross_reference: GO:0019085

Axiom
annotated source: phage class I gene transcription
annotated property: has_related_synonym
annotated target: phage early transcription
database_cross_reference: PHI:AT

phage class II gene transcription
type: Class
subclass of: phage gene transcription
definition: The second round of viral gene transcription, usually of replication genes.
database_cross_reference: GO:0019084
has_exact_synonym: (delayed) early viral mRNA transcription
has_obo_namespace: Phage ontology
id: phi:0000036

Axiom
annotated source: phage class II gene transcription
annotated property: definition
annotated target: The second round of viral gene transcription, usually of replication genes.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage class II gene transcription
annotated property: has_exact_synonym
annotated target: (delayed) early viral mRNA transcription
database_cross_reference: GO:0019084

phage class IIB gene transcription
type: Class
subclass of: phage gene transcription
definition: The third round of phage transcription, usually of regulators involved in the progression of induction of the phage late gene expression.
has_exact_synonym: middle promoter transcription
has_obo_namespace: Phage ontology
id: phi:0000037

Axiom
annotated source: phage class IIB gene transcription
annotated property: definition
annotated target: The third round of phage transcription, usually of regulators involved in the progression of induction of the phage late gene expression.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage class IIB gene transcription
annotated property: has_exact_synonym
annotated target: middle promoter transcription
database_cross_reference: PHI:AT

phage class III gene transcription
type: Class
subclass of: phage gene transcription
definition: The transcriptional period of the latest expressed viral genes mainly encoding phage capsid components, morphogenesis proteins and cell wall degradation enzymes.
database_cross_reference: GO:0019086
has_exact_synonym: late viral mRNA transcription
has_obo_namespace: Phage ontology
has_related_synonym: phage late transcription
id: phi:0000038
comment: Typically turned on by phage-encoded transcription factors.

Axiom
annotated source: phage class III gene transcription
annotated property: definition
annotated target: The transcriptional period of the latest expressed viral genes mainly encoding phage capsid components, morphogenesis proteins and cell wall degradation enzymes.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage class III gene transcription
annotated property: has_exact_synonym
annotated target: late viral mRNA transcription
database_cross_reference: GO:0019086

Axiom
annotated source: phage class III gene transcription
annotated property: has_related_synonym
annotated target: phage late transcription
database_cross_reference: PHI:AT

phage transcription termination
type: Class
subclass of: Restriction
  on property: part_of
  some values from: negative transcriptional regulation of phage gene expression
definition: Process by which phage gene transcription stops and RNA-polymerase is released from the DNA template.
database_cross_reference: GO:0030401
has_obo_namespace: Phage ontology
id: phi:0000039

Axiom
annotated source: phage transcription termination
annotated property: definition
annotated target: Process by which phage gene transcription stops and RNA-polymerase is released from the DNA template.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage transcription anti termination
type: Class
subclass of: Restriction
  on property: part_of
  some values from: positive transcriptional regulation of phage gene expression
definition: Functions to prevent the termination of RNA synthesis. Acts as a regulatory device, e.g. in phage lambda, enabling a terminator to be masked from RNA polymerase so that distal genes can be expressed.
database_cross_reference: GO:0030401
has_obo_namespace: Phage ontology
id: phi:0000040

Axiom
annotated source: phage transcription anti termination
annotated property: definition
annotated target: Functions to prevent the termination of RNA synthesis. Acts as a regulatory device, e.g. in phage lambda, enabling a terminator to be masked from RNA polymerase so that distal genes can be expressed.
database_cross_reference: GO:0030401

regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage gene expression
definition: Any process that activates or represses phage gene expression.
has_obo_namespace: Phage ontology
id: phi:0000041

Axiom
annotated source: regulation of phage gene expression
annotated property: definition
annotated target: Any process that activates or represses phage gene expression.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

positive regulation of phage replication
type: Class
subclass of: Restriction
  on property: part_of
  some values from: regulation of phage replication
definition: Any process that stimulates the frequency, rate or extent of the phage genome replication.
has_broad_synonym: positive regulation of viral genome replication
database_cross_reference: GO:0045070
has_obo_namespace: Phage ontology
id: phi:0000042

Axiom
annotated source: positive regulation of phage replication
annotated property: definition
annotated target: Any process that stimulates the frequency, rate or extent of the phage genome replication.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: positive regulation of phage replication
annotated property: has_broad_synonym
annotated target: positive regulation of viral genome replication
database_cross_reference: GO:0045070

negative regulation of phage replication
type: Class
subclass of: Restriction
  on property: part_of
  some values from: regulation of phage replication
definition: Any process that decreases the frequency, rate or extent of the phage genome replication.
has_broad_synonym: negative regulation of viral genome replication
database_cross_reference: GO:0045071
has_obo_namespace: Phage ontology
id: phi:0000043

Axiom
annotated source: negative regulation of phage replication
annotated property: definition
annotated target: Any process that decreases the frequency, rate or extent of the phage genome replication.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: negative regulation of phage replication
annotated property: has_broad_synonym
annotated target: negative regulation of viral genome replication
database_cross_reference: GO:0045071

transcriptional-regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: regulation of phage gene expression
definition: Any process that activates or represses the transcription of phage genes. Typically turned on by phage-encoded transcription factors.
has_broad_synonym: regulation of viral transcription
database_cross_reference: GO:0046782
has_obo_namespace: Phage ontology
id: phi:0000044

Axiom
annotated source: transcriptional-regulation of phage gene expression
annotated property: definition
annotated target: Any process that activates or represses the transcription of phage genes. Typically turned on by phage-encoded transcription factors.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: transcriptional-regulation of phage gene expression
annotated property: has_broad_synonym
annotated target: regulation of viral transcription
database_cross_reference: GO:0046782

negative post transcriptional regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: post-transcriptional regulation of phage gene expression
definition: Any process that represses the expression of phage genes at the post-transcriptional level.
has_obo_namespace: Phage ontology
id: phi:0000045

Axiom
annotated source: negative post transcriptional regulation of phage gene expression
annotated property: definition
annotated target: Any process that represses the expression of phage genes at the post-transcriptional level.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

positive post transcriptional regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: post-transcriptional regulation of phage gene expression
definition: Any process that activates the expression of phage genes at the post-transcriptional level.
has_obo_namespace: Phage ontology
id: phi:0000046

Axiom
annotated source: positive post transcriptional regulation of phage gene expression
annotated property: definition
annotated target: Any process that activates the expression of phage genes at the post-transcriptional level.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

post-transcriptional regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: regulation of phage gene expression
definition: Any process that activates or represses the expression of phage genes at a post-trasncriptional level.
has_obo_namespace: Phage ontology
id: phi:0000047

Axiom
annotated source: post-transcriptional regulation of phage gene expression
annotated property: definition
annotated target: Any process that activates or represses the expression of phage genes at a post-trasncriptional level.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

negative transcriptional regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: positive transcriptional regulation of phage gene expression
definition: Any process that represses the expression of phage genes at the transcriptional level.
has_broad_synonym: negative regulation of viral transcription
database_cross_reference: GO:0032897
has_obo_namespace: Phage ontology
id: phi:0000048
comment: Typically turned off by phage-encoded transcription factors.

Axiom
annotated source: negative transcriptional regulation of phage gene expression
annotated property: definition
annotated target: Any process that represses the expression of phage genes at the transcriptional level.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: negative transcriptional regulation of phage gene expression
annotated property: has_broad_synonym
annotated target: negative regulation of viral transcription
database_cross_reference: GO:0032897

positive transcriptional regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transcriptional-regulation of phage gene expression
definition: Any process that activates the expression of phage genes at the transcriptional level.
has_broad_synonym: positive regulation of viral transcription
database_cross_reference: GO:0050434
has_obo_namespace: Phage ontology
id: phi:0000049
comment: Typically turned on by phage-encoded transcription factors.

Axiom
annotated source: positive transcriptional regulation of phage gene expression
annotated property: definition
annotated target: Any process that activates the expression of phage genes at the transcriptional level.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: positive transcriptional regulation of phage gene expression
annotated property: has_broad_synonym
annotated target: positive regulation of viral transcription
database_cross_reference: GO:0050434

post-translational regulation of phage gene expression
type: Class
subclass of: Restriction
  on property: part_of
  some values from: regulation of phage gene expression
definition: Any process that up or down-regulates protein activity or stability.
has_obo_namespace: Phage ontology
id: phi:0000050

Axiom
annotated source: post-translational regulation of phage gene expression
annotated property: definition
annotated target: Any process that up or down-regulates protein activity or stability.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

establishment as a plasmid prophage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
definition: A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a plasmid.
has_obo_namespace: Phage ontology
id: phi:0000051

Axiom
annotated source: establishment as a plasmid prophage
annotated property: definition
annotated target: A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a plasmid.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage lysogenic conversion
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
definition: Process through which a prophage induces a hereditary change in the phenotype or fitness of the lysogen.
database_cross_reference: GO:0019087
has_obo_namespace: Phage ontology
has_related_synonym: transformation of host cell by virus
id: phi:0000052

Axiom
annotated source: phage lysogenic conversion
annotated property: definition
annotated target: Process through which a prophage induces a hereditary change in the phenotype or fitness of the lysogen.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage lysogenic conversion
annotated property: has_related_synonym
annotated target: transformation of host cell by virus
database_cross_reference: GO:0019087

establishment as a linear plasmid prophage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: establishment as a plasmid prophage
definition: A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a linear plasmid.
has_obo_namespace: Phage ontology
id: phi:0000053

Axiom
annotated source: establishment as a linear plasmid prophage
annotated property: definition
annotated target: A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a linear plasmid.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

establishment as a circular plasmid prophage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: establishment as a plasmid prophage
definition: A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a circular plasmid.
has_obo_namespace: Phage ontology
id: phi:0000054

Axiom
annotated source: establishment as a circular plasmid prophage
annotated property: definition
annotated target: A process by which a phage genome establishes a repressed prophage in its host cytoplasm as a circular plasmid.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

establishment as an integrated prophage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
definition: A process by which the phage integrates in the host genomes and establishes as a stable prophage.
has_obo_namespace: Phage ontology
id: phi:0000055

Axiom
annotated source: establishment as an integrated prophage
annotated property: definition
annotated target: A process by which the phage integrates in the host genomes and establishes as a stable prophage.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

prophage DNA integration
type: Class
subclass of: site-specific DNA integration
subclass of: Restriction
  on property: part_of
  some values from: establishment as an integrated prophage
definition: Process by which the phage DNA integrates into the host genome by recombination. Integration usually proceeds via site-specific recombination into the host chromosome.
database_cross_reference: GO:0019047
has_exact_synonym: provirus integration
has_obo_namespace: Phage ontology
id: phi:0000056

Axiom
annotated source: prophage DNA integration
annotated property: definition
annotated target: Process by which the phage DNA integrates into the host genome by recombination. Integration usually proceeds via site-specific recombination into the host chromosome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: prophage DNA integration
annotated property: has_exact_synonym
annotated target: provirus integration
database_cross_reference: GO:0019047

maintenance of prophage immunity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: establishment as a linear plasmid prophage
subclass of: Restriction
  on property: part_of
  some values from: establishment as a circular plasmid prophage
subclass of: Restriction
  on property: part_of
  some values from: establishment as an integrated prophage
definition: Process by which a latent prophage blocks the expression of its own lytic genes as well as expression of those genes by a related superinfecting phage with the same immunity. The host bacterium is thus "immune" to superinfection by such related phages.
has_broad_synonym: provirus maintenance
database_cross_reference: GO:0032360
has_obo_namespace: Phage ontology
id: phi:0000057

Axiom
annotated source: maintenance of prophage immunity
annotated property: definition
annotated target: Process by which a latent prophage blocks the expression of its own lytic genes as well as expression of those genes by a related superinfecting phage with the same immunity. The host bacterium is thus "immune" to superinfection by such related phages.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: maintenance of prophage immunity
annotated property: has_broad_synonym
annotated target: provirus maintenance
database_cross_reference: GO:0032360

phage latent infection
type: Class
subclass of: phage process
definition: To be written.
has_obo_namespace: Phage ontology
id: phi:0000058
comment: IS this term really necessary?

Axiom
annotated source: phage latent infection
annotated property: definition
annotated target: To be written.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage abortive infection
type: Class
subclass of: phage process
definition: Process of infection by a phage, which does not complete the lytic cycle and produces no viable phage burst. It may or may not provoke cell death.
has_obo_namespace: Phage ontology
id: phi:0000059

Axiom
annotated source: phage abortive infection
annotated property: definition
annotated target: Process of infection by a phage, which does not complete the lytic cycle and produces no viable phage burst. It may or may not provoke cell death.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage pseudolysogeny
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage infectious cycle
definition: Simulated lysogeny in a mixed population of phage-infected bacteria, non-infected phage-sensitive bacteria, and free phages.
has_obo_namespace: Phage ontology
id: phi:0000060

Axiom
annotated source: phage pseudolysogeny
annotated property: definition
annotated target: Simulated lysogeny in a mixed population of phage-infected bacteria, non-infected phage-sensitive bacteria, and free phages.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: bacteriophage
definition: All macromolecules, proteins, nucleic acids, sugars, lipids etc. that are part or participate in the assembly of the mature virion particle.
has_obo_namespace: Phage ontology
id: phi:0000061

Axiom
annotated source: phage component
annotated property: definition
annotated target: All macromolecules, proteins, nucleic acids, sugars, lipids etc. that are part or participate in the assembly of the mature virion particle.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

prophage induction
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage infectious cycle
definition: Process by which a prophage is made to switch from the latent/lysogenic state to the lytic cycle and production of phage progeny.
has_broad_synonym: reactivation of latent virus
database_cross_reference: GO:0019046
has_obo_namespace: Phage ontology
id: phi:0000062

Axiom
annotated source: prophage induction
annotated property: definition
annotated target: Process by which a prophage is made to switch from the latent/lysogenic state to the lytic cycle and production of phage progeny.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: prophage induction
annotated property: has_broad_synonym
annotated target: reactivation of latent virus
database_cross_reference: GO:0019046

prophage DNA excision
type: Class
subclass of: site-specific DNA excision
subclass of: Restriction
  on property: part_of
  some values from: prophage induction
definition: Process by which a prophage DNA is excised from the host genome.
database_cross_reference: GO:0032359
has_exact_synonym: provirus excision
has_obo_namespace: Phage ontology
id: phi:0000063

Axiom
annotated source: prophage DNA excision
annotated property: definition
annotated target: Process by which a prophage DNA is excised from the host genome.
database_cross_reference: PHI:AT

Axiom
annotated source: prophage DNA excision
annotated property: has_exact_synonym
annotated target: provirus excision
database_cross_reference: GO:0032359

phage head/capsid protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: head/capsid
definition: Component of the closed shell (head or capsid) of the phage.
has_obo_namespace: Phage ontology
id: phi:0000064

Axiom
annotated source: phage head/capsid protein
annotated property: definition
annotated target: Component of the closed shell (head or capsid) of the phage.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

capsid scaffolding protein
type: Class
subclass of: prohead/procapsid
definition: Transient internal component of the phage prohead, which allows for its assembly. It is degraded or leaves the prohead without being degraded and is replaced by the phage DNA upon maturation.
has_obo_namespace: Phage ontology
id: phi:0000065

Axiom
annotated source: capsid scaffolding protein
annotated property: definition
annotated target: Transient internal component of the phage prohead, which allows for its assembly. It is degraded or leaves the prohead without being degraded and is replaced by the phage DNA upon maturation.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage head/capsid major protein
type: Class
subclass of: phage head/capsid protein
definition: Abbreviated MHP, the major subunit component that forms the closed shell (capsid) of the phage head.
database_cross_reference: GO:0046727
has_exact_synonym: capsomer
has_obo_namespace: Phage ontology
id: phi:0000066

Axiom
annotated source: phage head/capsid major protein
annotated property: definition
annotated target: Abbreviated MHP, the major subunit component that forms the closed shell (capsid) of the phage head.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage head/capsid major protein
annotated property: has_exact_synonym
annotated target: capsomer
database_cross_reference: GO:0046727

phage portal associated protein
type: Class
subclass of: phage head/capsid protein
definition: Also called gate keepers, these proteins close the head after packaging and maturation of the phage genome, are part of the completed head, allow for the binding of the tail and are part of the complete phage particle.
has_obo_namespace: Phage ontology
id: phi:0000067

Axiom
annotated source: phage portal associated protein
annotated property: definition
annotated target: Also called gate keepers, these proteins close the head after packaging and maturation of the phage genome, are part of the completed head, allow for the binding of the tail and are part of the complete phage particle.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage portal protein
type: Class
subclass of: phage head/capsid protein
definition: Protein component that forms the junction between the Caudovirales phage head and tail and serves as a gate through which DNA passes during packaging and translocation.
has_obo_namespace: Phage ontology
id: phi:0000068

Axiom
annotated source: phage portal protein
annotated property: definition
annotated target: Protein component that forms the junction between the Caudovirales phage head and tail and serves as a gate through which DNA passes during packaging and translocation.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage head/capsid decoration protein
type: Class
subclass of: phage head/capsid protein
definition: Component of the phage head/capsid. Located on the outer head surface they are involved in the stabilization of the head structure and, usually, are not essential.
has_obo_namespace: Phage ontology
id: phi:0000069

Axiom
annotated source: phage head/capsid decoration protein
annotated property: definition
annotated target: Component of the phage head/capsid. Located on the outer head surface they are involved in the stabilization of the head structure and, usually, are not essential.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage head/capsid fiber protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage head/capsid fiber
definition: Protein component of fiber structures, which decorate the head/capsid of some phages.
has_obo_namespace: Phage ontology
id: phi:0000070

Axiom
annotated source: phage head/capsid fiber protein
annotated property: definition
annotated target: Protein component of fiber structures, which decorate the head/capsid of some phages.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage terminal protein
type: Class
subclass of: phage head/capsid protein
definition: Protein covalently linked to the ends of dsDNA phages that use protein primed DNA replication.
has_obo_namespace: Phage ontology
id: phi:0000071
comment: The protein primes DNA replication and may have other functions including cell wall hydrolase.

