ontology: go/extensions/go_annotation_extension_examples
default-namespace: go/extensions/go_annotation_extension_examples
remark: These examples are intended to illustrate how to use relations in c16 of a GO annotation file.
remark: Each stanza corresponds to an actual or hypothetical annotation.
remark: The identifier is autogenerated can be ignored.
remark: Some understanding of how OBO-Format relates to OWL class expressions helps.
remark: Each collection of 1..n intersection_of tags corresponds to a class expression (x1 and x2 ... and xn), where each element is either a plain class (the genus)
remark: or a relationship (differentia). The genus corresponds to the pre-composed annotation in c5, and the differentia to c16.
remark: a has_participant relationship to the gene or gene product is shown, but this is for illustrative purposes only; this would go in c1 and c2 of an actual GAF.
remark: -- 
remark: The basic idea is to show what the term would look like if it were to be pre-composed in the ontology.
remark: Definitions that correspond to what the actual definition would look like are helpful here.

[Term]
id: PomBase:association-PomBase:SPAC13A11.03-GO:0006302-0
name: double-strand break repair during meiotic cell cycle
namespace: PomBase
comment: A straightforward example of happens_during
def: "A process of double-strand break repair that occurs during a meiotic cell cycle." [GO_REF:0000001, GOC:mah]
relationship: has_participant PomBase:SPAC13A11.03 ! mcp7
intersection_of: GO:0006302  ! double-strand break repair
intersection_of: happens_during GO:0051321 ! meiotic cell cycle

[Term]
id: PomBase:association-PomBase:SPAC1834.06c-GO:0005816-0
name: spindle pole body dependent on septation initiation signaling cascade
namespace: PomBase
comment: An example of gene product localization dependent on a process occurring. Note: see comments for independent_of. The definition below isn't really a very good cell component definition, but it accurately captures the intent of the curator, who wants to talk about the circumstances of the location rather than the component itself
def: "Gene product is located at to the spindle pole body that occurs if and only if a septation initiation cascade process occurs." [PMID:16096637, PMID:16823372, GOC:mah]
relationship: has_participant PomBase:SPAC1834.06c ! pmo25
intersection_of: GO:0005816  ! spindle pole body
intersection_of: localization_dependent_on GO:0031028 ! septation initiation signaling cascade

[Term]
id: PomBase:association-PomBase:SPAC637.13c-GO:0035091-0
name: phosphatidylinositol binding dependent on Pleckstrin homology domain
namespace: PomBase
comment: An example of a MF/BP dependent on protein domain. **VAL**: can you add more detail? Presumably the pleckstrin is on the binding partner
def: "Phosphatidylinositol binding that is mediated by and requires the gene product's pleckstrin homology domain." [GO_REF:0000001, GOC:mah]
relationship: has_participant PomBase:SPAC637.13c ! SPAC637.13c
intersection_of: GO:0035091  ! phosphatidylinositol binding
intersection_of: requires_sequence_feature Pfam:PF00169

[Term]
id: PomBase:association-GeneDB_Spombe:SPCC1281.01-GO:0009897-0
namespace: GeneDB_Spombe
name: external side of plasma membrane dependent_on Alpha-Amylase
comment: TODO!!! VAL: Not quite clear on what this means!!
def: "Gene product is located at the external side of the plasma membrane that is mediated by and requires the gene product's alpha-amylase domain." [PMID:17472966, GOC:mah]
relationship: has_participant GeneDB_Spombe:SPCC1281.01 ! ags1
intersection_of: GO:0009897  ! external side of plasma membrane
intersection_of: dependent_on Pfam:PF00128
is_obsolete: true
! not sure how accurate def is ... based on TAS evidence, and I'm having trouble figuring out which statement(s) lead to the conclusion represented by the def
! could just be that it's the alpha-amylase domain that's on the external side ... if so, dependent_on is misleading
! update 2011-07-20: Val has removed this from our internal annotations, so it'll be gone in the next pombe GAF. Neither of us could figure out what it meant!
! update 2012-04-24: obsolete; not replaced

[Term]
id: GeneDB_Spombe:association-GeneDB_Spombe:SPBC27B12.03c-GO:0090002-0
name: establishment of protein localization in plasma membrane dependent_on sterol
namespace: GeneDB_Spombe
comment: BP dependent_on CHEBI example. (just curious - the PMID refers to subclasses of CHEBI:sterol - worth capturing these?)
def: "The directed movement of a protein to a specific location in the plasma membrane that occurs only in the presence of some sterol." [PMID:18310029, GOC:mah]
relationship: has_participant GeneDB_Spombe:SPBC27B12.03c ! erg32
intersection_of: GO:0090002  ! establishment of protein localization in plasma membrane
intersection_of: dependent_on CHEBI:15889 ! sterol
is_obsolete: true
! not sure I see where this comes from in the paper ... pma1 localization looks similar in mutant vs wild type; aat1 is mislocalized but where's the sterol dependency?
! have guessed at def based on terms & extensions anyway
! update: Val has removed erg2 and erg32 annotations, and added erg6 annotations
! update 2012-04-24: obsolete; not replaced

[Term]
id: PomBase:association-PomBase:SPBC4F6.12-GO:0005826-0
name: actomyosin contractile ring independent_of septation initiation signaling cascade
namespace: PomBase
comment: CC independent_of BP examples. We need to document what it means for a physical entity to be dependent/independent..
def: "Gene product is located at the actomyosin contractile ring that occurs whether or not a septation initiation signaling cascade occurs." [PMID:18256290, PMID:18272786, GOC:mah]
relationship: has_participant PomBase:SPBC4F6.12 ! pxl1
intersection_of: GO:0005826  ! actomyosin contractile ring
intersection_of: independent_of GO:0031028 ! septation initiation signaling cascade

[Term]
id: GeneDB_Spombe:association-GeneDB_Spombe:SPAC31G5.18c-GO:0034629-0
name: SHREC complex localization
namespace: GeneDB_Spombe
comment: This is an example of a post-composed annotation that