Axiom
annotated source: phage terminal protein
annotated property: definition
annotated target: Protein covalently linked to the ends of dsDNA phages that use protein primed DNA replication.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:MS
database_cross_reference: PHI:SC

phage terminase complex
type: Class
subclass of: phage head/capsid protein
definition: A complex of large and small terminase subunits. It is responsible for binding to and thereby choosing the DNA that will be packaged; it also carries the ATPase motor (DNA translocase) that drives the DNA into the prohead during packaging and has the nuclease activity that cleaves virion-length DNA from overlength or circular replicating DNA. The name refers to the nuclease activity that creates the termini of the virion DNA. Some phage terminases exist as single polypeptides and some terminase complexes include an RNA component.
database_cross_reference: GO:0043493
has_obo_namespace: Phage ontology
id: phi:0000072

Axiom
annotated source: phage terminase complex
annotated property: definition
annotated target: A complex of large and small terminase subunits. It is responsible for binding to and thereby choosing the DNA that will be packaged; it also carries the ATPase motor (DNA translocase) that drives the DNA into the prohead during packaging and has the nuclease activity that cleaves virion-length DNA from overlength or circular replicating DNA. The name refers to the nuclease activity that creates the termini of the virion DNA. Some phage terminases exist as single polypeptides and some terminase complexes include an RNA component.
database_cross_reference: GO:0043493
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage terminase large subunit
type: Class
subclass of: phage terminase complex
definition: Phage component that forms a complex with the terminase small subunit at the base of the phage head.
has_obo_namespace: Phage ontology
id: phi:0000073

Axiom
annotated source: phage terminase large subunit
annotated property: definition
annotated target: Phage component that forms a complex with the terminase small subunit at the base of the phage head.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage terminase small subunit
type: Class
subclass of: phage terminase complex
definition: Phage component that forms a complex with the terminase large subunit at the base of the phage head.
has_obo_namespace: Phage ontology
id: phi:0000074

Axiom
annotated source: phage terminase small subunit
annotated property: definition
annotated target: Phage component that forms a complex with the terminase large subunit at the base of the phage head.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

capsid neck fiber protein
type: Class
subclass of: capsid structural protein
subclass of: Restriction
  on property: part_of
  some values from: capsid neck fiber
definition: Protein component of fiber structures appended at the neck at the base of some phage heads.
has_obo_namespace: Phage ontology
id: phi:0000075

Axiom
annotated source: capsid neck fiber protein
annotated property: definition
annotated target: Protein component of fiber structures appended at the neck at the base of some phage heads.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

injected protein
type: Class
subclass of: phage component
subclass of: capsid structural protein
definition: Protein component of a phage, which is injected into the host cytoplasm upon phage infection.
has_obo_namespace: Phage ontology
id: phi:0000076

Axiom
annotated source: injected protein
annotated property: definition
annotated target: Protein component of a phage, which is injected into the host cytoplasm upon phage infection.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

pre DNA injected protein
type: Class
subclass of: injected protein
definition: Protein component of a phage, which is injected into the host cytoplasm upon phage infection prior to phage DNA translocation.
has_obo_namespace: Phage ontology
id: phi:0000077

Axiom
annotated source: pre DNA injected protein
annotated property: definition
annotated target: Protein component of a phage, which is injected into the host cytoplasm upon phage infection prior to phage DNA translocation.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

post DNA injected protein
type: Class
subclass of: injected protein
definition: Protein component of a phage, which is injected into the host cytoplasm upon phage infection after phage DNA translocation.
has_obo_namespace: Phage ontology
id: phi:0000078

Axiom
annotated source: post DNA injected protein
annotated property: definition
annotated target: Protein component of a phage, which is injected into the host cytoplasm upon phage infection after phage DNA translocation.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

translocation protein
type: Class
subclass of: injected protein
definition: Protein component of a phage, which is injected into the host membrane upon phage infection, creating a channel for phage DNA translocation.
has_obo_namespace: Phage ontology
id: phi:0000079

Axiom
annotated source: translocation protein
annotated property: definition
annotated target: Protein component of a phage, which is injected into the host membrane upon phage infection, creating a channel for phage DNA translocation.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage inner vesicle
type: Class
subclass of: phage head/capsid protein
definition: Biochemical assembly that contains both proteins and lipids and is part_of some (Tectiviridae) phage capsids.
has_obo_namespace: Phage ontology
id: phi:0000080

Axiom
annotated source: phage inner vesicle
annotated property: definition
annotated target: Biochemical assembly that contains both proteins and lipids and is part_of some (Tectiviridae) phage capsids.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

phage tail protein
type: Class
subclass of: capsid structural protein
subclass of: Restriction
  on property: part_of
  some values from: capsid tail
definition: Protein component of the assembled tail of tailed phages (caudovirale).
has_obo_namespace: Phage ontology
id: phi:0000081

Axiom
annotated source: phage tail protein
annotated property: definition
annotated target: Protein component of the assembled tail of tailed phages (caudovirale).
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage major tail protein
type: Class
subclass of: phage tail protein
definition: Abbreviated MTP, the term refers to protein component found in large amount, easily detectable upon electrophoresis of tailed phage particles of the types Myoviridae and Siphoviridae.
has_obo_namespace: Phage ontology
id: phi:0000082

Axiom
annotated source: phage major tail protein
annotated property: definition
annotated target: Abbreviated MTP, the term refers to protein component found in large amount, easily detectable upon electrophoresis of tailed phage particles of the types Myoviridae and Siphoviridae.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail tube protein
type: Class
subclass of: phage tail protein
definition: Protein that forms the internal tube of the contractile tails of Myovirirdae phages. It is the channel for DNA ejection into the host cytoplasm.
has_obo_namespace: Phage ontology
id: phi:0000083

Axiom
annotated source: phage tail tube protein
annotated property: definition
annotated target: Protein that forms the internal tube of the contractile tails of Myovirirdae phages. It is the channel for DNA ejection into the host cytoplasm.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail sheath protein
type: Class
subclass of: phage tail protein
definition: Protein that forms the external contractile envelope of the tails of Myoviridae phages. Its contraction ensures ejection of the phage DNA into the host cytoplasm.
has_obo_namespace: Phage ontology
id: phi:0000084

Axiom
annotated source: phage tail sheath protein
annotated property: definition
annotated target: Protein that forms the external contractile envelope of the tails of Myoviridae phages. Its contraction ensures ejection of the phage DNA into the host cytoplasm.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail shaft protein
type: Class
subclass of: phage tail protein
definition: Protein that forms the tube of the non-contractile tails of Siphoviridae phages. It is the channel for DNA translocation into the host cytoplasm.
has_obo_namespace: Phage ontology
id: phi:0000085

Axiom
annotated source: phage tail shaft protein
annotated property: definition
annotated target: Protein that forms the tube of the non-contractile tails of Siphoviridae phages. It is the channel for DNA translocation into the host cytoplasm.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail tape measure protein
type: Class
subclass of: phage tail protein
definition: Protein TMP that controls the tail tube length in Myoviridae and tail shaft length in Siphoviridae. The protein is part of the finished tail. Some phages inject their TMP with their DNA in the host cytoplasm.
has_obo_namespace: Phage ontology
id: phi:0000086

Axiom
annotated source: phage tail tape measure protein
annotated property: definition
annotated target: Protein TMP that controls the tail tube length in Myoviridae and tail shaft length in Siphoviridae. The protein is part of the finished tail. Some phages inject their TMP with their DNA in the host cytoplasm.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail tip protein
type: Class
subclass of: phage tail protein
subclass of: Restriction
  on property: part_of
  some values from: phage base plate protein
definition: Protein structure that forms the basal tip of the phage tail and is used by the phage to adsorb to the host cell.
has_obo_namespace: Phage ontology
id: phi:0000087

Axiom
annotated source: phage tail tip protein
annotated property: definition
annotated target: Protein structure that forms the basal tip of the phage tail and is used by the phage to adsorb to the host cell.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage base plate protein
type: Class
subclass of: phage tail protein
definition: Multiprotein component at the head-distal end of the tail and to which fibers of tailed phages may be attached (Caudovirales). Sometimes referred to as the tail tip or tip structure in Siphoviridae.
has_obo_namespace: Phage ontology
id: phi:0000088

Axiom
annotated source: phage base plate protein
annotated property: definition
annotated target: Multiprotein component at the head-distal end of the tail and to which fibers of tailed phages may be attached (Caudovirales). Sometimes referred to as the tail tip or tip structure in Siphoviridae.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail fiber protein
type: Class
definition: Protein component of the fiber, structure appended to the phage tail and used to scan, recognize and attach to the host cell.
term replaced by: phi:0000175
has_obo_namespace: Phage ontology
id: phi:0000089
comment: Fibers typically bind to particular LPS, polysaccharide or protein receptors on the cell surface
deprecated: true

Axiom
annotated source: phage tail fiber protein
annotated property: definition
annotated target: Protein component of the fiber, structure appended to the phage tail and used to scan, recognize and attach to the host cell.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

prophage
type: Class
subclass of: genomic island
definition: A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated island.
database_cross_reference: SO:0001006
has_obo_namespace: Phage ontology
id: phi:0000090

Axiom
annotated source: prophage
annotated property: definition
annotated target: A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated island.
database_cross_reference: SO:0001006

phage concatemer
type: Class
subclass of: SO term
definition: Tandem array or branched complex of DNA bacteriophage genomes generated in the bacterial host cytoplasm during phage replication and which is the substrate for DNA packaging.
has_obo_namespace: Phage ontology
id: phi:0000091

Axiom
annotated source: phage concatemer
annotated property: definition
annotated target: Tandem array or branched complex of DNA bacteriophage genomes generated in the bacterial host cytoplasm during phage replication and which is the substrate for DNA packaging.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

cryptic prophage
type: Class
subclass of: prophage
definition: A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
database_cross_reference: SO:0001007
has_obo_namespace: Phage ontology
has_related_synonym: defective prophage
id: phi:0000092

Axiom
annotated source: cryptic prophage
annotated property: definition
annotated target: A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes.
database_cross_reference: SO:0001007

Axiom
annotated source: cryptic prophage
annotated property: has_related_synonym
annotated target: defective prophage
database_cross_reference: SO:0001007

phage related bacterial component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: bacteriophage
definition: A bacterial component to be added in GO that had to do with the phage life cycle.
has_obo_namespace: Phage ontology
id: phi:0000093
comment: This is a temporary term.

Axiom
annotated source: phage related bacterial component
annotated property: definition
annotated target: A bacterial component to be added in GO that had to do with the phage life cycle.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage receptor
type: Class
subclass of: phage related bacterial component
definition: A bacterial component located on the cell surface and which is specifically recognized and used by the phage for adsorption.
has_obo_namespace: Phage ontology
id: phi:0000094

Axiom
annotated source: phage receptor
annotated property: definition
annotated target: A bacterial component located on the cell surface and which is specifically recognized and used by the phage for adsorption.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail fiber minor protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: capsid tail fiber
definition: Minor protein component of the phage tail fiber.
has_obo_namespace: Phage ontology
id: phi:0000095

Axiom
annotated source: phage tail fiber minor protein
annotated property: definition
annotated target: Minor protein component of the phage tail fiber.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage tail fiber major protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: capsid tail fiber
definition: Major protein component of the phage tail fiber.
has_obo_namespace: Phage ontology
id: phi:0000096

Axiom
annotated source: phage tail fiber major protein
annotated property: definition
annotated target: Major protein component of the phage tail fiber.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage activity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: bacteriophage
definition: Molecular functions of phage components.
has_obo_namespace: Phage ontology
id: phi:0000097

Axiom
annotated source: phage activity
annotated property: definition
annotated target: Molecular functions of phage components.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

anti holin activity
type: Class
subclass of: phage activity
definition: Inhibits holin activity.
has_obo_namespace: Phage ontology
id: phi:0000098
comment: Some anti-holins differ from their cognate holins by only a few terminal amino acids.

Axiom
annotated source: anti holin activity
annotated property: definition
annotated target: Inhibits holin activity.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

holin activity
type: Class
subclass of: phage activity
definition: Catalysis of the temporally regulated formation of a transmembrane protein hole that directly or indirectly allows murein hydrolyases to access their cell wall substrate.
database_cross_reference: GO:0034290
database_cross_reference: XX:<new dbxref>
has_obo_namespace: Phage ontology
id: phi:0000099

Axiom
annotated source: holin activity
annotated property: definition
annotated target: Catalysis of the temporally regulated formation of a transmembrane protein hole that directly or indirectly allows murein hydrolyases to access their cell wall substrate.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

anti repressor activity
type: Class
subclass of: phage activity
definition: Inhibition, inactivation or degradation of a transcriptional repressor.
has_obo_namespace: Phage ontology
id: phi:0000100
comment: An activity as that of the lambda Cro repressor that has opposing effects on gene expression than another repressor, here lambda CI by operator binding is NOT considered an anti-repressor.

Axiom
annotated source: anti repressor activity
annotated property: definition
annotated target: Inhibition, inactivation or degradation of a transcriptional repressor.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

ATPase activity
type: Class
subclass of: phage activity
definition: Catalysis of the reaction: ATP + H2O = ADP + phosphate. May or may not be coupled to another reaction.
database_cross_reference: GO:0016887
has_obo_namespace: Phage ontology
id: phi:0000101

Axiom
annotated source: ATPase activity
annotated property: definition
annotated target: Catalysis of the reaction: ATP + H2O = ADP + phosphate. May or may not be coupled to another reaction.
database_cross_reference: GO:0016887

CI/Cro transcriptional repressor activity
type: Class
definition: Transcriptional repressor activity involved in switching between lytic and lysogenic transcription.
has_obo_namespace: Phage ontology
id: phi:0000102
deprecated: true

Axiom
annotated source: CI/Cro transcriptional repressor activity
annotated property: definition
annotated target: Transcriptional repressor activity involved in switching between lytic and lysogenic transcription.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

endolysin activity
type: Class
subclass of: phage activity
definition: Cell wall degradation enzyme synthesized by a phage during its lytic cycle and responsible for host cell lysis.
has_obo_namespace: Phage ontology
id: phi:0000103

Axiom
annotated source: endolysin activity
annotated property: definition
annotated target: Cell wall degradation enzyme synthesized by a phage during its lytic cycle and responsible for host cell lysis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

exolysin activity
type: Class
subclass of: phage activity
definition: Cell wall hydrolase activity associated with phage structures (usually the tail or the base plate) and which helps DNA translocation by damaging the host cell envelope after adsorption.
has_obo_namespace: Phage ontology
id: phi:0000104

Axiom
annotated source: exolysin activity
annotated property: definition
annotated target: Cell wall hydrolase activity associated with phage structures (usually the tail or the base plate) and which helps DNA translocation by damaging the host cell envelope after adsorption.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

peptidase activity
type: Class
subclass of: phage activity
definition: Catalysis of the hydrolysis of peptide bonds.
database_cross_reference: GO:0008233
has_obo_namespace: Phage ontology
id: phi:0000105

Axiom
annotated source: peptidase activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of peptide bonds.
database_cross_reference: GO:0008233

coat chaperon activity
type: Class
subclass of: capsid protein chaperon activity
definition: Chaperon activity required for the assembly of the phage coat.
has_obo_namespace: Phage ontology
id: phi:0000106

Axiom
annotated source: coat chaperon activity
annotated property: definition
annotated target: Chaperon activity required for the assembly of the phage coat.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

tail chaperon activity
type: Class
subclass of: capsid protein chaperon activity
definition: Chaperon activity required for the assembly of the phage tail.
has_obo_namespace: Phage ontology
id: phi:0000107

Axiom
annotated source: tail chaperon activity
annotated property: definition
annotated target: Chaperon activity required for the assembly of the phage tail.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

tail fiber chaperon activity
type: Class
subclass of: capsid protein chaperon activity
definition: Chaperon activity required for the assembly of the phage fibers.
has_obo_namespace: Phage ontology
id: phi:0000108

Axiom
annotated source: tail fiber chaperon activity
annotated property: definition
annotated target: Chaperon activity required for the assembly of the phage fibers.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

DNA binding activity
type: Class
subclass of: phage activity
definition: Interacting selectively with DNA (deoxyribonucleic acid).
database_cross_reference: GO:0003677
has_obo_namespace: Phage ontology
id: phi:0000109

Axiom
annotated source: DNA binding activity
annotated property: definition
annotated target: Interacting selectively with DNA (deoxyribonucleic acid).
database_cross_reference: GO:0003677

single stranded DNA binding activity
type: Class
subclass of: DNA binding activity
definition: Interacting selectively with single stranded DNA (deoxyribonucleic acid).
database_cross_reference: GO:0003697
has_obo_namespace: Phage ontology
id: phi:0000110

Axiom
annotated source: single stranded DNA binding activity
annotated property: definition
annotated target: Interacting selectively with single stranded DNA (deoxyribonucleic acid).
database_cross_reference: GO:0003697

double stranded DNA binding activity
type: Class
subclass of: DNA binding activity
definition: Interacting selectively with double stranded DNA (deoxyribonucleic acid).
database_cross_reference: GO:0003690
has_obo_namespace: Phage ontology
id: phi:0000111

Axiom
annotated source: double stranded DNA binding activity
annotated property: definition
annotated target: Interacting selectively with double stranded DNA (deoxyribonucleic acid).
database_cross_reference: GO:0003690

DNA topoisomerase activity
type: Class
subclass of: phage activity
definition: Catalysis of a topological transformation in double-stranded DNA by a covalent or non-covalent mechanism.
database_cross_reference: GO:0003916
has_obo_namespace: Phage ontology
id: phi:0000112

Axiom
annotated source: DNA topoisomerase activity
annotated property: definition
annotated target: Catalysis of a topological transformation in double-stranded DNA by a covalent or non-covalent mechanism.
database_cross_reference: GO:0003916

DNA polymerase processivity factor activity
type: Class
subclass of: phage activity
definition: An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization.
database_cross_reference: GO:0030337
has_obo_namespace: Phage ontology
id: phi:0000113

Axiom
annotated source: DNA polymerase processivity factor activity
annotated property: definition
annotated target: An accessory subunit of DNA polymerase that acts to increase the processivity of polymerization.
database_cross_reference: GO:0030337

DNA helicase activity
type: Class
subclass of: phage activity
definition: Catalysis of the hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied.
database_cross_reference: GO:0003678
has_obo_namespace: Phage ontology
id: phi:0000114

Axiom
annotated source: DNA helicase activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of ATP to unwind the DNA helix at the replication fork, allowing the resulting single strands to be copied.
database_cross_reference: GO:0003678

DNA directed DNA polymerase activity
type: Class
subclass of: phage activity
definition: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from DNA replication.
database_cross_reference: GO:0003887
has_obo_namespace: Phage ontology
id: phi:0000115

Axiom
annotated source: DNA directed DNA polymerase activity
annotated property: definition
annotated target: Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from DNA replication.
database_cross_reference: GO:0003887

DNA directed RNA polymerase activity
type: Class
subclass of: phage activity
definition: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
database_cross_reference: GO:0003899
has_obo_namespace: Phage ontology
id: phi:0000116

Axiom
annotated source: DNA directed RNA polymerase activity
annotated property: definition
annotated target: Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
database_cross_reference: GO:0003899

DNA methyltransferase activity
type: Class
subclass of: phage activity
definition: Catalysis of the transfer of a methyl group to a DNA molecule.
database_cross_reference: GO:0009008
has_obo_namespace: Phage ontology
id: phi:0000117

Axiom
annotated source: DNA methyltransferase activity
annotated property: definition
annotated target: Catalysis of the transfer of a methyl group to a DNA molecule.
database_cross_reference: GO:0009008

DNA primase activity
type: Class
subclass of: phage activity
definition: Catalysis of the synthesis of short RNA primers for the Okazaki fragments on both DNA template strands at the replication fork. A DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase.
database_cross_reference: GO:0003896
has_obo_namespace: Phage ontology
id: phi:0000118

Axiom
annotated source: DNA primase activity
annotated property: definition
annotated target: Catalysis of the synthesis of short RNA primers for the Okazaki fragments on both DNA template strands at the replication fork. A DNA-directed RNA polymerase that forms a complex with alpha DNA polymerase.
database_cross_reference: GO:0003896

DNA exonuclease activity
type: Class
subclass of: phage activity
definition: Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
database_cross_reference: GO:0004527
has_obo_namespace: Phage ontology
id: phi:0000119

Axiom
annotated source: DNA exonuclease activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
database_cross_reference: GO:0004527

DNA 3'-5' exonuclease activity
type: Class
subclass of: DNA exonuclease activity
definition: Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
database_cross_reference: GO:0008408
has_obo_namespace: Phage ontology
id: phi:0000120

Axiom
annotated source: DNA 3'-5' exonuclease activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
database_cross_reference: GO:0008408

DNA 5'-3' exonuclease activity
type: Class
subclass of: DNA exonuclease activity
definition: Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
database_cross_reference: GO:0008409
has_obo_namespace: Phage ontology
id: phi:0000121

Axiom
annotated source: DNA 5'-3' exonuclease activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
database_cross_reference: GO:0008409

excisionase activity
type: Class
subclass of: phage activity
definition: DNA-binding activity that activates excision by a serine or tyrosine based integrase, of a DNA segment from another, usually larger, DNA molecule such as a chromosome.
has_obo_namespace: Phage ontology
id: phi:0000122

Axiom
annotated source: excisionase activity
annotated property: definition
annotated target: DNA-binding activity that activates excision by a serine or tyrosine based integrase, of a DNA segment from another, usually larger, DNA molecule such as a chromosome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

prohead protease activity
type: Class
subclass of: peptidase activity
definition: Protease activity involved in head maturation. Usually degrades the scaffolding or remove portions of coat or portal proteins in an assembly dependent manner. May be part_of the scaffolding protein or encoded by the same gene.
has_obo_namespace: Phage ontology
id: phi:0000123

Axiom
annotated source: prohead protease activity
annotated property: definition
annotated target: Protease activity involved in head maturation. Usually degrades the scaffolding or remove portions of coat or portal proteins in an assembly dependent manner. May be part_of the scaffolding protein or encoded by the same gene.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

cell-wall peptidase activity
type: Class
subclass of: peptidase activity
definition: Protease activity involved in breaking down of the cell wall as part of the phage lysis process.
has_obo_namespace: Phage ontology
id: phi:0000124

Axiom
annotated source: cell-wall peptidase activity
annotated property: definition
annotated target: Protease activity involved in breaking down of the cell wall as part of the phage lysis process.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage terminase activity
type: Class
subclass of: DNA endonuclease activity
definition: Catalysis of DNA cleavage involved in the packaging of DNA into phage heads.
has_obo_namespace: Phage ontology
id: phi:0000125

Axiom
annotated source: phage terminase activity
annotated property: definition
annotated target: Catalysis of DNA cleavage involved in the packaging of DNA into phage heads.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

DNA endonuclease activity
type: Class
subclass of: phage activity
definition: Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
database_cross_reference: GO:0004519
has_obo_namespace: Phage ontology
id: phi:0000126

Axiom
annotated source: DNA endonuclease activity
annotated property: definition
annotated target: Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
database_cross_reference: GO:0004519

transcriptional repressor activity
type: Class
subclass of: transcription factor activity
definition: Any transcription regulator activity that prevents or downregulates transcription.
database_cross_reference: GO:0016564
has_obo_namespace: Phage ontology
id: phi:0000127

Axiom
annotated source: transcriptional repressor activity
annotated property: definition
annotated target: Any transcription regulator activity that prevents or downregulates transcription.
database_cross_reference: GO:0016564

translation repressor activity
type: Class
subclass of: phage activity
definition: Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
database_cross_reference: GO:0030371
has_obo_namespace: Phage ontology
id: phi:0000128

Axiom
annotated source: translation repressor activity
annotated property: definition
annotated target: Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
database_cross_reference: GO:0030371

DNA recombination
type: Class
subclass of: recombination process
definition: The processes by which a new genotype is formed by reassortment of genes resulting in gene combinations. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur between chromosome and plasmid or those and horizontally acquired DNA introduced in the cell via genetic transformation, conjugation or transduction.
database_cross_reference: GO:0006310
has_obo_namespace: Phage ontology
id: phi:0000129
comment: This definition differs from that in GO.

Axiom
annotated source: DNA recombination
annotated property: definition
annotated target: The processes by which a new genotype is formed by reassortment of genes resulting in gene combinations. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur between chromosome and plasmid or those and horizontally acquired DNA introduced in the cell via genetic transformation, conjugation or transduction.
database_cross_reference: GO:0006310

homologous DNA recombination
type: Class
subclass of: DNA recombination
definition: The formation and repair of double strand breaks through a double Holliday junction intermediate that results in the equal exchange of genetic material between a pair of homologous DNA fragments (chromosome, plasmid, phage).
database_cross_reference: GO:0007131
has_obo_namespace: Phage ontology
id: phi:0000130
comment: This definition differs from that in GO.

Axiom
annotated source: homologous DNA recombination
annotated property: definition
annotated target: The formation and repair of double strand breaks through a double Holliday junction intermediate that results in the equal exchange of genetic material between a pair of homologous DNA fragments (chromosome, plasmid, phage).
database_cross_reference: GO:0007131

site-specific DNA recombination
type: Class
subclass of: DNA recombination
definition: Recombination between two DNA sites begins by the recognition and binding of these sites by the recombinase protein. This is followed by the synapsis i.e. bringing the sites together to form the synaptic complex. It is within this synaptic complex that the strand exchange takes place, as the DNA is cleaved and rejoined by controlled transesterification reactions. During strand exchange, the DNA cut at fixed points within crossover region of the site releases a deoxyribose hydroxyl group, while recombinase protein forms a transient covalent bond to a DNA backbone phosphate. This phosphodiester bond between hydroxyl group of the nucleophilic, serine or tyrosine residue conserves the energy that was expended in cleaving the DNA. Energy stored in this bond is subsequently used for the rejoining of the DNA to the corresponding deoxyribose hydroxyl group on the other site. The entire process therefore goes through without the need for external energy rich cofactors such as ATP.
database_cross_reference: XX:<new xref>
has_obo_namespace: Phage ontology
id: phi:0000131

Axiom
annotated source: site-specific DNA recombination
annotated property: definition
annotated target: Recombination between two DNA sites begins by the recognition and binding of these sites by the recombinase protein. This is followed by the synapsis i.e. bringing the sites together to form the synaptic complex. It is within this synaptic complex that the strand exchange takes place, as the DNA is cleaved and rejoined by controlled transesterification reactions. During strand exchange, the DNA cut at fixed points within crossover region of the site releases a deoxyribose hydroxyl group, while recombinase protein forms a transient covalent bond to a DNA backbone phosphate. This phosphodiester bond between hydroxyl group of the nucleophilic, serine or tyrosine residue conserves the energy that was expended in cleaving the DNA. Energy stored in this bond is subsequently used for the rejoining of the DNA to the corresponding deoxyribose hydroxyl group on the other site. The entire process therefore goes through without the need for external energy rich cofactors such as ATP.
database_cross_reference: XX:<new dbxref>

Axiom
annotated source: site-specific DNA recombination
annotated property: database_cross_reference
annotated target: XX:<new xref>
label: http://en.wikipedia.org/wiki/Site-specific_recombination

site-specific DNA integration
type: Class
subclass of: site-specific DNA recombination
definition: The process by which a segment of DNA is incorporated into another by a site-specific recombination event.
has_obo_namespace: Phage ontology
id: phi:0000132

Axiom
annotated source: site-specific DNA integration
annotated property: definition
annotated target: The process by which a segment of DNA is incorporated into another by a site-specific recombination event.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

DNA integration
type: Class
subclass of: DNA recombination
definition: The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
database_cross_reference: GO:0015074
has_obo_namespace: Phage ontology
id: phi:0000133

Axiom
annotated source: DNA integration
annotated property: definition
annotated target: The process by which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
database_cross_reference: GO:0015074

site-specific DNA excision
type: Class
subclass of: site-specific DNA recombination
definition: The process by which a segment of DNA is separated from another by a site-specific recombination event. The process occurs during prophage excision, the resolution of a cointegrate DNA molecule resulting from a process of replicative transposition into finished transposition products, the resolution of multimeric plasmids into monomers and the separation of entangled circular bacterial chromosomes prior to cell division.
has_obo_namespace: Phage ontology
id: phi:0000134

Axiom
annotated source: site-specific DNA excision
annotated property: definition
annotated target: The process by which a segment of DNA is separated from another by a site-specific recombination event. The process occurs during prophage excision, the resolution of a cointegrate DNA molecule resulting from a process of replicative transposition into finished transposition products, the resolution of multimeric plasmids into monomers and the separation of entangled circular bacterial chromosomes prior to cell division.
database_cross_reference: PHI:AT

replicative transpositional recombination
type: Class
subclass of: transpositional DNA recombination
definition: A process of transpositional recombination, which involves the replication of the transposed DNA segment.
has_obo_namespace: Phage ontology
id: phi:0000135

Axiom
annotated source: replicative transpositional recombination
annotated property: definition
annotated target: A process of transpositional recombination, which involves the replication of the transposed DNA segment.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

transpositional DNA recombination
type: Class
subclass of: DNA recombination
definition: A process that moves a DNA region from one to another location in a genome via a DNA intermediate.
database_cross_reference: GO:0006313
has_obo_namespace: Phage ontology
id: phi:0000136
comment: Synonyms recently associated with the GO term do not apply here. These are in fact much too specific.

Axiom
annotated source: transpositional DNA recombination
annotated property: definition
annotated target: A process that moves a DNA region from one to another location in a genome via a DNA intermediate.
database_cross_reference: GO:0006313

conservative transpositional recombination
type: Class
subclass of: transpositional DNA recombination
definition: A process of transpositional recombination, which does not involve the replication of the transposed DNA segment. This process can however lead to the duplication of the transposed DNA segment by recombinational repair.
has_obo_namespace: Phage ontology
id: phi:0000137

Axiom
annotated source: conservative transpositional recombination
annotated property: definition
annotated target: A process of transpositional recombination, which does not involve the replication of the transposed DNA segment. This process can however lead to the duplication of the transposed DNA segment by recombinational repair.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

recombinational repair
type: Class
subclass of: DNA recombination
definition: The repair of damaged DNA that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
database_cross_reference: GO:0000725
has_obo_namespace: Phage ontology
id: phi:0000138

Axiom
annotated source: recombinational repair
annotated property: definition
annotated target: The repair of damaged DNA that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA.
database_cross_reference: GO:0000725

telomere resolution
type: Class
subclass of: Restriction
  on property: part_of
  some values from: establishment as a linear plasmid prophage
definition: A process involving DNA breakage and reunion that converts replicated telomeres into covalently closed hairpin telomeres on the ends of linear DNA molecules.
has_obo_namespace: Phage ontology
id: phi:0000139

Axiom
annotated source: telomere resolution
annotated property: definition
annotated target: A process involving DNA breakage and reunion that converts replicated telomeres into covalently closed hairpin telomeres on the ends of linear DNA molecules.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

recombinase activity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage activity
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: Activities related to bacteria, phage, plasmid and transposon recombination.
has_obo_namespace: Phage ontology
id: phi:0000140

Axiom
annotated source: recombinase activity
annotated property: definition
annotated target: Activities related to bacteria, phage, plasmid and transposon recombination.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

recombination process
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: Processes related to bacteria, phage, plasmid and transposon recombination.
has_obo_namespace: Phage ontology
id: phi:0000141

Axiom
annotated source: recombination process
annotated property: definition
annotated target: Processes related to bacteria, phage, plasmid and transposon recombination.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

DNA breakage and rejoining enzymes
type: Class
subclass of: recombinase activity
definition: Catalysis of cleavage and formation of new phosphodiester bonds between a pair of DNA target sequences.
has_obo_namespace: Phage ontology
id: phi:0000142

Axiom
annotated source: DNA breakage and rejoining enzymes
annotated property: definition
annotated target: Catalysis of cleavage and formation of new phosphodiester bonds between a pair of DNA target sequences.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

tyrosine-based recombinase activity
type: Class
subclass of: DNA breakage and rejoining enzymes
definition: Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequence by cleavage of one DNA strand and formation of a covalent phosphotyrosyl enzyme intermediate. Depending on the enzyme families, this bond can be a 3' or 5',phosphotyrosyl, liberating a 5' or a 3'OH nucleophile involved in the reunion part of the reaction.
database_cross_reference: GO:0009037
has_obo_namespace: Phage ontology
id: phi:0000143
comment: Def different form existing GO.

Axiom
annotated source: tyrosine-based recombinase activity
annotated property: definition
annotated target: Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequence by cleavage of one DNA strand and formation of a covalent phosphotyrosyl enzyme intermediate. Depending on the enzyme families, this bond can be a 3' or 5',phosphotyrosyl, liberating a 5' or a 3'OH nucleophile involved in the reunion part of the reaction.
database_cross_reference: GO:0009037

serine-based recombinase activity
type: Class
subclass of: DNA breakage and rejoining enzymes
definition: Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a 5-prime phosphoseryl enzyme intermediate in which the target sequence is first cleaved by nucleophilic attack by a serine in the active site.
database_cross_reference: XX:<new xref>
has_obo_namespace: Phage ontology
id: phi:0000144

Axiom
annotated source: serine-based recombinase activity
annotated property: definition
annotated target: Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a 5-prime phosphoseryl enzyme intermediate in which the target sequence is first cleaved by nucleophilic attack by a serine in the active site.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM
database_cross_reference: XX:<new dbxref>

Axiom
annotated source: serine-based recombinase activity
annotated property: database_cross_reference
annotated target: XX:<new xref>
label: http://en.wikipedia.org/wiki/Site-specific_recombination

tyrosine based integrase activity
type: Class
definition: Tyrosine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another.
consider: phi:0000132
consider: phi:0000143
database_cross_reference: GO:0009037
has_obo_namespace: Phage ontology
id: phi:0000145
comment: Definition differs from GO:0009037
deprecated: true

Axiom
annotated source: tyrosine based integrase activity
annotated property: definition
annotated target: Tyrosine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another.
database_cross_reference: GO:0009037

tyrosine based resolvase activity
type: Class
definition: Tyrosine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two.
consider: phi:0000134
consider: phi:0000143
has_obo_namespace: Phage ontology
id: phi:0000146
deprecated: true

Axiom
annotated source: tyrosine based resolvase activity
annotated property: definition
annotated target: Tyrosine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

tyrosine based topoisomerase IB activity
type: Class
subclass of: tyrosine-based recombinase activity
definition: Catalysis of a topological transformation in DNA through the cleavage of one DNA strand and formation of a covalent 3-prime-phosphotyrosyl enzyme intermediate to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
has_obo_namespace: Phage ontology
id: phi:0000147

Axiom
annotated source: tyrosine based topoisomerase IB activity
annotated property: definition
annotated target: Catalysis of a topological transformation in DNA through the cleavage of one DNA strand and formation of a covalent 3-prime-phosphotyrosyl enzyme intermediate to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

protelomerase activity
type: Class
subclass of: tyrosine-based recombinase activity
definition: Catalysis of a site-specific breakage and reunion reaction that generates two hairpin telomeres from a replicated telomere substrate. Occurs via a two-step transesterification with a protein-DNA intermediate similar to that used by topoisomerases and site-specific recombinases.
database_cross_reference: GO:0043336
database_cross_reference: PHI:AT
database_cross_reference: PMID:11804598
has_obo_namespace: Phage ontology
id: phi:0000148

Axiom
annotated source: protelomerase activity
annotated property: definition
annotated target: Catalysis of a site-specific breakage and reunion reaction that generates two hairpin telomeres from a replicated telomere substrate. Occurs via a two-step transesterification with a protein-DNA intermediate similar to that used by topoisomerases and site-specific recombinases.
database_cross_reference: GO:0043336
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

tyrosine-based transposase activity
type: Class
definition: Tyrosine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome.
has_obo_namespace: Phage ontology
id: phi:0000149
deprecated: true

Axiom
annotated source: tyrosine-based transposase activity
annotated property: definition
annotated target: Tyrosine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

serine based integrase activity
type: Class
definition: Serine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another.
consider: phi:0000132
consider: phi:0000144
has_obo_namespace: Phage ontology
id: phi:0000150
deprecated: true

Axiom
annotated source: serine based integrase activity
annotated property: definition
annotated target: Serine based DNA breakage and reunion activity that leads to the integration of one DNA molecule into another.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

serine based resolvase activity
type: Class
definition: Serine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two.
consider: phi:0000134
consider: phi:0000144
has_obo_namespace: Phage ontology
id: phi:0000151
deprecated: true

Axiom
annotated source: serine based resolvase activity
annotated property: definition
annotated target: Serine based DNA breakage and reunion activity that leads to the conversion of one DNA molecule into two.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

serine based transposase activity
type: Class
definition: Serine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome.
has_obo_namespace: Phage ontology
id: phi:0000152
deprecated: true

Axiom
annotated source: serine based transposase activity
annotated property: definition
annotated target: Serine based DNA breakage and reunion activity that moves a DNA segment from one to another location in a genome.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

DDE-based recombinase activity
type: Class
subclass of: DNA breakage and rejoining enzymes
subclass of: Restriction
  on property: part_of
  some values from: transpososome
definition: Recomoinases with aDDE transposase have a related amino-acid motif (the DDE motif), which forms the active site of the transposase and is responsible for coordinating the cleavage and joining steps of transposition. Breakage of the DNA occurs at the end of the element (usually a hydrolysis) and is followed by breakage and integration at the target site (a transesterification reaction).
has_obo_namespace: Phage ontology
id: phi:0000153

Axiom
annotated source: DDE-based recombinase activity
annotated property: definition
annotated target: Recomoinases with aDDE transposase have a related amino-acid motif (the DDE motif), which forms the active site of the transposase and is responsible for coordinating the cleavage and joining steps of transposition. Breakage of the DNA occurs at the end of the element (usually a hydrolysis) and is followed by breakage and integration at the target site (a transesterification reaction).
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

recombination component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: Any multiprotein recombinogenic complex containing DNA, recombinase and accessory proteins.
has_obo_namespace: Phage ontology
id: phi:0000154

Axiom
annotated source: recombination component
annotated property: definition
annotated target: Any multiprotein recombinogenic complex containing DNA, recombinase and accessory proteins.
database_cross_reference: PHI:AT

intasome
type: Class
subclass of: phage component
subclass of: recombination component
definition: Any multiprotein recombinogenic complex containing DNA, site-specific tyrosine or serine based integrase and accessory proteins and involved in the intgeration or ecision of DNA fragments.
has_obo_namespace: Phage ontology
id: phi:0000155

Axiom
annotated source: intasome
annotated property: definition
annotated target: Any multiprotein recombinogenic complex containing DNA, site-specific tyrosine or serine based integrase and accessory proteins and involved in the intgeration or ecision of DNA fragments.
database_cross_reference: PHI:AT

relaxosome
type: Class
subclass of: recombination component
subclass of: plasmid component
definition: A multi-component enzymatic machine including a relaxase, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition.
has_obo_namespace: Phage ontology
id: phi:0000156

Axiom
annotated source: relaxosome
annotated property: definition
annotated target: A multi-component enzymatic machine including a relaxase, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition.
database_cross_reference: PHI:AT

transpososome
type: Class
subclass of: phage component
subclass of: recombination component
subclass of: plasmid component
definition: A multi-component enzymatic machine, which mediates DNA transposition; it Includes the DDE (DDD?) transposase and accessory proteins including nucleoid associated proteins such as HU or IHF.
has_obo_namespace: Phage ontology
id: phi:0000157

Axiom
annotated source: transpososome
annotated property: definition
annotated target: A multi-component enzymatic machine, which mediates DNA transposition; it Includes the DDE (DDD?) transposase and accessory proteins including nucleoid associated proteins such as HU or IHF.
database_cross_reference: PHI:AT

resolvasome
type: Class
subclass of: plasmid component
definition: A multi-component enzymatic machine including a tyrosine or serine based resolvase, which mediates resolution of chromosome dimers and replicon fusions.
has_obo_namespace: Phage ontology
id: phi:0000158

Axiom
annotated source: resolvasome
annotated property: definition
annotated target: A multi-component enzymatic machine including a tyrosine or serine based resolvase, which mediates resolution of chromosome dimers and replicon fusions.
database_cross_reference: PHI:AT

Y2 transposase activity
type: Class
subclass of: DNA breakage and rejoining enzymes
definition: Y2-transposases catalyze the rolling circle transposition. They contain several conserved motifs including a pair of tyrosine residues, that are conserved among plasmid and phage rolling-circle replication proteins, which are important for DNA binding, breakage and reunion.
has_obo_namespace: Phage ontology
id: phi:0000159

Axiom
annotated source: Y2 transposase activity
annotated property: definition
annotated target: Y2-transposases catalyze the rolling circle transposition. They contain several conserved motifs including a pair of tyrosine residues, that are conserved among plasmid and phage rolling-circle replication proteins, which are important for DNA binding, breakage and reunion.
database_cross_reference: PHI:AL
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: PHI:GH
database_cross_reference: PHI:IM

rolling circle transposition
type: Class
subclass of: transpositional DNA recombination
definition: Movement of a DNA segment form one to another location in a genome by a mechanism that resembles rolling-circle replication carried out by many bacterial plasmids and phage.
has_obo_namespace: Phage ontology
id: phi:0000160

Axiom
annotated source: rolling circle transposition
annotated property: definition
annotated target: Movement of a DNA segment form one to another location in a genome by a mechanism that resembles rolling-circle replication carried out by many bacterial plasmids and phage.
database_cross_reference: PHI:A
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

head/capsid
type: Class
subclass of: phage component
definition: The protein coat that surrounds the infective nucleic acid in phage particles. It comprises numerous regularly arranged subunits.
has_obo_namespace: Phage ontology
id: phi:0000161

Axiom
annotated source: head/capsid
annotated property: definition
annotated target: The protein coat that surrounds the infective nucleic acid in phage particles. It comprises numerous regularly arranged subunits.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

inhibitor of RNA polymerase
type: Class
subclass of: phage activity
definition: Activity that represses RNA polymerase activity.
has_obo_namespace: Phage ontology
id: phi:0000162
comment: Typically expressed by phages to turn off host egne expression.

Axiom
annotated source: inhibitor of RNA polymerase
annotated property: definition
annotated target: Activity that represses RNA polymerase activity.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

inhibitor of RecBCD nuclease
type: Class
subclass of: phage activity
definition: Activity that inhibits DNA degradation by the phage host protein complex RecBCD.
has_obo_namespace: Phage ontology
id: phi:0000163

Axiom
annotated source: inhibitor of RecBCD nuclease
annotated property: definition
annotated target: Activity that inhibits DNA degradation by the phage host protein complex RecBCD.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

plasmid mediated regulation of host gene expression
type: Class
subclass of: phage mediated modulation of host functions
subclass of: plasmid mediated modulation of host functions
definition: Any process that modulates host gene expression as a result of phage gene expression.
has_obo_namespace: Phage ontology
id: phi:0000164

Axiom
annotated source: plasmid mediated regulation of host gene expression
annotated property: definition
annotated target: Any process that modulates host gene expression as a result of phage gene expression.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

plasmid mediated positive regulation of host gene expression
type: Class
subclass of: plasmid mediated regulation of host gene expression
definition: Any process that up-regulates host gene expression as a result of phage gene expression.
has_obo_namespace: Phage ontology
id: phi:0000165

Axiom
annotated source: plasmid mediated positive regulation of host gene expression
annotated property: definition
annotated target: Any process that up-regulates host gene expression as a result of phage gene expression.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

plasmid mediated negative regulation of host gene expression
type: Class
subclass of: plasmid mediated regulation of host gene expression
definition: Any process that down-regulates host gene expression as a result of phage gene expression.
has_obo_namespace: Phage ontology
id: phi:0000166

Axiom
annotated source: plasmid mediated negative regulation of host gene expression
annotated property: definition
annotated target: Any process that down-regulates host gene expression as a result of phage gene expression.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

inhibitor of FtsH protease activity
type: Class
subclass of: phage activity
definition: Activity that inhibits protein breakdown by the phage host protease FtsH.
has_obo_namespace: Phage ontology
id: phi:0000167

Axiom
annotated source: inhibitor of FtsH protease activity
annotated property: definition
annotated target: Activity that inhibits protein breakdown by the phage host protease FtsH.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

modulator of nucleoid associated protein HNS
type: Class
subclass of: phage activity
definition: Activity that modulates the nucleoid associated protein/DNA chaperon HNS.
has_obo_namespace: Phage ontology
id: phi:0000168

Axiom
annotated source: modulator of nucleoid associated protein HNS
annotated property: definition
annotated target: Activity that modulates the nucleoid associated protein/DNA chaperon HNS.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

inhibitor-of deoxyguanosine triphospho hydrolase
type: Class
subclass of: phage activity
definition: Activity that decreases deoxyguanosine triphospho-hydrolase activity.
has_obo_namespace: Phage ontology
id: phi:0000169
comment: Typically expressed by phages to turn off host egne expression.

Axiom
annotated source: inhibitor-of deoxyguanosine triphospho hydrolase
annotated property: definition
annotated target: Activity that decreases deoxyguanosine triphospho-hydrolase activity.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

plasmid mediated modulation of host protein activity
type: Class
subclass of: phage mediated modulation of host functions
subclass of: plasmid mediated modulation of host functions
definition: Any process that activates or represses the activity of a host protein.
has_obo_namespace: Phage ontology
id: phi:0000170

Axiom
annotated source: plasmid mediated modulation of host protein activity
annotated property: definition
annotated target: Any process that activates or represses the activity of a host protein.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

host cell killing activity
type: Class
subclass of: phage activity
subclass of: plasmid activity
definition: Activity that provokes host cell kiling independently of any other phage lytic or plasmid activity.
has_obo_namespace: Phage ontology
id: phi:0000171

Axiom
annotated source: host cell killing activity
annotated property: definition
annotated target: Activity that provokes host cell kiling independently of any other phage lytic or plasmid activity.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

SO term
type: Class
definition: To be (or already) transferred to SO
has_obo_namespace: Phage ontology
id: phi:0000172

Axiom
annotated source: SO term
annotated property: definition
annotated target: To be (or already) transferred to SO
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

major capsid structural protein
type: Class
subclass of: capsid structural protein
definition: Protein that is a major component of the phage particle.
database_cross_reference: GO:0042001
has_obo_namespace: Phage ontology
id: phi:0000173

Axiom
annotated source: major capsid structural protein
annotated property: definition
annotated target: Protein that is a major component of the phage particle.
database_cross_reference: PHI:AT

capsid tail
type: Class
subclass of: phage component
definition: Component of the tailed phages i.e. the Caudovirales, which have a double stranded DNA genome. The tail can be short (Podoviridae), long and non-contractile (Siphoviridae) or long and contractile (Myoviridae). The tail is the channel through which the phage genome is injected into the host bacterial cell.
has_obo_namespace: Phage ontology
id: phi:0000174

Axiom
annotated source: capsid tail
annotated property: definition
annotated target: Component of the tailed phages i.e. the Caudovirales, which have a double stranded DNA genome. The tail can be short (Podoviridae), long and non-contractile (Siphoviridae) or long and contractile (Myoviridae). The tail is the channel through which the phage genome is injected into the host bacterial cell.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

capsid tail fiber
type: Class
subclass of: phage component
definition: Tail fibers are appended at the phage tail tip and serve to scan, recognize and attach to the cognate receptor on bacterial host cell surface. Tail fibers typically bind to particular LPS, polysaccharide, protein or other components of the cell surface.
has_obo_namespace: Phage ontology
id: phi:0000175

Axiom
annotated source: capsid tail fiber
annotated property: definition
annotated target: Tail fibers are appended at the phage tail tip and serve to scan, recognize and attach to the cognate receptor on bacterial host cell surface. Tail fibers typically bind to particular LPS, polysaccharide, protein or other components of the cell surface.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage head/capsid fiber
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage head/capsid protein
definition: Fiber structures, which decorate the head of some phages.
has_obo_namespace: Phage ontology
id: phi:0000176

Axiom
annotated source: phage head/capsid fiber
annotated property: definition
annotated target: Fiber structures, which decorate the head of some phages.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

prohead/procapsid
type: Class
subclass of: phage component
definition: The precursor protein complex that will evolve into the coat that surrounds the infective nucleic acid in phage particles. It builds up around the scaffolding, which assembles on top of the portal complex and is later degraded or leaves the prohead without degradation to be replaced by DNA.
has_obo_namespace: Phage ontology
id: phi:0000177

Axiom
annotated source: prohead/procapsid
annotated property: definition
annotated target: The precursor protein complex that will evolve into the coat that surrounds the infective nucleic acid in phage particles. It builds up around the scaffolding, which assembles on top of the portal complex and is later degraded or leaves the prohead without degradation to be replaced by DNA.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage minor tail protein
type: Class
subclass of: phage tail protein
definition: Protein component found in low number of copies in the tail of phage particles of the types myoviridae and siphoviridae.
has_obo_namespace: Phage ontology
id: phi:0000178

Axiom
annotated source: phage minor tail protein
annotated property: definition
annotated target: Protein component found in low number of copies in the tail of phage particles of the types myoviridae and siphoviridae.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

phage head/capsid internal protein
type: Class
subclass of: phage head/capsid protein
definition: Phage head/capsid protein component located inside the finished head.
has_obo_namespace: Phage ontology
id: phi:0000179

Axiom
annotated source: phage head/capsid internal protein
annotated property: definition
annotated target: Phage head/capsid protein component located inside the finished head.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

inhibitor of RecA protease activity
type: Class
subclass of: phage activity
definition: Activity that inhibits the protease activity of the host RecA protein.
has_obo_namespace: Phage ontology
id: phi:0000180

Axiom
annotated source: inhibitor of RecA protease activity
annotated property: definition
annotated target: Activity that inhibits the protease activity of the host RecA protein.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

capsid protein chaperon activity
type: Class
subclass of: phage activity
definition: Chaperon activity required for the assembly of phage components.
has_obo_namespace: Phage ontology
id: phi:0000181

Axiom
annotated source: capsid protein chaperon activity
annotated property: definition
annotated target: Chaperon activity required for the assembly of phage components.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

DNA excision
type: Class
subclass of: DNA recombination
definition: The process by which a segment of DNA is separated from another, usually larger, DNA molecule such as a chromosome.
database_cross_reference: GO:0007131
has_exact_synonym: DNA resolution
has_obo_namespace: Phage ontology
id: phi:0000182

Axiom
annotated source: DNA excision
annotated property: definition
annotated target: The process by which a segment of DNA is separated from another, usually larger, DNA molecule such as a chromosome.
database_cross_reference: PHI:AT

Axiom
annotated source: DNA excision
annotated property: has_exact_synonym
annotated target: DNA resolution
database_cross_reference: GO:0007131

RNA directed RNA polymerase activity
type: Class
subclass of: phage activity
definition: Catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
database_cross_reference: GO:0003899
has_obo_namespace: Phage ontology
id: phi:0000183

Axiom
annotated source: RNA directed RNA polymerase activity
annotated property: definition
annotated target: Catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
database_cross_reference: GO:0003968

transcription factor activity
type: Class
subclass of: DNA binding activity
definition: Any transcription regulator activity that prevents or downregulates transcription.
database_cross_reference: GO:0003700
has_obo_namespace: Phage ontology
id: phi:0000184

Axiom
annotated source: transcription factor activity
annotated property: definition
annotated target: Any transcription regulator activity that prevents or downregulates transcription.
database_cross_reference: GO:0003700

phage head/capsid minor protein
type: Class
subclass of: phage head/capsid protein
definition: Protein component found in low number of copies in the shell/head/capsid of phage particles.
has_obo_namespace: Phage ontology
id: phi:0000185

Axiom
annotated source: phage head/capsid minor protein
annotated property: definition
annotated target: Protein component found in low number of copies in the shell/head/capsid of phage particles.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

minor capsid structural protein
type: Class
subclass of: capsid structural protein
definition: Protein that is a minor component of the phage particle.
database_cross_reference: GO:0042001
has_obo_namespace: Phage ontology
id: phi:0000186

Axiom
annotated source: minor capsid structural protein
annotated property: definition
annotated target: Protein that is a minor component of the phage particle.
database_cross_reference: PHI:AT

capsid structural protein
type: Class
subclass of: phage component
definition: Protein component of the phage virion.
database_cross_reference: GO:0042001
has_obo_namespace: Phage ontology
id: phi:0000187

Axiom
annotated source: capsid structural protein
annotated property: definition
annotated target: Protein component of the phage virion.
database_cross_reference: PHI:AT

shiga toxin activity
type: Class
subclass of: intracellular AB toxin activity
definition: Usually taken in with food or water contaminated with bacteria that express it, the Shiga toxin is composed of two subunits, A and B. It acts on the lining of the blood vessels, the vascular endothelium. After it enters the cell, the toxin inhibits the ribosomes, leading to cell death.
database_cross_reference: CBWInfo:Verotox.html#0003
has_obo_namespace: Phage ontology
id: phi:0000188

Axiom
annotated source: shiga toxin activity
annotated property: definition
annotated target: Usually taken in with food or water contaminated with bacteria that express it, the Shiga toxin is composed of two subunits, A and B. It acts on the lining of the blood vessels, the vascular endothelium. After it enters the cell, the toxin inhibits the ribosomes, leading to cell death.
database_cross_reference: PHI:AT

shiga toxin subunit A
type: Class
subclass of: Restriction
  on property: part_of
  some values from: shiga toxin activity
definition: One of the two subunits. The A subunit of the Shiga toxin is an N-glycosidase that modifies the RNA component of the ribosome to inactivate it and so brings a halt to protein synthesis leading to cell death.
database_cross_reference: CBWInfo:Verotox.html#0003
has_obo_namespace: Phage ontology
id: phi:0000189

Axiom
annotated source: shiga toxin subunit A
annotated property: definition
annotated target: One of the two subunits. The A subunit of the Shiga toxin is an N-glycosidase that modifies the RNA component of the ribosome to inactivate it and so brings a halt to protein synthesis leading to cell death.
database_cross_reference: PHI:AT

shiga toxin subunit B
type: Class
subclass of: Restriction
  on property: part_of
  some values from: shiga toxin activity
definition: Shiga toxin subunit B binds to a component of the cell membrane known as Gb3 allowing the complex AB toxin to enter the cell.
database_cross_reference: CBWInfo:Verotox.html#0003
has_obo_namespace: Phage ontology
id: phi:0000190

Axiom
annotated source: shiga toxin subunit B
annotated property: definition
annotated target: Shiga toxin subunit B binds to a component of the cell membrane known as Gb3 allowing the complex AB toxin to enter the cell.
database_cross_reference: PHI:AT

unclassified
type: Class
definition: Yet...
has_obo_namespace: Phage ontology
id: phi:0000191

Axiom
annotated source: unclassified
annotated property: definition
annotated target: Yet...
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:MS
database_cross_reference: PHI:SC

thioredoxin
type: Class
subclass of: phage activity
definition: Thioredoxins are proteins that act as antioxidants by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange. Thioredoxins are found in nearly all known organisms and are essential for life in mammals. Thioredoxin is a co-factor of some phage DNA-polymerases.
database_cross_reference: GO:0030508
database_cross_reference: Wikipedia:thioredoxin
has_exact_synonym: thiol-disulfide exchange intermediate activity
has_obo_namespace: Phage ontology
id: phi:0000192

Axiom
annotated source: thioredoxin
annotated property: definition
annotated target: Thioredoxins are proteins that act as antioxidants by facilitating the reduction of other proteins by cysteine thiol-disulfide exchange. Thioredoxins are found in nearly all known organisms and are essential for life in mammals. Thioredoxin is a co-factor of some phage DNA-polymerases.
database_cross_reference: PHI:AT

Axiom
annotated source: thioredoxin
annotated property: has_exact_synonym
annotated target: thiol-disulfide exchange intermediate activity
database_cross_reference: GO:0030508

restriction alleviation
type: Class
subclass of: phage mediated modulation of host functions
subclass of: plasmid mediated modulation of host functions
definition: Any process that results into the inhibition of a host restriction.
has_obo_namespace: Phage ontology
id: phi:0000193

Axiom
annotated source: restriction alleviation
annotated property: definition
annotated target: Any process that results into the inhibition of a host restriction.
database_cross_reference: PHI:AT

plasmid maintenance
type: Class
subclass of: plasmid process
subclass of: Restriction
  on property: part_of
  some values from: establishment as a linear plasmid prophage
subclass of: Restriction
  on property: part_of
  some values from: establishment as a circular plasmid prophage
definition: The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
database_cross_reference: GO:n0006276
has_obo_namespace: Phage ontology
id: phi:0000194

Axiom
annotated source: plasmid maintenance
annotated property: definition
annotated target: The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
database_cross_reference: GO:0006276

phage translation repressor activity
type: Class
subclass of: translation repressor activity
definition: Phage encoded protein that antagonizes ribosome-mediated translation of mRNA into a polypeptide.
database_cross_reference: GO:0030371
has_obo_namespace: Phage ontology
id: phi:0000195

Axiom
annotated source: phage translation repressor activity
annotated property: definition
annotated target: Phage encoded protein that antagonizes ribosome-mediated translation of mRNA into a polypeptide.
database_cross_reference: PHI:AT

plasmid copy number control
type: Class
subclass of: Restriction
  on property: part_of
  some values from: establishment as a linear plasmid prophage
subclass of: Restriction
  on property: part_of
  some values from: establishment as a circular plasmid prophage
subclass of: Restriction
  on property: part_of
  some values from: plasmid vegetative DNA replication
definition: Any process that controls the number of copies of a plasmid per host cell.
has_obo_namespace: Phage ontology
id: phi:0000196

Axiom
annotated source: plasmid copy number control
annotated property: definition
annotated target: Any process that controls the number of copies of a plasmid per host cell.
database_cross_reference: PHI:AT

virulent phage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: Phage which upon infection has no other choice than entering the lytic cycle.
has_obo_namespace: Phage ontology
id: phi:0000197

Axiom
annotated source: virulent phage
annotated property: definition
annotated target: Phage which upon infection has no other choice than entering the lytic cycle.
database_cross_reference: PHI:AT

temperate phage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: Phage which upon infection has the choice between going lytic or lysogenic.
database_cross_reference: Wikipedia:thioredoxin
has_obo_namespace: Phage ontology
id: phi:0000198
comment: Needs revision

Axiom
annotated source: temperate phage
annotated property: definition
annotated target: Phage which upon infection has the choice between going lytic or lysogenic.
database_cross_reference: PHI:AT

hyaluronidase activity
type: Class
subclass of: phage activity
subclass of: toxin
definition: Activity resulting in the degradation of hyaluronic acid.
database_cross_reference: KEGG:EC 3.2.1.35
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Hyaluronidase
has_obo_namespace: Phage ontology
id: phi:0000199

Axiom
annotated source: hyaluronidase activity
annotated property: definition
annotated target: Activity resulting in the degradation of hyaluronic acid.
database_cross_reference: PHI:AT

leukocidin cativity
type: Class
subclass of: phage activity
subclass of: toxin
definition: Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes, and macrophages.
database_cross_reference: PMID:16794307
has_obo_namespace: Phage ontology
id: phi:0000200
comment: Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes and macrophages.

Axiom
annotated source: leukocidin cativity
annotated property: definition
annotated target: Staphylococcal leukocidin (Luk) consists of LukS and LukF, which cooperatively lyse human polymorphonuclear leukocytes (HPMNLs), monocytes, and macrophages.
database_cross_reference: PHI:AT

superantigen activity
type: Class
subclass of: phage activity
subclass of: toxin
definition: Family of potent immunostimulators able to simultaneously bind to the MHC class 2 molecules and the T cell receptor bacterial, resulting in alpha-beta T cell activation.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Superantigen
has_obo_namespace: Phage ontology
id: phi:0000201

Axiom
annotated source: superantigen activity
annotated property: definition
annotated target: Family of potent immunostimulators able to simultaneously bind to the MHC class 2 molecules and the T cell receptor bacterial, resulting in alpha-beta T cell activation.
database_cross_reference: PHI:AT

staphylokinase
type: Class
subclass of: phage activity
subclass of: toxin
definition: Staphylokinases (SAK) are enzymes, which activate plasminogen, which in turn can degrade various host proteins during infection.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Staphylokinase
has_obo_namespace: Phage ontology
id: phi:0000202

Axiom
annotated source: staphylokinase
annotated property: definition
annotated target: Staphylokinases (SAK) are enzymes, which activate plasminogen, which in turn can degrade various host proteins during infection.
database_cross_reference: PHI:AT

streptodornase
type: Class
subclass of: phage activity
subclass of: toxin
definition: Streptodornases are DNases secreted by S. pyogenes and which protect the bacteria from being trapped in neutrophil extracellular traps (NETs) by digesting the NET's web of DNA, to which are bound neutrophil serine proteases that can kill the bacteria.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Streptococcus_pyogenes
has_exact_synonym: streptokinase
has_obo_namespace: Phage ontology
id: phi:0000203

Axiom
annotated source: streptodornase
annotated property: definition
annotated target: Streptodornases are DNases secreted by S. pyogenes and which protect the bacteria from being trapped in neutrophil extracellular traps (NETs) by digesting the NET's web of DNA, to which are bound neutrophil serine proteases that can kill the bacteria.
database_cross_reference: PHI:AT

exfoliative toxin A
type: Class
subclass of: phage activity
subclass of: toxin
definition: Exfoliative toxin A is a Staphylococcus aureus protease activity, which causes peeling of the skin observed in staphylococcal scalded-skin syndrome.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/Staphylococcus_aureus
has_obo_namespace: Phage ontology
id: phi:0000204

Axiom
annotated source: exfoliative toxin A
annotated property: definition
annotated target: Exfoliative toxin A is a Staphylococcus aureus protease activity, which causes peeling of the skin observed in staphylococcal scalded-skin syndrome.
database_cross_reference: PHI:AT

capsid neck protein
type: Class
subclass of: capsid structural protein
subclass of: Restriction
  on property: part_of
  some values from: capsid neck
definition: Protein component of a constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae).
has_obo_namespace: Phage ontology
id: phi:0000205

Axiom
annotated source: capsid neck protein
annotated property: definition
annotated target: Protein component of a constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae).
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

capsid collar protein
type: Class
subclass of: capsid structural protein
subclass of: Restriction
  on property: part_of
  some values from: capsid collar
definition: Protein component of a small disk located below some phage heads.
has_obo_namespace: Phage ontology
id: phi:0000206

Axiom
annotated source: capsid collar protein
annotated property: definition
annotated target: Protein component of a small disk located below some phage heads.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

capsid collar fiber protein
type: Class
subclass of: capsid structural protein
subclass of: Restriction
  on property: part_of
  some values from: capsid collar fiber
definition: Protein component of the fibers attached to the collar structure of some phages.
has_obo_namespace: Phage ontology
id: phi:0000207

Axiom
annotated source: capsid collar fiber protein
annotated property: definition
annotated target: Protein component of the fibers attached to the collar structure of some phages.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

phage spike
type: Class
subclass of: phage head/capsid protein
definition: Short stuctures (generally 30 nm long) at the tail tip of some phages and used for attachment.
has_obo_namespace: Phage ontology
id: phi:0000208

Axiom
annotated source: phage spike
annotated property: definition
annotated target: Short stuctures (generally 30 nm long) at the tail tip of some phages and used for attachment.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

pathogenicity island
type: Class
subclass of: genomic island
definition: Genomic island which carries genes encoding proteins related to pathogenicity such as attachment, invasion of the host, other virulence factors, toxins, etc.
database_cross_reference: SO:0000773
has_exact_synonym: pathogenic island
has_obo_namespace: Phage ontology
id: phi:0000209
comment: SO definition: Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species.

Axiom
annotated source: pathogenicity island
annotated property: definition
annotated target: Genomic island which carries genes encoding proteins related to pathogenicity such as attachment, invasion of the host, other virulence factors, toxins, etc.
database_cross_reference: SO:0000773

phage capsid triangulation number
type: Class
subclass of: unclassified
definition: Number of triangles into which an icosahedral virus capsid can be subdivided.
has_obo_namespace: Phage ontology
id: phi:0000210

Axiom
annotated source: phage capsid triangulation number
annotated property: definition
annotated target: Number of triangles into which an icosahedral virus capsid can be subdivided.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

attachment site
type: Class
subclass of: SO term
definition: Short DNA sequence, which is a target region for site-specific integration and/or excision and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
database_cross_reference: SO:0000342
has_exact_synonym: site specific recombination target region
has_obo_namespace: Phage ontology
id: phi:0000211

Axiom
annotated source: attachment site
annotated property: definition
annotated target: Short DNA sequence, which is a target region for site-specific integration and/or excision and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: attachment site
annotated property: has_exact_synonym
annotated target: site specific recombination target region
database_cross_reference: SO:0000342

attB site
type: Class
subclass of: attachment site
definition: Integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
database_cross_reference: SO:0000943
has_obo_namespace: Phage ontology
id: phi:0000212

Axiom
annotated source: attB site
annotated property: definition
annotated target: Integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site.
database_cross_reference: SO:0000943

attP site
type: Class
subclass of: attachment site
subclass of: Restriction
  on property: part_of
  some values from: phage concatemer
definition: Attachment site located on the on the phage genome.
database_cross_reference: SO:0000942
has_obo_namespace: Phage ontology
id: phi:0000213

Axiom
annotated source: attP site
annotated property: definition
annotated target: Attachment site located on the on the phage genome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: SO:0000942

attL site
type: Class
subclass of: attachment site
subclass of: Restriction
  on property: part_of
  some values from: prophage
subclass of: Restriction
  on property: part_of
  some values from: transposable prophage
definition: Attachment site located on the bacterial chromosome at the left of a prophage region and which is used for prophage site-specific excision.
database_cross_reference: SO:0000944
has_exact_synonym: attBP'
has_obo_namespace: Phage ontology
id: phi:0000214

Axiom
annotated source: attL site
annotated property: definition
annotated target: Attachment site located on the bacterial chromosome at the left of a prophage region and which is used for prophage site-specific excision.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: SO:0000944

Axiom
annotated source: attL site
annotated property: has_exact_synonym
annotated target: attBP'
database_cross_reference: PHI:AT

attR site
type: Class
subclass of: attachment site
subclass of: Restriction
  on property: part_of
  some values from: prophage
subclass of: Restriction
  on property: part_of
  some values from: transposable prophage
definition: A region that results from recombination between attP site and attB site, composed of the 5' portion of attP site and the 3' portion of attB site.
database_cross_reference: SO:0000945
has_exact_synonym: attPB'
has_obo_namespace: Phage ontology
id: phi:0000215

Axiom
annotated source: attR site
annotated property: definition
annotated target: A region that results from recombination between attP site and attB site, composed of the 5' portion of attP site and the 3' portion of attB site.
database_cross_reference: SO:0000945

Axiom
annotated source: attR site
annotated property: has_exact_synonym
annotated target: attPB'
database_cross_reference: PHI:AT

attCTn site
type: Class
subclass of: attachment site
subclass of: Restriction
  on property: part_of
  some values from: conjugative transposon
subclass of: Restriction
  on property: part_of
  some values from: defective conjugative transposon
definition: An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
database_cross_reference: SO:0001043
has_obo_namespace: Phage ontology
id: phi:0000216

Axiom
annotated source: attCTn site
annotated property: definition
annotated target: An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon.
database_cross_reference: SO:0001043

attI site
type: Class
subclass of: attachment site
subclass of: Restriction
  on property: part_of
  some values from: integron platform
definition: A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
database_cross_reference: SO:0000367
has_obo_namespace: Phage ontology
id: phi:0000217

Axiom
annotated source: attI site
annotated property: definition
annotated target: A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place.
database_cross_reference: SO:0000367

attC site
type: Class
subclass of: attachment site
subclass of: Restriction
  on property: part_of
  some values from: gene cassette (sensu integrons)
definition: Attachment site located on a gene cassette (sensu integron) and used for site-specific integration in an integron.
database_cross_reference: SO:0000950
has_exact_synonym: 59 base pairs sequence
has_obo_namespace: Phage ontology
id: phi:0000218
comment: Exists in SO but I prefer my definition, because SO's does not mention the cassette.

Axiom
annotated source: attC site
annotated property: definition
annotated target: Attachment site located on a gene cassette (sensu integron) and used for site-specific integration in an integron.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

resolution site
type: Class
subclass of: Restriction
  on property: part_of
  some values from: unitary transposon
subclass of: Restriction
  on property: part_of
  some values from: cointegrate
definition: Target region for site-specific recombination leading to the resolution of a chromosome or plasmid dimer or a cointegrate resulting from replicative transposition.
database_cross_reference: SO:0000947
has_exact_synonym: res site
has_obo_namespace: Phage ontology
has_related_synonym: cer site
has_related_synonym: dif site
has_related_synonym: loxP site
id: phi:0000219

Axiom
annotated source: resolution site
annotated property: definition
annotated target: Target region for site-specific recombination leading to the resolution of a chromosome or plasmid dimer or a cointegrate resulting from replicative transposition.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: SO:0000947

transposon end
type: Class
subclass of: inverted repeat
definition: Region located at either end of an integrated transposon; it includes binding sites for the cognate transposase enzyme, which nicks the transposon at its last base pair.
has_obo_namespace: Phage ontology
id: phi:0000220

Axiom
annotated source: transposon end
annotated property: definition
annotated target: Region located at either end of an integrated transposon; it includes binding sites for the cognate transposase enzyme, which nicks the transposon at its last base pair.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

IRLI
type: Class
subclass of: transposon end
subclass of: Restriction
  on property: part_of
  some values from: composite transposon
definition: The left transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence.
has_obo_namespace: Phage ontology
id: phi:0000221

Axiom
annotated source: IRLI
annotated property: definition
annotated target: The left transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

IRL
type: Class
subclass of: transposon end
subclass of: Restriction
  on property: part_of
  some values from: unitary transposon
subclass of: Restriction
  on property: part_of
  some values from: insertion sequence
definition: The left end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRR.
has_obo_namespace: Phage ontology
has_related_synonym: inverted repeat
id: phi:0000222
comment: In the case of transposable (pro)phages it is called attL and includes several subsites, attL1, attL2 and attL3.

Axiom
annotated source: IRL
annotated property: definition
annotated target: The left end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRR.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: IRL
annotated property: has_related_synonym
annotated target: inverted repeat
database_cross_reference: SO:0000294

IRR
type: Class
subclass of: transposon end
subclass of: Restriction
  on property: part_of
  some values from: unitary transposon
subclass of: Restriction
  on property: part_of
  some values from: insertion sequence
definition: The right end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRL.
has_obo_namespace: Phage ontology
has_related_synonym: inverted repeat
id: phi:0000223
comment: In the case of transposable (pro)phages it is called attR and includes several subsites, attR1, attR2 and attR3.

Axiom
annotated source: IRR
annotated property: definition
annotated target: The right end of an IS or a transposon. During transpososome synapsis it is brought together with its counterpart imperfect inverted repeat IRL.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: IRR
annotated property: has_related_synonym
annotated target: inverted repeat
database_cross_reference: SO:0000294

IRLO
type: Class
subclass of: transposon end
subclass of: Restriction
  on property: part_of
  some values from: composite transposon
definition: The left transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence.
has_obo_namespace: Phage ontology
id: phi:0000224

Axiom
annotated source: IRLO
annotated property: definition
annotated target: The left transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

IRRO
type: Class
subclass of: transposon end
subclass of: Restriction
  on property: part_of
  some values from: composite transposon
definition: The right transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence.
has_obo_namespace: Phage ontology
id: phi:0000225

Axiom
annotated source: IRRO
annotated property: definition
annotated target: The right transposon end of an IS, which is part of a composite transposon and is on the outside end of the transposon sequence.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

IRRI
type: Class
subclass of: transposon end
subclass of: Restriction
  on property: part_of
  some values from: composite transposon
definition: The right transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence.
has_obo_namespace: Phage ontology
id: phi:0000226

Axiom
annotated source: IRRI
annotated property: definition
annotated target: The right transposon end of an IS, which is part of a composite transposon and is on the inside end of the transposon sequence.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type I secretion membrane fusion protein activity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type I protein secretion system complex
definition: To be added.
has_obo_namespace: Phage ontology
id: phi:0000227

Axiom
annotated source: type I secretion membrane fusion protein activity
annotated property: definition
annotated target: To be added.
database_cross_reference: PHI:AT

inversion site
type: Class
subclass of: inverted repeat
definition: A region specifically recognized by a recombinase, which inverts the region flanked by a pair of sites.
database_cross_reference: SO:0000948
has_exact_synonym: inv site
has_obo_namespace: Phage ontology
has_related_synonym: ftr site
id: phi:0000228

Axiom
annotated source: inversion site
annotated property: definition
annotated target: A region specifically recognized by a recombinase, which inverts the region flanked by a pair of sites.
database_cross_reference: SO:0000948

IRLinv site
type: Class
subclass of: inversion site
definition: Component of the inversion site located at the left of a region susceptible to site-specific inversion.
has_obo_namespace: Phage ontology
id: phi:0000229

Axiom
annotated source: IRLinv site
annotated property: definition
annotated target: Component of the inversion site located at the left of a region susceptible to site-specific inversion.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

IRRinv site
type: Class
subclass of: inversion site
definition: Component of the inversion site located at the right of a region susceptible to site-specific inversion.
database_cross_reference: SO:0001047
has_obo_namespace: Phage ontology
id: phi:0000230

Axiom
annotated source: IRRinv site
annotated property: definition
annotated target: Component of the inversion site located at the right of a region susceptible to site-specific inversion.
database_cross_reference: SO:0001047

pac site
type: Class
subclass of: Restriction
  on property: part_of
  some values from: prophage
subclass of: Restriction
  on property: part_of
  some values from: phage concatemer
subclass of: Restriction
  on property: part_of
  some values from: transposable prophage
definition: DNA region recognized by the terminase small subunit as the first step in synapsis of the double stranded DNA phage full head packaging complex.
has_obo_namespace: Phage ontology
id: phi:0000231

Axiom
annotated source: pac site
annotated property: definition
annotated target: DNA region recognized by the terminase small subunit as the first step in synapsis of the double stranded DNA phage full head packaging complex.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

cos site
type: Class
subclass of: Restriction
  on property: part_of
  some values from: prophage
subclass of: Restriction
  on property: part_of
  some values from: phage concatemer
definition: DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates double stranded DNA phage genomes with sticky ends.
has_obo_namespace: Phage ontology
id: phi:0000232

Axiom
annotated source: cos site
annotated property: definition
annotated target: DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates double stranded DNA phage genomes with sticky ends.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

3'extended cos site
type: Class
subclass of: cos site
definition: DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates phage genomes with 3'-extended protruding sticky ends.
has_obo_namespace: Phage ontology
id: phi:0000233

Axiom
annotated source: 3'extended cos site
annotated property: definition
annotated target: DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex that generates phage genomes with 3'-extended protruding sticky ends.
database_cross_reference: PHI:AT

5'extended cos site
type: Class
subclass of: cos site
definition: DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex, which generates phage genomes with 5'-extended protruding sticky ends.
has_obo_namespace: Phage ontology
id: phi:0000234

Axiom
annotated source: 5'extended cos site
annotated property: definition
annotated target: DNA region recognized by the terminase small subunit as the first step in synapsis of the packaging complex, which generates phage genomes with 5'-extended protruding sticky ends.
database_cross_reference: PHI:AT

genomic island
type: Class
subclass of: integrated mobile genetic element
definition: Chromosomal DNA region that has features suggesting a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
database_cross_reference: SO:0000772
has_obo_namespace: Phage ontology
id: phi:0000235
comment: revise SO definition.

Axiom
annotated source: genomic island
annotated property: definition
annotated target: Chromosomal DNA region that has features suggesting a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility.
database_cross_reference: SO:0000772

integron
type: Class
subclass of: genomic island
definition: A DNA region encoding an integrase, which acts at an adjacent attI site to insert a gene cassette with an attC site through attI-attC recombination. The integron also carries a promoter that controls expression of the gene on the cassette.
database_cross_reference: SO:0000365
has_obo_namespace: Phage ontology
id: phi:0000236
comment: A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. DEF in SO not really complete.

Axiom
annotated source: integron
annotated property: definition
annotated target: A DNA region encoding an integrase, which acts at an adjacent attI site to insert a gene cassette with an attC site through attI-attC recombination. The integron also carries a promoter that controls expression of the gene on the cassette.
database_cross_reference: SO:0000365

integron platform
type: Class
subclass of: Restriction
  on property: part_of
  some values from: integron
definition: DNA region that contains a tyrosine based recombinase gene, a primary recombination site attI and a strong outward promoter Pc.
has_obo_namespace: Phage ontology
id: phi:0000237

Axiom
annotated source: integron platform
annotated property: definition
annotated target: DNA region that contains a tyrosine based recombinase gene, a primary recombination site attI and a strong outward promoter Pc.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

gene cassette (sensu integrons)
type: Class
subclass of: Restriction
  on property: part_of
  some values from: integron
definition: Discrete DNA region which can exist either as discrete circular region with an attC site, or integrated after attI by attC recombination, downstream of the integron Pc promoter, which controls the expression of its usually single encoded gene.
has_obo_namespace: Phage ontology
id: phi:0000238

Axiom
annotated source: gene cassette (sensu integrons)
annotated property: definition
annotated target: Discrete DNA region which can exist either as discrete circular region with an attC site, or integrated after attI by attC recombination, downstream of the integron Pc promoter, which controls the expression of its usually single encoded gene.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

transposable element
type: Class
subclass of: genomic island
definition: Transposable DNA region that encodes mobility and its regulatory functions and other phenotypic traits such as antibiotic resistance, catabolic enzymes etc.
database_cross_reference: SO:0000101
has_obo_namespace: Phage ontology
id: phi:0000239
comment: SO definition: A transposon or insertion sequence. An element that can insert in a variety of DNA sequence.

Axiom
annotated source: transposable element
annotated property: definition
annotated target: Transposable DNA region that encodes mobility and its regulatory functions and other phenotypic traits such as antibiotic resistance, catabolic enzymes etc.
database_cross_reference: SO:0000101

unitary transposon
type: Class
subclass of: DNA transposon
definition: Transposon in which mobility genes and phenotypic genes are surrounded by imperfect inverted repeats.
has_obo_namespace: Phage ontology
id: phi:0000240

Axiom
annotated source: unitary transposon
annotated property: definition
annotated target: Transposon in which mobility genes and phenotypic genes are surrounded by imperfect inverted repeats.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

composite transposon
type: Class
subclass of: DNA transposon
definition: Transposon composed of two identical IS sequences in the same or opposite orientation flanking a region containing the phenotypic genes.
has_obo_namespace: Phage ontology
id: phi:0000241

Axiom
annotated source: composite transposon
annotated property: definition
annotated target: Transposon composed of two identical IS sequences in the same or opposite orientation flanking a region containing the phenotypic genes.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

conjugative transposon
type: Class
subclass of: DNA transposon
definition: A genomic island which contains genes for integration/excision and intercellular transfer by conjugation.
database_cross_reference: SO:0000371
has_exact_synonym: CTn
has_exact_synonym: ICE
has_obo_namespace: Phage ontology
id: phi:0000242
comment: Diiferes fro OS def (A transposon that encodes function required for conjugation).

Axiom
annotated source: conjugative transposon
annotated property: definition
annotated target: A genomic island which contains genes for integration/excision and intercellular transfer by conjugation.
database_cross_reference: SO:0000371

defective conjugative transposon
type: Class
subclass of: conjugative transposon
definition: A genomic island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
database_cross_reference: SO:0001049
has_obo_namespace: Phage ontology
id: phi:0000243

Axiom
annotated source: defective conjugative transposon
annotated property: definition
annotated target: A genomic island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon.
database_cross_reference: SO:0001049

transfer agent
type: Class
subclass of: cryptic prophage
definition: DNA region that contains genes for phage head and tail formation but no replication genes. The produced heads only encapsidate host DNA, generating defective generalized transducing particles.
has_obo_namespace: Phage ontology
id: phi:0000244

Axiom
annotated source: transfer agent
annotated property: definition
annotated target: DNA region that contains genes for phage head and tail formation but no replication genes. The produced heads only encapsidate host DNA, generating defective generalized transducing particles.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

insertion sequence
type: Class
subclass of: DNA transposon
definition: DNA region flanked by inverted repeats and containing genes coding for transposition enzymes and regulators of transposition.
database_cross_reference: SO:0000973
has_obo_namespace: Phage ontology
id: phi:0000245

Axiom
annotated source: insertion sequence
annotated property: definition
annotated target: DNA region flanked by inverted repeats and containing genes coding for transposition enzymes and regulators of transposition.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC
database_cross_reference: SO:0000973

cointegrate
type: Class
subclass of: SO term
definition: A DNA region consisting of two fused replicons/plasmids resulting from a replicative transposition event.
database_cross_reference: SO:0001045
has_obo_namespace: Phage ontology
has_related_synonym: cointegrate replicon
id: phi:0000246
comment: SO definition for cointegrate replicon: A MGE region consisting of two fused replicons/plasmids resulting from a replicative transposition event.

Axiom
annotated source: cointegrate
annotated property: definition
annotated target: A DNA region consisting of two fused replicons/plasmids resulting from a replicative transposition event.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: cointegrate
annotated property: has_related_synonym
annotated target: cointegrate replicon
database_cross_reference: SO:0001045

generalized transduction
type: Class
subclass of: transduction
definition: When bacteriophages complete their lytic cycle, random bacterial chromosomal DNA segments or plasmid DNA instead of viral DNA may be inserted into the viral capsid. The phage particle loaded with a piece of bacterial DNA may infect another bacterial cell. This newly acquired DNA can fall to one of three fates. It can be recycled. If the DNA was originally a plasmid, it can recircularize inside the new cell and become a plasmid again. If the new DNA matches with a homologous region of the recipient chromosome, it will recombine so that part or most of that DNA material is incorporated into the new host chromosome.
database_cross_reference: GO:0007131
database_cross_reference: Wiki:http://en.wikipedia.org/wiki/Transduction_(genetics)#Generalized_transduction
has_obo_namespace: Phage ontology
id: phi:0000247
comment: This definition differs from that in GO:0009293.

Axiom
annotated source: generalized transduction
annotated property: definition
annotated target: When bacteriophages complete their lytic cycle, random bacterial chromosomal DNA segments or plasmid DNA instead of viral DNA may be inserted into the viral capsid. The phage particle loaded with a piece of bacterial DNA may infect another bacterial cell. This newly acquired DNA can fall to one of three fates. It can be recycled. If the DNA was originally a plasmid, it can recircularize inside the new cell and become a plasmid again. If the new DNA matches with a homologous region of the recipient chromosome, it will recombine so that part or most of that DNA material is incorporated into the new host chromosome.
database_cross_reference: Phi:AT

specialized transduction
type: Class
subclass of: transduction
definition: While excising from the chromosome incorrectly, a prophage can leave part of its DNA in the chromosome and pick up adjacent bacterial DNA. This DNA may be packaged into a mature phage particle, which can be released and infect a new host. Depending on which part of the phage DNA has been lost, this new genome may or not be able to complete a lytic cycle. If its bacterial DNA moiety is homologous to the recipient cell chromosome, integration can occur by homologous recombination. If the integrase and attachment site components of the phage are still present, integration can also occur by site-specific recombination. In both cases the recipient chromosome will contain two copies of the bacterial DNA segment carried by the transducing genome. The genes most susceptible to transfer by this mechanism are those in the direct vicinity of the original prophage.
database_cross_reference: GO:0007131
has_obo_namespace: Phage ontology
id: phi:0000248
comment: This definition differs from that in GO:0009293.

Axiom
annotated source: specialized transduction
annotated property: definition
annotated target: While excising from the chromosome incorrectly, a prophage can leave part of its DNA in the chromosome and pick up adjacent bacterial DNA. This DNA may be packaged into a mature phage particle, which can be released and infect a new host. Depending on which part of the phage DNA has been lost, this new genome may or not be able to complete a lytic cycle. If its bacterial DNA moiety is homologous to the recipient cell chromosome, integration can occur by homologous recombination. If the integrase and attachment site components of the phage are still present, integration can also occur by site-specific recombination. In both cases the recipient chromosome will contain two copies of the bacterial DNA segment carried by the transducing genome. The genes most susceptible to transfer by this mechanism are those in the direct vicinity of the original prophage.
database_cross_reference: Phi:AT

transduction
type: Class
subclass of: phage process
subclass of: homologous DNA recombination
definition: Transfer of a DNA segment from one to another cell by a virus (usually a bacteriophage).
database_cross_reference: GO:0007131
database_cross_reference: Wiki:http://en.wikipedia.org/wiki/Transduction_(genetics)
has_obo_namespace: Phage ontology
id: phi:0000249
comment: This definition differs from that in GO:0009293.

Axiom
annotated source: transduction
annotated property: definition
annotated target: Transfer of a DNA segment from one to another cell by a virus (usually a bacteriophage).
database_cross_reference: Phi:AT

phage extrusion
type: Class
subclass of: phage release
definition: Process of releasing mature phage particles (filamentous phages) by passing through bacterial membranes.
has_broad_synonym: non-lytic viral release
database_cross_reference: GO:0046753
has_exact_synonym: phage excretion
has_obo_namespace: Phage ontology
id: phi:0000250

Axiom
annotated source: phage extrusion
annotated property: definition
annotated target: Process of releasing mature phage particles (filamentous phages) by passing through bacterial membranes.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: phage extrusion
annotated property: has_broad_synonym
annotated target: non-lytic viral release
database_cross_reference: GO:0046753

Axiom
annotated source: phage extrusion
annotated property: has_exact_synonym
annotated target: phage excretion
database_cross_reference: Phi:AT

catabolic island
type: Class
subclass of: genomic island
definition: Genomic island which carries genes encoding proteins involved in catabolism, usually of man-made toxic compounds (chlorinated aromatic and aliphatic compounds for instance).
has_obo_namespace: Phage ontology
has_related_synonym: metabolic island
id: phi:0000251

Axiom
annotated source: catabolic island
annotated property: definition
annotated target: Genomic island which carries genes encoding proteins involved in catabolism, usually of man-made toxic compounds (chlorinated aromatic and aliphatic compounds for instance).
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: catabolic island
annotated property: has_related_synonym
annotated target: metabolic island
database_cross_reference: SO:0000774

symbiosis island
type: Class
subclass of: genomic island
definition: Genomic island that carries genes encoding proteins involved in symbiosis, usually with plants.
database_cross_reference: SO:0000776
has_obo_namespace: Phage ontology
id: phi:0000252
comment: SO definition: A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria.

Axiom
annotated source: symbiosis island
annotated property: definition
annotated target: Genomic island that carries genes encoding proteins involved in symbiosis, usually with plants.
database_cross_reference: SO:0000776

fitness island
type: Class
subclass of: genomic island
definition: Genomic island whose presence increases the fitness of the host.
database_cross_reference: SO:0000775
has_exact_synonym: adaptive island
has_obo_namespace: Phage ontology
id: phi:0000253

Axiom
annotated source: fitness island
annotated property: definition
annotated target: Genomic island whose presence increases the fitness of the host.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: fitness island
annotated property: has_exact_synonym
annotated target: adaptive island
database_cross_reference: SO:0000775

integrative conjugative transposon
type: Class
definition: Genomic island that carries determinants for integration and excision of the host genome and for inter-cellular transfer by conjugation. The former include an integrase of the tyrosine or serine base integrase and cognate att sites. The latter can or not be related to plasmid encoded conjugation machinery.
has_obo_namespace: Phage ontology
id: phi:0000254
deprecated: true

Axiom
annotated source: integrative conjugative transposon
annotated property: definition
annotated target: Genomic island that carries determinants for integration and excision of the host genome and for inter-cellular transfer by conjugation. The former include an integrase of the tyrosine or serine base integrase and cognate att sites. The latter can or not be related to plasmid encoded conjugation machinery.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

phage genome
type: Class
subclass of: SO term
definition: The nucleotide sequence of a virus that infects bacteria.
database_cross_reference: SO:0001042
has_exact_synonym: phage sequence
has_obo_namespace: Phage ontology
id: phi:0000255

Axiom
annotated source: phage genome
annotated property: definition
annotated target: The nucleotide sequence of a virus that infects bacteria.
database_cross_reference: SO:0001042

Axiom
annotated source: phage genome
annotated property: has_exact_synonym
annotated target: phage sequence
database_cross_reference: SO:0001042

transposable phage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: A DS DNA phage that integrates and replicates by transpositional recombination.
has_obo_namespace: Phage ontology
id: phi:0000256

Axiom
annotated source: transposable phage
annotated property: definition
annotated target: A DS DNA phage that integrates and replicates by transpositional recombination.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

bacteriophage
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: Virus that infect bacteria.
has_exact_synonym: phage
has_exact_synonym: phage particle
has_obo_namespace: Phage ontology
id: phi:0000257

Axiom
annotated source: bacteriophage
annotated property: definition
annotated target: Virus that infect bacteria.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: bacteriophage
annotated property: has_exact_synonym
annotated target: phage
database_cross_reference: PHI:AT

Axiom
annotated source: bacteriophage
annotated property: has_exact_synonym
annotated target: phage particle
database_cross_reference: PHI:AT

plasmid component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid
definition: Components associated with plasmids.
database_cross_reference: Wikipedia:thioredoxin
has_obo_namespace: Phage ontology
id: phi:0000258

Axiom
annotated source: plasmid component
annotated property: definition
annotated target: Components associated with plasmids.
database_cross_reference: PHI:AT

plasmid process
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid
definition: Any process that changes the level of transcription of plasmid genes.
has_alternative_id: phi:0000362
database_cross_reference: Wikipedia:thioredoxin
has_obo_namespace: Phage ontology
id: phi:0000259

Axiom
annotated source: plasmid process
annotated property: definition
annotated target: Any process that changes the level of transcription of plasmid genes.
database_cross_reference: PHI:AT

transposable phage genome
type: Class
subclass of: phage genome
definition: Genome of a DS DNA phage that integrates and replicates by transpositional recombination.
has_obo_namespace: Phage ontology
id: phi:0000260

Axiom
annotated source: transposable phage genome
annotated property: definition
annotated target: Genome of a DS DNA phage that integrates and replicates by transpositional recombination.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type V protein secretion system complex
type: Class
subclass of: protein secretion
definition: A complex of proteins that permits the transfer of proteins into the extracellular milieu or directly into host cells via the type V secretion system.
has_obo_namespace: Phage ontology
id: phi:0000261

Axiom
annotated source: type V protein secretion system complex
annotated property: definition
annotated target: A complex of proteins that permits the transfer of proteins into the extracellular milieu or directly into host cells via the type V secretion system.
database_cross_reference: PHI:AT

toxin
type: Class
subclass of: unclassified
definition: Poisonous activity, especially of proteins or conjugated proteins produced by certain animals, higher plants, and pathogenic bacteria.
database_cross_reference: :
has_narrow_synonym: effector
has_obo_namespace: Phage ontology
id: phi:0000262

Axiom
annotated source: toxin
annotated property: definition
annotated target: Poisonous activity, especially of proteins or conjugated proteins produced by certain animals, higher plants, and pathogenic bacteria.
database_cross_reference: PHI:AT

Dorland's Medical Dictionary
type: Axiom
annotated source: toxin
annotated property: database_cross_reference
annotated target: :

type IV protein secretion/mating pair formation system complex
type: Class
subclass of: plasmid component
subclass of: protein secretion
definition: A complex of proteins that permits the transfer of nucleoprotein DNA conjugation intermediates or proteins directly into host cells or into the extracellular milieu In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s).
database_cross_reference: GO:0043684
has_obo_namespace: Phage ontology
id: phi:0000263
comment: Term and definition differ from those in GO.

Axiom
annotated source: type IV protein secretion/mating pair formation system complex
annotated property: definition
annotated target: A complex of proteins that permits the transfer of nucleoprotein DNA conjugation intermediates or proteins directly into host cells or into the extracellular milieu In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s).
database_cross_reference: GO:0043684

nucleoid associated protein
type: Class
subclass of: unclassified
definition: Protein associated with the bacterial nucleoid.
has_obo_namespace: Phage ontology
id: phi:0000264

Axiom
annotated source: nucleoid associated protein
annotated property: definition
annotated target: Protein associated with the bacterial nucleoid.
database_cross_reference: PHI:AT

type I protein secretion system complex
type: Class
subclass of: protein secretion
definition: A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space.
database_cross_reference: GO:0030256
has_obo_namespace: Phage ontology
id: phi:0000265

Axiom
annotated source: type I protein secretion system complex
annotated property: definition
annotated target: A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space.
database_cross_reference: GO:0030256

type II protein secretion system complex
type: Class
subclass of: protein secretion
definition: A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of secreted proteins from the cytoplasm into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane.
database_cross_reference: GO:0015627
has_obo_namespace: Phage ontology
id: phi:0000266

Axiom
annotated source: type II protein secretion system complex
annotated property: definition
annotated target: A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of secreted proteins from the cytoplasm into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane.
database_cross_reference: GO:0015627

type III protein secretion system complex
type: Class
subclass of: protein secretion
definition: A complex nanomachine of approximately 20 proteins that carries out protein secretion in the type III secretion system. It contains an ATPase, spans the inner membrane, the peptidoglycan layer and the outer membrane and secretes a stiff needle like structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In some T3S the needle is not complete and the structure serves as the conduit for protein secretion.
database_cross_reference: GO:0030257
has_obo_namespace: Phage ontology
has_related_synonym: injectisome
id: phi:0000267
comment: Definition differs from GO.

Axiom
annotated source: type III protein secretion system complex
annotated property: definition
annotated target: A complex nanomachine of approximately 20 proteins that carries out protein secretion in the type III secretion system. It contains an ATPase, spans the inner membrane, the peptidoglycan layer and the outer membrane and secretes a stiff needle like structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In some T3S the needle is not complete and the structure serves as the conduit for protein secretion.
database_cross_reference: GO:0030257

plasmid vegetative DNA replication
type: Class
subclass of: plasmid process
definition: Process of bidirectional (theta) vegetative replication of a plasmid DNA genome.
has_obo_namespace: Phage ontology
id: phi:0000268

Axiom
annotated source: plasmid vegetative DNA replication
annotated property: definition
annotated target: Process of bidirectional (theta) vegetative replication of a plasmid DNA genome.
database_cross_reference: PHI:AT

plasmid conjugative DNA replication
type: Class
subclass of: Restriction
  on property: part_of
  some values from: intercellular transfer by conjugation
definition: Process of sigma-type replication of a plasmid DNA genome from the origin of transfer oriT, during conjugation.
has_obo_namespace: Phage ontology
id: phi:0000269

Axiom
annotated source: plasmid conjugative DNA replication
annotated property: definition
annotated target: Process of sigma-type replication of a plasmid DNA genome from the origin of transfer oriT, during conjugation.
database_cross_reference: PHI:AT

oriT
type: Class
subclass of: origin of replication
subclass of: Restriction
  on property: part_of
  some values from: conjugative transposon
subclass of: Restriction
  on property: part_of
  some values from: plasmid genome
definition: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
database_cross_reference: SO:0000724
has_obo_namespace: Phage ontology
id: phi:0000270

Axiom
annotated source: oriT
annotated property: definition
annotated target: A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization.
database_cross_reference: SO:0000724

intercellular transfer by conjugation
type: Class
subclass of: plasmid process
definition: The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell (donor) is then transferred into the other cell (recipient) unidirectional conjugation occurs between cells of different mating types.
database_cross_reference: GO:0009291
has_obo_namespace: Phage ontology
has_related_synonym: unidirectional conjugation
id: phi:0000271
comment: It is essential NOT to use 'male' and female' because any bacterium can be donor and recipient even at the same time.

Axiom
annotated source: intercellular transfer by conjugation
annotated property: definition
annotated target: The process of unidirectional (polarized) transfer of genetic information involving direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell (donor) is then transferred into the other cell (recipient) unidirectional conjugation occurs between cells of different mating types.
database_cross_reference: GO:0009291

Axiom
annotated source: intercellular transfer by conjugation
annotated property: has_related_synonym
annotated target: unidirectional conjugation
database_cross_reference: GO:0009291

type IV secretion system coupling protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV secretion system motor
definition: Inner membrane ATPase (TraG/VirD4) that recruits the DNA substrate including the conjugative relaxase to the T4SS and powers the intercellular transfer of DNA by conjugation.
has_obo_namespace: Phage ontology
id: phi:0000272

Axiom
annotated source: type IV secretion system coupling protein
annotated property: definition
annotated target: Inner membrane ATPase (TraG/VirD4) that recruits the DNA substrate including the conjugative relaxase to the T4SS and powers the intercellular transfer of DNA by conjugation.
database_cross_reference: PHI:AT

pilin
type: Class
subclass of: unclassified
subclass of: Restriction
  on property: part_of
  some values from: type II protein secretion system complex
definition: Alpha-beta fibrous proteins found in pilus structures in bacteria. Bacterial pili are used in partner recognition and exchange of genetic material during bacterial conjugation. Pili are more common in gram-negative bacteria, where, individual pilin molecules are linked by noncovalent protein-protein interactions. Gram-positive bacteria often have polymerized pilin.
has_obo_namespace: Phage ontology
has_related_synonym: flagellin
id: phi:0000273
comment: Several terms associated to pilus and flagllum as components and their biogenesis are in GO.

Axiom
annotated source: pilin
annotated property: definition
annotated target: Alpha-beta fibrous proteins found in pilus structures in bacteria. Bacterial pili are used in partner recognition and exchange of genetic material during bacterial conjugation. Pili are more common in gram-negative bacteria, where, individual pilin molecules are linked by noncovalent protein-protein interactions. Gram-positive bacteria often have polymerized pilin.
database_cross_reference: PHI:AT

fimbrium
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter.
database_cross_reference: GO:0009289
has_obo_namespace: Phage ontology
id: phi:0000274

Axiom
annotated source: fimbrium
annotated property: definition
annotated target: A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter.
database_cross_reference: GO:0009289

type IV secretion system pilin
type: Class
subclass of: pilin
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Structural subunit of the T4SS Secretion pilus of the T4SS formed or VirB2/TrbC/TraA/TraX structural subunits, some of which when mature assumes a circular configuration. The pilus is involved in mating pair formation prior to unidirectional conjugation.
has_obo_namespace: Phage ontology
id: phi:0000275

Axiom
annotated source: type IV secretion system pilin
annotated property: definition
annotated target: Structural subunit of the T4SS Secretion pilus of the T4SS formed or VirB2/TrbC/TraA/TraX structural subunits, some of which when mature assumes a circular configuration. The pilus is involved in mating pair formation prior to unidirectional conjugation.
database_cross_reference: PHI:AT

VirB3 related outer membrane protein
type: Class
definition: Outer membrane component (TrbD/TraL) of the T4SS also involved in mating pair formation prior to unidirectional conjugation. VirB3 interacts with T4SS VirB6 and VirB4 related proteins.
has_obo_namespace: Phage ontology
id: phi:0000276
deprecated: true

Axiom
annotated source: VirB3 related outer membrane protein
annotated property: definition
annotated target: Outer membrane component (TrbD/TraL) of the T4SS also involved in mating pair formation prior to unidirectional conjugation. VirB3 interacts with T4SS VirB6 and VirB4 related proteins.
database_cross_reference: PHI:AT

type IV secretion system motor
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Heart of the T4SS, this complex consists of a Walker A- Walker B hexameric ATPase (VirB4/TrwK/TrbE/TraC/TraU), possibly cytosolic and anchored to the inner membrane through interaction with the integral inner membrane protein (VirB3/TrwM/?), an hexameric ATP dependent chaperon (VirB11/TrwD/?) and a third ATPase devoted to DNA trasnfer (TraG/VirD4) also called coupling protein. VirB4 and alike are supposed to power transfer of the pilin protein, VirB11 and alike to power unfolding of the secreted pilin, and TraG and alike to power DNA transfer.
has_obo_namespace: Phage ontology
id: phi:0000277

Axiom
annotated source: type IV secretion system motor
annotated property: definition
annotated target: Heart of the T4SS, this complex consists of a Walker A- Walker B hexameric ATPase (VirB4/TrwK/TrbE/TraC/TraU), possibly cytosolic and anchored to the inner membrane through interaction with the integral inner membrane protein (VirB3/TrwM/?), an hexameric ATP dependent chaperon (VirB11/TrwD/?) and a third ATPase devoted to DNA trasnfer (TraG/VirD4) also called coupling protein. VirB4 and alike are supposed to power transfer of the pilin protein, VirB11 and alike to power unfolding of the secreted pilin, and TraG and alike to power DNA transfer.
database_cross_reference: PHI:AT

type IV secretion system minor pilus component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Component (TrbJ/TraE) of the T4SS pilus that may be involved in adhesion.
has_obo_namespace: Phage ontology
id: phi:0000278

Axiom
annotated source: type IV secretion system minor pilus component
annotated property: definition
annotated target: Component (TrbJ/TraE) of the T4SS pilus that may be involved in adhesion.
database_cross_reference: PHI:AT

VirB1 related cell wall hydrolase activity
type: Class
definition: Protein of the T4SS, also involved in mating pair formation prior to unidirectional conjugation and that perforates the peptidoglycan cell wall.
has_obo_namespace: Phage ontology
id: phi:0000279
deprecated: true

Axiom
annotated source: VirB1 related cell wall hydrolase activity
annotated property: definition
annotated target: Protein of the T4SS, also involved in mating pair formation prior to unidirectional conjugation and that perforates the peptidoglycan cell wall.
database_cross_reference: PHI:AT

type IV secretion system-Mpf stabilizer
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Polytopic inner membrane protein (VirB6/TrbL/TraG/), which is part of the lumen of the T4SS-Mating pair formation channel.
has_obo_namespace: Phage ontology
id: phi:0000280

Axiom
annotated source: type IV secretion system-Mpf stabilizer
annotated property: definition
annotated target: Polytopic inner membrane protein (VirB6/TrbL/TraG/), which is part of the lumen of the T4SS-Mating pair formation channel.
database_cross_reference: PHI:AT

type IV secretion system pilus associated lipoprotein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Lipoprotein component (VirB7/TrbH/TraV/TraI) that connects the pilus to the core of the T4SS-Mating pair formation complex.
has_obo_namespace: Phage ontology
id: phi:0000281

Axiom
annotated source: type IV secretion system pilus associated lipoprotein
annotated property: definition
annotated target: Lipoprotein component (VirB7/TrbH/TraV/TraI) that connects the pilus to the core of the T4SS-Mating pair formation complex.
database_cross_reference: PHI:AT

VirB8 related inner-outer membrane bridging protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Protein that forms a bridge over the periplasm connecting the inner membrane and outer membrane components of the T4SS-Mating pair formation complex. Interacts with VirB1, VirB3, VirB4, VirB9 and VirB10.
has_obo_namespace: Phage ontology
id: phi:0000282

Axiom
annotated source: VirB8 related inner-outer membrane bridging protein
annotated property: definition
annotated target: Protein that forms a bridge over the periplasm connecting the inner membrane and outer membrane components of the T4SS-Mating pair formation complex. Interacts with VirB1, VirB3, VirB4, VirB9 and VirB10.
database_cross_reference: PHI:AT

type IV secretion system secretin
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: Periplasm spanning and outer membrane component of T4SS formed of the VirB9/TrbG/TraK/TraN subunit.
has_obo_namespace: Phage ontology
id: phi:0000283

Axiom
annotated source: type IV secretion system secretin
annotated property: definition
annotated target: Periplasm spanning and outer membrane component of T4SS formed of the VirB9/TrbG/TraK/TraN subunit.
database_cross_reference: PHI:AT

type IV secretion system bridging component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type IV protein secretion/mating pair formation system complex
definition: A nodal point connecting the inner and outer membrane components of the T4SS formed of VirB10/TrbI/TraB/TraO subunits.
has_obo_namespace: Phage ontology
id: phi:0000284

Axiom
annotated source: type IV secretion system bridging component
annotated property: definition
annotated target: A nodal point connecting the inner and outer membrane components of the T4SS formed of VirB10/TrbI/TraB/TraO subunits.
database_cross_reference: PHI:AT

VirB11 typeII/IV secretion NTPase activity
type: Class
definition: Hexameric ring shaped NTPase similar to the F1-ATPase molecular motors and that fuels the T4SS and TIISS.
database_cross_reference: GO:0015219
has_obo_namespace: Phage ontology
id: phi:0000285
deprecated: true

Axiom
annotated source: VirB11 typeII/IV secretion NTPase activity
annotated property: definition
annotated target: Hexameric ring shaped NTPase similar to the F1-ATPase molecular motors and that fuels the T4SS and TIISS.
database_cross_reference: PHI:AT

type III secretion system needle ruler
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III protein secretion system complex
definition: Protein involved in the determination of the length of the needle from the injectisome. This protein (YscP, Spa32, InvJ) is thought to operate as a molecular ruler coupled to a substrate-specificity switch.
database_cross_reference: PMID:16458574
has_obo_namespace: Phage ontology
id: phi:0000286

Axiom
annotated source: type III secretion system needle ruler
annotated property: definition
annotated target: Protein involved in the determination of the length of the needle from the injectisome. This protein (YscP, Spa32, InvJ) is thought to operate as a molecular ruler coupled to a substrate-specificity switch.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type III secretion outer membrane ring
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III protein secretion system complex
definition: Located in the outer membrane of the bacterial cell this part of the injectisome contains the pilotin (YscW, MxiA), a lipoprotein ancillary to the secretin (YscW) and the secretin ( YscC ) .
has_obo_namespace: Phage ontology
id: phi:0000287

Axiom
annotated source: type III secretion outer membrane ring
annotated property: definition
annotated target: Located in the outer membrane of the bacterial cell this part of the injectisome contains the pilotin (YscW, MxiA), a lipoprotein ancillary to the secretin (YscW) and the secretin ( YscC ) .
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type III secretion system extracellular needle
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III protein secretion system complex
definition: Needle component of the TIIISS system, which is formed of YscF (MxiH, EscF) proteins and protrudes outside from the bacterial surface by about 60 nm.
has_obo_namespace: Phage ontology
id: phi:0000288

Axiom
annotated source: type III secretion system extracellular needle
annotated property: definition
annotated target: Needle component of the TIIISS system, which is formed of YscF (MxiH, EscF) proteins and protrudes outside from the bacterial surface by about 60 nm.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type III secretion system needle tip
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III secretion system translocator
definition: Terminal structure of the needle made of protein LcrV (PcrV, AcrV, IpaD) serving as a scaffold for the translocation pore YopBD.
has_obo_namespace: Phage ontology
id: phi:0000289

Axiom
annotated source: type III secretion system needle tip
annotated property: definition
annotated target: Terminal structure of the needle made of protein LcrV (PcrV, AcrV, IpaD) serving as a scaffold for the translocation pore YopBD.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type III secretion system secretin
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III secretion outer membrane ring
definition: Component of the injectisome that spans the outer membrane and contains YscC subunits.
has_obo_namespace: Phage ontology
id: phi:0000290

Axiom
annotated source: type III secretion system secretin
annotated property: definition
annotated target: Component of the injectisome that spans the outer membrane and contains YscC subunits.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type III secretion system translocator
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III protein secretion system complex
definition: A set of two hydrophobic (YopB/YopD in Yersinia, PopB/PopD in Pseudomonas aeruginosa) and one hydrophilic (LcrV in Yersinia, PcrV in P.aeruginosa) proteins, exported by the injectisome and which form a pore in the host cell membrane to allow effector translocation.
has_exact_synonym: translocation pore
has_obo_namespace: Phage ontology
id: phi:0000291

Axiom
annotated source: type III secretion system translocator
annotated property: definition
annotated target: A set of two hydrophobic (YopB/YopD in Yersinia, PopB/PopD in Pseudomonas aeruginosa) and one hydrophilic (LcrV in Yersinia, PcrV in P.aeruginosa) proteins, exported by the injectisome and which form a pore in the host cell membrane to allow effector translocation.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type II secretion T2SO protein activity
type: Class
definition: Peptidase component of the TIISS system.
has_obo_namespace: Phage ontology
id: phi:0000292
deprecated: true

Axiom
annotated source: type II secretion T2SO protein activity
annotated property: definition
annotated target: Peptidase component of the TIISS system.
database_cross_reference: PHI:AT

type II secretion system outer membrane component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type II protein secretion system complex
definition: T2SF Out etc?
has_obo_namespace: Phage ontology
id: phi:0000293

Axiom
annotated source: type II secretion system outer membrane component
annotated property: definition
annotated target: T2SF Out etc?
database_cross_reference: PHI:AT

type II secretion envelope protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type II protein secretion system complex
definition: Envelope protein component of TIISS. PulD, Out? etc.
has_obo_namespace: Phage ontology
has_related_synonym: secretin
id: phi:0000294

Axiom
annotated source: type II secretion envelope protein
annotated property: definition
annotated target: Envelope protein component of TIISS. PulD, Out? etc.
database_cross_reference: PHI:AT

type III secretion inner membrane ring
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III protein secretion system complex
definition: Inner membrane ring component of the type III secretion machine, which includes lipoprotein YscJ (PrgK, EscJ), YscS, T, U and V and probably the YscR and D subunits.
has_exact_synonym: MS ring
has_obo_namespace: Phage ontology
id: phi:0000295

Axiom
annotated source: type III secretion inner membrane ring
annotated property: definition
annotated target: Inner membrane ring component of the type III secretion machine, which includes lipoprotein YscJ (PrgK, EscJ), YscS, T, U and V and probably the YscR and D subunits.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

Axiom
annotated source: type III secretion inner membrane ring
annotated property: has_exact_synonym
annotated target: MS ring
database_cross_reference: PHI:GC

type III secretion system cytoplasmic ring component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: type III protein secretion system complex
definition: Cytoplasmic ring component of the type III secretion machine, which includes YscQ subunits and probably YScK and YscL and the YscN ATpase.
has_obo_namespace: Phage ontology
id: phi:0000296

Axiom
annotated source: type III secretion system cytoplasmic ring component
annotated property: definition
annotated target: Cytoplasmic ring component of the type III secretion machine, which includes YscQ subunits and probably YScK and YscL and the YscN ATpase.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

oriV
type: Class
subclass of: origin of replication
subclass of: Restriction
  on property: part_of
  some values from: phage concatemer
subclass of: Restriction
  on property: part_of
  some values from: phage genome
subclass of: Restriction
  on property: part_of
  some values from: plasmid genome
definition: An origin of vegetative replication in plasmids and phages.
database_cross_reference: SO:0000952
has_obo_namespace: Phage ontology
id: phi:0000297

Axiom
annotated source: oriV
annotated property: definition
annotated target: An origin of vegetative replication in plasmids and phages.
database_cross_reference: SO:0000952

plasmid genome
type: Class
subclass of: SO term
definition: A self-replicating linear or circular DNA molecule that is distinct from a chromosome in the organism.
database_cross_reference: SO:00155
has_exact_synonym: plasmid
has_obo_namespace: Phage ontology
id: phi:0000298
comment: "Plasmid" in SO. Add "linear" in SO definition as it is.

Axiom
annotated source: plasmid genome
annotated property: definition
annotated target: A self-replicating linear or circular DNA molecule that is distinct from a chromosome in the organism.
database_cross_reference: SO:0000155

origin of replication
type: Class
subclass of: SO term
subclass of: Restriction
  on property: part_of
  some values from: plasmid genome
definition: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
database_cross_reference: SO:0000296
has_obo_namespace: Phage ontology
id: phi:0000299

Axiom
annotated source: origin of replication
annotated property: definition
annotated target: The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies.
database_cross_reference: SO:0000296

integrated mobile genetic element
type: Class
subclass of: SO term
definition: An MGE that is integrated into the host chromosome.
database_cross_reference: SO:0001039
has_obo_namespace: Phage ontology
id: phi:0000300

Axiom
annotated source: integrated mobile genetic element
annotated property: definition
annotated target: An MGE that is integrated into the host chromosome.
database_cross_reference: SO:0001039

DNA transposon
type: Class
subclass of: transposable element
definition: A transposon where the mechanism of transposition is via a DNA intermediate.
database_cross_reference: SO:0000182
has_obo_namespace: Phage ontology
id: phi:0000301

Axiom
annotated source: DNA transposon
annotated property: definition
annotated target: A transposon where the mechanism of transposition is via a DNA intermediate.
database_cross_reference: SO:0000182

inverted repeat
type: Class
subclass of: SO term
subclass of: Restriction
  on property: part_of
  some values from: composite transposon
definition: The sequence is complementary and repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
database_cross_reference: SO:0000294
has_obo_namespace: Phage ontology
id: phi:0000302

Axiom
annotated source: inverted repeat
annotated property: definition
annotated target: The sequence is complementary and repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC.
database_cross_reference: SO:0000294

plasmid partitioning
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid maintenance
definition: Any process by which plasmids are segregated or distributed into daughter cells upon cell division. As in, but not restricted to, the taxon Bacteria.
database_cross_reference: GO:0030542
has_obo_namespace: Phage ontology
id: phi:0000303
comment: Should be connected to chromsome segregation? GO:0007059?

Axiom
annotated source: plasmid partitioning
annotated property: definition
annotated target: Any process by which plasmids are segregated or distributed into daughter cells upon cell division. As in, but not restricted to, the taxon Bacteria.
database_cross_reference: GO:0030542

plasmid dimer resolution
type: Class
subclass of: site-specific DNA excision
subclass of: Restriction
  on property: part_of
  some values from: plasmid maintenance
definition: The recombination process that separates plasmid dimers or higher multimers into monomers.
has_obo_namespace: Phage ontology
id: phi:0000304

Axiom
annotated source: plasmid dimer resolution
annotated property: definition
annotated target: The recombination process that separates plasmid dimers or higher multimers into monomers.
database_cross_reference: PHI:AT

regulation of vegetative plasmid DNA replication
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid vegetative DNA replication
definition: Any process that controls the initiation of bidirectional (theta) vegetative replication of a plasmid DNA genome.
has_obo_namespace: Phage ontology
has_related_synonym: copy number control
id: phi:0000305

Axiom
annotated source: regulation of vegetative plasmid DNA replication
annotated property: definition
annotated target: Any process that controls the initiation of bidirectional (theta) vegetative replication of a plasmid DNA genome.
database_cross_reference: PHI:AT

Axiom
annotated source: regulation of vegetative plasmid DNA replication
annotated property: has_related_synonym
annotated target: copy number control
database_cross_reference: PHI:AT

regulation of plasmid DNA conjugation
type: Class
subclass of: plasmid process
definition: Any process that controls plasmid DNA conjugation.
has_obo_namespace: Phage ontology
id: phi:0000306

Axiom
annotated source: regulation of plasmid DNA conjugation
annotated property: definition
annotated target: Any process that controls plasmid DNA conjugation.
database_cross_reference: PHI:AT

capsid collar fiber
type: Class
subclass of: phage component
definition: Fiber attached to the collar structure of some phages.
has_obo_namespace: Phage ontology
id: phi:0000307

Axiom
annotated source: capsid collar fiber
annotated property: definition
annotated target: Fiber attached to the collar structure of some phages.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

capsid collar
type: Class
subclass of: phage component
definition: Small disk located below some phage heads.
has_obo_namespace: Phage ontology
id: phi:0000308

Axiom
annotated source: capsid collar
annotated property: definition
annotated target: Small disk located below some phage heads.
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

capsid neck
type: Class
subclass of: phage component
definition: A constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae).
has_obo_namespace: Phage ontology
id: phi:0000309

Axiom
annotated source: capsid neck
annotated property: definition
annotated target: A constriction located below the head and above the tail sheath, of phages with contractile tails (Myoviridae).
database_cross_reference: PHI:AT
database_cross_reference: PHI:HWA

capsid neck fiber
type: Class
subclass of: phage component
definition: Fiber appended at the neck at the base of some phage heads.
has_exact_synonym: wisker
has_obo_namespace: Phage ontology
id: phi:0000310

Axiom
annotated source: capsid neck fiber
annotated property: definition
annotated target: Fiber appended at the neck at the base of some phage heads.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: capsid neck fiber
annotated property: has_exact_synonym
annotated target: wisker
database_cross_reference: PHI:AT

transposable prophage
type: Class
subclass of: prophage
subclass of: DNA transposon
definition: Integrated genome of a transposable phage.
has_obo_namespace: Phage ontology
id: phi:0000311

Axiom
annotated source: transposable prophage
annotated property: definition
annotated target: Integrated genome of a transposable phage.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

IAS
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transposable prophage
definition: Internal activating sequence for transposition in transposable phages. It transiently binds transposase to stimulate transpososome synapsis.
has_obo_namespace: Phage ontology
id: phi:0000312

Axiom
annotated source: IAS
annotated property: definition
annotated target: Internal activating sequence for transposition in transposable phages. It transiently binds transposase to stimulate transpososome synapsis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

type IV secretion system pilin maturation
type: Class
subclass of: Restriction
  on property: part_of
  some values from: intercellular transfer by conjugation
definition: Process that during assembly of the T4SS removes the C-terminal aa from the pilin and generates the final cyclic pilin product by introducing a new peptide bond. This process requires the TraF/TrhI component of the T4SS.
has_obo_namespace: Phage ontology
id: phi:0000313

Axiom
annotated source: type IV secretion system pilin maturation
annotated property: definition
annotated target: Process that during assembly of the T4SS removes the C-terminal aa from the pilin and generates the final cyclic pilin product by introducing a new peptide bond. This process requires the TraF/TrhI component of the T4SS.
database_cross_reference: PHI:AT

MeGO
type: Class
definition: Ontology for non-phage prokaryotic mobile genetic elements.
has_obo_namespace: Phage ontology
id: phi:0000314

Axiom
annotated source: MeGO
annotated property: definition
annotated target: Ontology for non-phage prokaryotic mobile genetic elements.
database_cross_reference: PHI:AT

plasmid entry exclusion
type: Class
subclass of: Restriction
  on property: part_of
  some values from: intercellular transfer by conjugation
definition: Definition?
has_obo_namespace: Phage ontology
id: phi:0000315

Axiom
annotated source: plasmid entry exclusion
annotated property: definition
annotated target: Definition?
database_cross_reference: PHI:AT

protein secretion
type: Class
subclass of: unclassified
definition: The regulated release of proteins from a cell or group of cells.
database_cross_reference: GO:0009306
has_obo_namespace: Phage ontology
id: phi:0000316

Axiom
annotated source: protein secretion
annotated property: definition
annotated target: The regulated release of proteins from a cell or group of cells.
database_cross_reference: GO:0009306

relaxase activity
type: Class
subclass of: plasmid activity
definition: Relaxase is an enzyme in prokaryotes that is involved bacterial conjugation. It forms part of the relaxosome multi protein complex and nicks double-stranded DNA at the OriT origin of transfer on a bacterial plasmid forming a covalent 5'phosphotyrosyl bond.
database_cross_reference: PMID:19396961
database_cross_reference: XX:<new dbxref>
has_obo_namespace: Phage ontology
id: phi:0000317

Axiom
annotated source: relaxase activity
annotated property: definition
annotated target: Relaxase is an enzyme in prokaryotes that is involved bacterial conjugation. It forms part of the relaxosome multi protein complex and nicks double-stranded DNA at the OriT origin of transfer on a bacterial plasmid forming a covalent 5'phosphotyrosyl bond.
database_cross_reference: Wiki:

plasmid fertility inhibition
type: Class
subclass of: Restriction
  on property: part_of
  some values from: intercellular transfer by conjugation
definition: Def?
has_obo_namespace: Phage ontology
id: phi:0000318

Axiom
annotated source: plasmid fertility inhibition
annotated property: definition
annotated target: Def?
database_cross_reference: PHI:AT

autoinducer synthesis
type: Class
subclass of: unclassified
definition: Any step required for the synthesis of an autoinducer (AI) molecule, otherwise called a pheromone, a signaling molecule used by bacteria participating in quorum sensing. One common type of autoinducer is an acyl homoserine lactone (AHL).
database_cross_reference: http://en.wikipedia.org/wiki/Autoinducer
has_obo_namespace: Phage ontology
id: phi:0000319

Axiom
annotated source: autoinducer synthesis
annotated property: definition
annotated target: Any step required for the synthesis of an autoinducer (AI) molecule, otherwise called a pheromone, a signaling molecule used by bacteria participating in quorum sensing. One common type of autoinducer is an acyl homoserine lactone (AHL).
database_cross_reference: PHI:AT

lantibiotic biosynthesis
type: Class
subclass of: unclassified
definition: Lantibiotics are a class of peptide antibiotics that contain polycyclic thioether amino acids as well as the unsaturated amino acids dehydroalanine and 2-aminoisobutyric acid. These characteristic cyclic thioether amino acids are composed of either lanthionine or methyllanthionine. Lantibiotics are produced by a large number of Gram positive bacteria such as Streptococcus and Streptomyces to attack other gram positive bacteria and as such they are considered a member of the bacteriocins. They are synthesised with a leader polypeptide sequence that is only removed during the transport of the molecule out of the synthesizing cell.
database_cross_reference: http://en.wikipedia.org/wiki/Lantibiotics
has_obo_namespace: Phage ontology
id: phi:0000320

Axiom
annotated source: lantibiotic biosynthesis
annotated property: definition
annotated target: Lantibiotics are a class of peptide antibiotics that contain polycyclic thioether amino acids as well as the unsaturated amino acids dehydroalanine and 2-aminoisobutyric acid. These characteristic cyclic thioether amino acids are composed of either lanthionine or methyllanthionine. Lantibiotics are produced by a large number of Gram positive bacteria such as Streptococcus and Streptomyces to attack other gram positive bacteria and as such they are considered a member of the bacteriocins. They are synthesised with a leader polypeptide sequence that is only removed during the transport of the molecule out of the synthesizing cell.
database_cross_reference: PHI:AT

intracellular AB toxin activity
type: Class
subclass of: cytotoxin
definition: Toxin that exerts its activity within the target eukaryotic cell. The B subunit attaches to target regions on cell membranes, the A subunit enters through the membrane and possesses enzymatic function that affects internal cellular bio-mechanisms.
database_cross_reference: http://en.wikipedia.org/wiki/Exotoxin#Injected_toxins
has_obo_namespace: Phage ontology
id: phi:0000321

Axiom
annotated source: intracellular AB toxin activity
annotated property: definition
annotated target: Toxin that exerts its activity within the target eukaryotic cell. The B subunit attaches to target regions on cell membranes, the A subunit enters through the membrane and possesses enzymatic function that affects internal cellular bio-mechanisms.
database_cross_reference: PHI:AT

post-segregational killing
type: Class
subclass of: plasmid process
subclass of: Restriction
  on property: part_of
  some values from: plasmid maintenance
definition: Plasmid-sensu, process of increased plasmid prevalence (number of plasmid-containing cells/total number of cells) in growing bacterial populations by selective elimination of daughter cells that did not inherit a plasmid copy at cell division.
database_cross_reference: PMID:19325885
has_obo_namespace: Phage ontology
id: phi:0000322
comment: Needs to be checked by Laurence.

Axiom
annotated source: post-segregational killing
annotated property: definition
annotated target: Plasmid-sensu, process of increased plasmid prevalence (number of plasmid-containing cells/total number of cells) in growing bacterial populations by selective elimination of daughter cells that did not inherit a plasmid copy at cell division.
database_cross_reference: PHI:AT

cytotoxin
type: Class
subclass of: toxin
definition: A molecular entity with a toxin disposition\, the realization of which damages host cells.
database_cross_reference: IDO:0000584
has_obo_namespace: Phage ontology
id: phi:0000323

Axiom
annotated source: cytotoxin
annotated property: definition
annotated target: A molecular entity with a toxin disposition\, the realization of which damages host cells.
database_cross_reference: IDO:0000584

plasmid mobilization
type: Class
subclass of: plasmid process
definition: Def to be provided.
has_obo_namespace: Phage ontology
has_related_synonym: copy number control
id: phi:0000324

Axiom
annotated source: plasmid mobilization
annotated property: definition
annotated target: Def to be provided.
database_cross_reference: PHI:AT

plasmid activity
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid
definition: Molecular functions associated with plasmids.
has_obo_namespace: Phage ontology
id: phi:0000325

Axiom
annotated source: plasmid activity
annotated property: definition
annotated target: Molecular functions associated with plasmids.
database_cross_reference: PHI:AT

phage function unknown
type: Class
subclass of: Restriction
  on property: part_of
  some values from: bacteriophage
definition: No process, component or activity can yet be assigned to this phage function.
has_obo_namespace: Phage ontology
id: phi:0000326

Axiom
annotated source: phage function unknown
annotated property: definition
annotated target: No process, component or activity can yet be assigned to this phage function.
database_cross_reference: PHI:AT

PhiGO
type: Class
definition: Phage ontoloy
has_obo_namespace: Phage ontology
id: phi:0000327
deprecated: true

Axiom
annotated source: PhiGO
annotated property: definition
annotated target: Phage ontoloy
database_cross_reference: PHI:AT

phage base plate assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage assembly
definition: Process by which tailed phage base plates are assembled.
has_obo_namespace: Phage ontology
id: phi:0000328

Axiom
annotated source: phage base plate assembly
annotated property: definition
annotated target: Process by which tailed phage base plates are assembled.
database_cross_reference: PHI:AT

DNA inversion
type: Class
subclass of: DNA recombination
definition: The process by which a segment of DNA is inverted from its original orientation.
has_obo_namespace: Phage ontology
id: phi:0000329

Axiom
annotated source: DNA inversion
annotated property: definition
annotated target: The process by which a segment of DNA is inverted from its original orientation.
database_cross_reference: PHI:AT

site-specific DNA inversion
type: Class
subclass of: site-specific DNA recombination
definition: The process by which a segment of DNA is inverted from its original orientation through the action of a site-specific recombinase.
has_obo_namespace: Phage ontology
id: phi:0000330

Axiom
annotated source: site-specific DNA inversion
annotated property: definition
annotated target: The process by which a segment of DNA is inverted from its original orientation through the action of a site-specific recombinase.
database_cross_reference: PHI:AT

phage genome circularization
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage genome replication
subclass of: Restriction
  on property: part_of
  some values from: establishment as a circular plasmid prophage
subclass of: Restriction
  on property: part_of
  some values from: establishment as an integrated prophage
definition: The process that converts a linear double stranded DNA phage genome into the circular form, either by homologous recombination between redundant ends or by association of complementary single stranded ends (sticky ends). The circular form is the template for genome replication and for most temperate phages it is also necessary for lysogenisation, either as a circular plasmid or as an integrated prophage.
has_obo_namespace: Phage ontology
id: phi:0000331

Axiom
annotated source: phage genome circularization
annotated property: definition
annotated target: The process that converts a linear double stranded DNA phage genome into the circular form, either by homologous recombination between redundant ends or by association of complementary single stranded ends (sticky ends). The circular form is the template for genome replication and for most temperate phages it is also necessary for lysogenisation, either as a circular plasmid or as an integrated prophage.
database_cross_reference: PHI:AT

prophage mediated phage exclusion
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage lysogeny
definition: Any process through which a prophage inhibits the development of an unrelated, usually virulent superinfecting phage.
has_obo_namespace: Phage ontology
id: phi:0000332

Axiom
annotated source: prophage mediated phage exclusion
annotated property: definition
annotated target: Any process through which a prophage inhibits the development of an unrelated, usually virulent superinfecting phage.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM

plasmid function unknown
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid
definition: No process, component or activity can yet be assigned to this plasmid function.
has_obo_namespace: Phage ontology
id: phi:0000333

Axiom
annotated source: plasmid function unknown
annotated property: definition
annotated target: No process, component or activity can yet be assigned to this plasmid function.
database_cross_reference: PHI:AT

plasmid mediated phage exclusion
type: Class
subclass of: plasmid process
definition: Any process through which a plasmid inhibits the development of an infecting phage.
has_obo_namespace: Phage ontology
id: phi:0000334

Axiom
annotated source: plasmid mediated phage exclusion
annotated property: definition
annotated target: Any process through which a plasmid inhibits the development of an infecting phage.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM

phage mediated modulation of host functions
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage gene expression
definition: Any process by which a phage activates or represses the expression or the activity of one or more of its host proteins.
database_cross_reference: GO:0019054
database_cross_reference: GO:0019057
database_cross_reference: GO:0043921
has_narrow_synonym: regulation of host mRNA translation by virus
has_obo_namespace: Phage ontology
has_related_synonym: modification by virus of host cellular process
has_related_synonym: modulation by virus of host transcription
id: phi:0000335

Axiom
annotated source: phage mediated modulation of host functions
annotated property: definition
annotated target: Any process by which a phage activates or represses the expression or the activity of one or more of its host proteins.
database_cross_reference: PHI:AT

Axiom
annotated source: phage mediated modulation of host functions
annotated property: has_narrow_synonym
annotated target: regulation of host mRNA translation by virus
database_cross_reference: GO:0019057

Axiom
annotated source: phage mediated modulation of host functions
annotated property: has_related_synonym
annotated target: modification by virus of host cellular process
database_cross_reference: GO:001905

Axiom
annotated source: phage mediated modulation of host functions
annotated property: has_related_synonym
annotated target: modulation by virus of host transcription
database_cross_reference: GO:0043921

plasmid mediated modulation of host functions
type: Class
subclass of: Restriction
  on property: part_of
  some values from: plasmid process
definition: Any process by which a plasmid activates or represses the expression or the activity of one or more of its host proteins.
has_obo_namespace: Phage ontology
id: phi:0000336

Axiom
annotated source: plasmid mediated modulation of host functions
annotated property: definition
annotated target: Any process by which a plasmid activates or represses the expression or the activity of one or more of its host proteins.
database_cross_reference: PHI:AT

plasmid mediated inhibition of host SOS repsonse
type: Class
subclass of: phage mediated modulation of host functions
subclass of: plasmid mediated modulation of host functions
definition: Any process that results in preventing or decreasing the SOS response of the bacterial host.
has_obo_namespace: Phage ontology
id: phi:0000337

Axiom
annotated source: plasmid mediated inhibition of host SOS repsonse
annotated property: definition
annotated target: Any process that results in preventing or decreasing the SOS response of the bacterial host.
database_cross_reference: PHI:AT

chaperon activity
type: Class
subclass of: unclassified
definition: A protein activity necessary for the correct non-covalent folding or unfolding of another protein.
database_cross_reference: http://en.wikipedia.org/wiki/Autoinducer
has_obo_namespace: Phage ontology
id: phi:0000338

Axiom
annotated source: chaperon activity
annotated property: definition
annotated target: A protein activity necessary for the correct non-covalent folding or unfolding of another protein.
database_cross_reference: PHI:AT

cell wall degrading lysozyme activity
type: Class
subclass of: endolysin activity
definition: Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
has_obo_namespace: Phage ontology
id: phi:0000339

Axiom
annotated source: cell wall degrading lysozyme activity
annotated property: definition
annotated target: Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

cell wall degrading amidase activity
type: Class
subclass of: endolysin activity
definition: Cell wall amidase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
has_obo_namespace: Phage ontology
id: phi:0000340

Axiom
annotated source: cell wall degrading amidase activity
annotated property: definition
annotated target: Cell wall amidase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

cell wall degrading endopeptidase activity
type: Class
subclass of: endolysin activity
definition: Cell wall endopeptidase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
has_obo_namespace: Phage ontology
id: phi:0000341

Axiom
annotated source: cell wall degrading endopeptidase activity
annotated property: definition
annotated target: Cell wall endopeptidase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

spanin
type: Class
subclass of: phage component
definition: Nearly ubiquitous among phages of Gram-negative hosts, these proteins are predicted to span the bacterial host periplasm providing a physical connection between the inner and outer membranes. They are required for phage release by lysis.
database_cross_reference: PMID:17900620
has_obo_namespace: Phage ontology
id: phi:0000342

Axiom
annotated source: spanin
annotated property: definition
annotated target: Nearly ubiquitous among phages of Gram-negative hosts, these proteins are predicted to span the bacterial host periplasm providing a physical connection between the inner and outer membranes. They are required for phage release by lysis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

Rz/Rz1-type spanin
type: Class
subclass of: spanin
definition: Rz/Rz1 type spanins are two component spanins. The Rz protein has a predicted N-terminal transmembrane domain that spans the bacterial host inner membrane. The Rz1 protein is tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moeities of the N-terminal cysteine.
database_cross_reference: PMID:17900620
has_obo_namespace: Phage ontology
id: phi:0000343

Axiom
annotated source: Rz/Rz1-type spanin
annotated property: definition
annotated target: Rz/Rz1 type spanins are two component spanins. The Rz protein has a predicted N-terminal transmembrane domain that spans the bacterial host inner membrane. The Rz1 protein is tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moeities of the N-terminal cysteine.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

phage T1-type spanin
type: Class
subclass of: spanin
definition: T1 type spanins are one component spanins tethered to the bacterial host outer membrane by the fatty acid and lipid moieties of the N-terminal cysteine and to the host inner membrane by a predicted C-terminal transmembrane domain.
database_cross_reference: PMID:17900620
has_obo_namespace: Phage ontology
id: phi:0000344

Axiom
annotated source: phage T1-type spanin
annotated property: definition
annotated target: T1 type spanins are one component spanins tethered to the bacterial host outer membrane by the fatty acid and lipid moieties of the N-terminal cysteine and to the host inner membrane by a predicted C-terminal transmembrane domain.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

Rz-type spanin component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Rz/Rz1-type spanin
definition: The Rz proteins have a predicted N-terminal transmembrane domain, which spans the bacterial host inner membrane. There C-terminal domain interact with the C-terminal domain of cognate Rz1 spanin components.
database_cross_reference: PMID:17900620
has_obo_namespace: Phage ontology
id: phi:0000345

Axiom
annotated source: Rz-type spanin component
annotated property: definition
annotated target: The Rz proteins have a predicted N-terminal transmembrane domain, which spans the bacterial host inner membrane. There C-terminal domain interact with the C-terminal domain of cognate Rz1 spanin components.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

Rz1-type spanin component
type: Class
subclass of: Restriction
  on property: part_of
  some values from: Rz/Rz1-type spanin
definition: Rz1-like proteins are tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moieties of their N-terminal cysteine and interact with the Rz-like C-terminal domains through their C-terminal domain. The Rz1 coding sequence is either embedded within or adjacent to the Rz gene.
database_cross_reference: PMID:17900620
has_obo_namespace: Phage ontology
id: phi:0000346

Axiom
annotated source: Rz1-type spanin component
annotated property: definition
annotated target: Rz1-like proteins are tethered to the inner leaflet of the host outer membrane by the fatty acid and lipid moieties of their N-terminal cysteine and interact with the Rz-like C-terminal domains through their C-terminal domain. The Rz1 coding sequence is either embedded within or adjacent to the Rz gene.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

phage tail needle
type: Class
subclass of: Restriction
  on property: part_of
  some values from: capsid tail fiber
definition: Tail fiber component, which during infection is injected into the host, likely piercing a hole in the host cell envelope.
database_cross_reference: PMID:18059287
has_obo_namespace: Phage ontology
id: phi:0000347

Axiom
annotated source: phage tail needle
annotated property: definition
annotated target: Tail fiber component, which during infection is injected into the host, likely piercing a hole in the host cell envelope.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

cell wall degrading transglycosylase activity
type: Class
subclass of: endolysin activity
definition: Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
has_obo_namespace: Phage ontology
id: phi:0000348

Axiom
annotated source: cell wall degrading transglycosylase activity
annotated property: definition
annotated target: Cell wall transglycosylase synthesized by a phage during its lytic cycle and responsible for host cell lysis.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:RY
database_cross_reference: PHI:SC

target site selection protein
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transpososome
definition: Component of the transpososme, this protein contributes to target site selction. Some proteins in the family select specific sites (as the Tn7 TnsE protein) others more or less random sites (as the Tn7 TnsD protein).
has_obo_namespace: Phage ontology
id: phi:0000349

Axiom
annotated source: target site selection protein
annotated property: definition
annotated target: Component of the transpososme, this protein contributes to target site selction. Some proteins in the family select specific sites (as the Tn7 TnsE protein) others more or less random sites (as the Tn7 TnsD protein).
database_cross_reference: PHI:AT

regulation of DNA transposition
type: Class
subclass of: Restriction
  on property: part_of
  some values from: transpositional DNA replication
subclass of: Restriction
  on property: part_of
  some values from: transpositional DNA recombination
definition: Any process that controls the process of DNA transposition.
has_obo_namespace: Phage ontology
id: phi:0000350

Axiom
annotated source: regulation of DNA transposition
annotated property: definition
annotated target: Any process that controls the process of DNA transposition.
database_cross_reference: PHI:AT

positive regulation of DNA transposition
type: Class
subclass of: regulation of DNA transposition
definition: Any process that stimulates the process of DNA transposition.
has_obo_namespace: Phage ontology
id: phi:0000351

Axiom
annotated source: positive regulation of DNA transposition
annotated property: definition
annotated target: Any process that stimulates the process of DNA transposition.
database_cross_reference: PHI:AT

negative regulation of DNA transposition
type: Class
subclass of: regulation of DNA transposition
definition: Any process that inhibits the process of DNA transposition.
has_obo_namespace: Phage ontology
id: phi:0000352

Axiom
annotated source: negative regulation of DNA transposition
annotated property: definition
annotated target: Any process that inhibits the process of DNA transposition.
database_cross_reference: PHI:AT

host nucleoid disruption activity
type: Class
subclass of: host cell killing activity
definition: Any phage activity that provokes the disruption of the host bacterial nuceloid.
has_obo_namespace: Phage ontology
id: phi:0000353

Axiom
annotated source: host nucleoid disruption activity
annotated property: definition
annotated target: Any phage activity that provokes the disruption of the host bacterial nuceloid.
database_cross_reference: PHI:AT

genome segregation
type: Class
subclass of: unclassified
definition: The process by which genetic material is organized and physically separated and apportioned to two daughter bacterial cells.
has_obo_namespace: Phage ontology
has_related_synonym: chromosome segregation
id: phi:0000354

Axiom
annotated source: genome segregation
annotated property: definition
annotated target: The process by which genetic material is organized and physically separated and apportioned to two daughter bacterial cells.
database_cross_reference: PHI:AT

Axiom
annotated source: genome segregation
annotated property: has_related_synonym
annotated target: chromosome segregation
database_cross_reference: GO:0007059

phage entry exclusion
type: Class
subclass of: phage process
definition: A phage or plasmid-mediated process that prevents entry of an infecting phage into the host cell.
has_obo_namespace: Phage ontology
has_related_synonym: abortive infection
id: phi:0000355
comment: This process differs from immunity established by a prophage through the synthesis of a repressor protein that blocks gene expression by a superinfecting phage with the same immunity region.

Axiom
annotated source: phage entry exclusion
annotated property: definition
annotated target: A phage or plasmid-mediated process that prevents entry of an infecting phage into the host cell.
database_cross_reference: PHI:AT

Axiom
annotated source: phage entry exclusion
annotated property: has_related_synonym
annotated target: abortive infection
database_cross_reference: phi:0000059

site-specific endoribonuclease activity
type: Class
subclass of: phage activity
definition: Definition?
database_cross_reference: PMID:17046813
has_obo_namespace: Phage ontology
id: phi:0000356

Axiom
annotated source: site-specific endoribonuclease activity
annotated property: definition
annotated target: Definition?
database_cross_reference: PHI:AT

type III secretion complex injectisome
type: Class
definition: Structure found in many T3S nanomachines that possess a stiff needlelike structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In other T3S the needle is not complete and the structure serves as the conduit for protein secretion.
has_obo_namespace: Phage ontology
id: phi:0000357
comment: Is a synonym of type III secretion complex
deprecated: true

Axiom
annotated source: type III secretion complex injectisome
annotated property: definition
annotated target: Structure found in many T3S nanomachines that possess a stiff needlelike structure of a defined length. The needle is thought to function as the conduit for protein translocation into the target eukaryotic host cell. In other T3S the needle is not complete and the structure serves as the conduit for protein secretion.
database_cross_reference: PHI:AT
database_cross_reference: PHI:GC

relaxosome assembly
type: Class
subclass of: Restriction
  on property: part_of
  some values from: intercellular transfer by conjugation
definition: The process that leads to the assembly of the relaxosome, a multi-component enzymatic machine, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition.
has_obo_namespace: Phage ontology
id: phi:0000358

Axiom
annotated source: relaxosome assembly
annotated property: definition
annotated target: The process that leads to the assembly of the relaxosome, a multi-component enzymatic machine, which mediates cleavage and initiation of rolling circle replication on a doubles stranded DNA molecule during conjugation, phage replication and transposition.
database_cross_reference: PHI:AT

plasmid
type: Class
subclass of: Restriction
  on property: part_of
  some values from: MeGO
definition: This is a temporary term: parent to all functions related to plasmid processes, components and molecular activities.
has_obo_namespace: Phage ontology
id: phi:0000359

Axiom
annotated source: plasmid
annotated property: definition
annotated target: This is a temporary term: parent to all functions related to plasmid processes, components and molecular activities.
database_cross_reference: PHI:AT

negative regulation of plasmid gene expression
type: Class
subclass of: regulation of plasmid gene expression
definition: Any process that inhibits the process of transcription of plasmid genes.
has_obo_namespace: Phage ontology
id: phi:0000360

Axiom
annotated source: negative regulation of plasmid gene expression
annotated property: definition
annotated target: Any process that inhibits the process of transcription of plasmid genes.
database_cross_reference: PHI:AT

positive regulation of plasmid gene expression
type: Class
subclass of: regulation of plasmid gene expression
definition: Any process that stimulates the process of transcription of plasmid genes.
has_obo_namespace: Phage ontology
id: phi:0000361

Axiom
annotated source: positive regulation of plasmid gene expression
annotated property: definition
annotated target: Any process that stimulates the process of transcription of plasmid genes.
database_cross_reference: PHI:AT

phi_0000362
type: Class
IAO_0000231: IAO_0000227
term replaced by: plasmid process
deprecated: true

regulation of plasmid gene expression
type: Class
subclass of: plasmid process
definition: Any process that influences the level of plasmid gene transcription.
has_obo_namespace: Phage ontology
id: phi:0000363

Axiom
annotated source: regulation of plasmid gene expression
annotated property: definition
annotated target: Any process that influences the level of plasmid gene transcription.
database_cross_reference: PHI:AT

bacteriocin
type: Class
subclass of: plasmid activity
subclass of: exotoxin
definition: Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s).
database_cross_reference: Wiki:http://en.wikipedia.org/wiki/Bacteriocin
has_obo_namespace: Phage ontology
id: phi:0000364

Axiom
annotated source: bacteriocin
annotated property: definition
annotated target: Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s).
database_cross_reference: PH:AT

cobalamin biosynthesis
type: Class
subclass of: unclassified
definition: Any step required for the synthesis of cobalamin, a term that may refer to several substances depending on the upper axial ligand of the cobalt ion.
has_obo_namespace: Phage ontology
id: phi:0000365

Axiom
annotated source: cobalamin biosynthesis
annotated property: definition
annotated target: Any step required for the synthesis of cobalamin, a term that may refer to several substances depending on the upper axial ligand of the cobalt ion.
database_cross_reference: PHI:AT

establishment as a prophage
type: Class
subclass of: site-specific DNA integration
subclass of: Restriction
  on property: part_of
  some values from: establishment as an integrated prophage
definition: Process by which a phage genome reaches a latent state, becoming a component of its host genome.
has_broad_synonym: establishment of viral latency
database_cross_reference: GO:0019043
has_obo_namespace: Phage ontology
id: phi:0000366

Axiom
annotated source: establishment as a prophage
annotated property: definition
annotated target: Process by which a phage genome reaches a latent state, becoming a component of its host genome.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

Axiom
annotated source: establishment as a prophage
annotated property: has_broad_synonym
annotated target: establishment of viral latency
database_cross_reference: GO:0019043

negative regulation by host of phage transcription
type: Class
subclass of: Restriction
  on property: part_of
  some values from: negative transcriptional regulation of phage gene expression
definition: Any process by which a host bacterium stops, prevents or reduces the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template.
has_broad_synonym: negative regulation by host of viral transcription
database_cross_reference: GO:0043922
has_obo_namespace: Phage ontology
id: phi:0000367

Axiom
annotated source: negative regulation by host of phage transcription
annotated property: definition
annotated target: Any process by which a host bacterium stops, prevents or reduces the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template.
database_cross_reference: PHI:AT

Axiom
annotated source: negative regulation by host of phage transcription
annotated property: has_broad_synonym
annotated target: negative regulation by host of viral transcription
database_cross_reference: GO:0043922

positive regulation by host of phage transcription
type: Class
subclass of: Restriction
  on property: part_of
  some values from: regulation of phage gene expression
definition: Any process by which a host bacterium activates the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template.
has_broad_synonym: positive regulation by host of viral transcription
database_cross_reference: GO:0043923
has_obo_namespace: Phage ontology
id: phi:0000368

Axiom
annotated source: positive regulation by host of phage transcription
annotated property: definition
annotated target: Any process by which a host bacterium activates the frequency, rate or extent of phage transcription, the synthesis of RNA on either a DNA or an RNA template.
database_cross_reference: PHI:AT

phage capsid envelopment
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage head/capsid assembly
definition: The process by which a capsid acquires a membrane envelope.
has_broad_synonym: viral capsid envelopment
database_cross_reference: GO:0046744
has_obo_namespace: Phage ontology
id: phi:0000369

Axiom
annotated source: phage capsid envelopment
annotated property: definition
annotated target: The process by which a capsid acquires a membrane envelope.
database_cross_reference: PHI:AT

Axiom
annotated source: phage capsid envelopment
annotated property: has_broad_synonym
annotated target: viral capsid envelopment
database_cross_reference: GO:0046744

lysis-inhibition
type: Class
subclass of: phage process
definition: Lysis inhibition (LIN) refers to a highly adaptive attribute of the T4-related phages, which delay lysis for several hours in response to sensing the presence of external related phages attacking the cell. A block in expressing LIN results in large-plaque morphology.
created by: Ariane
creation date: 2009-06-02T04:00:05Z
has_obo_namespace: Phage ontology
id: phi:0000370

Axiom
annotated source: lysis-inhibition
annotated property: definition
annotated target: Lysis inhibition (LIN) refers to a highly adaptive attribute of the T4-related phages, which delay lysis for several hours in response to sensing the presence of external related phages attacking the cell. A block in expressing LIN results in large-plaque morphology.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

antibiotic resistance
type: Class
subclass of: unclassified
definition: A resistance to drug that mitigates the damaging effects of an antibiotic.
created by: Ariane
creation date: 2009-06-02T04:47:24Z
database_cross_reference: IDO:0000581
has_obo_namespace: Phage ontology
id: phi:0000371
comment: is_a response to drug, GO:0042493.

Axiom
annotated source: antibiotic resistance
annotated property: definition
annotated target: A resistance to drug that mitigates the damaging effects of an antibiotic.
database_cross_reference: IDO:0000581

phage lytic cycle
type: Class
subclass of: Restriction
  on property: part_of
  some values from: phage infectious cycle
definition: The set of processes by which a bacteriophage produces infectious progeny.
created by: Ariane
creation date: 2010-04-21T05:45:42Z
has_obo_namespace: Phage ontology
id: phi:0000372
comment: Formerly Ejection/injection.

Axiom
annotated source: phage lytic cycle
annotated property: definition
annotated target: The set of processes by which a bacteriophage produces infectious progeny.
database_cross_reference: PHI:AT
database_cross_reference: PHI:IM
database_cross_reference: PHI:SC

endotoxin
type: Class
subclass of: toxin
definition: A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
created by: Ariane
creation date: 2010-04-23T02:50:09Z
database_cross_reference: :
has_narrow_synonym: effector
has_obo_namespace: Phage ontology
id: phi:0000373

Axiom
annotated source: endotoxin
annotated property: definition
annotated target: A molecular entity with a toxin disposition and that is a structural component of a pathogen and is released from the pathogen only upon cytolysis.
database_cross_reference: IDO:0000552

Axiom
annotated source: endotoxin
annotated property: database_cross_reference
annotated target: :
label: http://en.wikipedia.org/wiki/Endotoxin

exotoxin
type: Class
subclass of: toxin
definition: A toxin excreted by a microorganism, including bacteria, fungi, algae, and protozoa. Exotoxins can cause damage by destroying host cells or disrupting normal host cellular metabolism. Exotoxins are either secreted, or, similar to endotoxins, released during lysis of the cell.
created by: Ariane
creation date: 2010-04-23T02:52:50Z
database_cross_reference: :
database_cross_reference: IDO:0000550
has_narrow_synonym: effector
has_obo_namespace: Phage ontology
id: phi:0000374

Axiom
annotated source: exotoxin
annotated property: definition
annotated target: A toxin excreted by a microorganism, including bacteria, fungi, algae, and protozoa. Exotoxins can cause damage by destroying host cells or disrupting normal host cellular metabolism. Exotoxins are either secreted, or, similar to endotoxins, released during lysis of the cell.
database_cross_reference: IDO:0000550
database_cross_reference: PHI:AT

Axiom
annotated source: exotoxin
annotated property: database_cross_reference
annotated target: :
label: http://en.wikipedia.org/wiki/Exotoxin

predicted prophage function unknown
type: Class
subclass of: Restriction
  on property: part_of
  some values from: bacteriophage
definition: No process, component or activity can yet be assigned to this predicted prophage function.
created by: ariane
creation date: 2011-07-12T01:43:27Z
has_obo_namespace: Phage ontology
id: phi:0000375

Axiom
annotated source: predicted prophage function unknown
annotated property: definition
annotated target: No process, component or activity can yet be assigned to this predicted prophage function.
database_cross_reference: PHI:AT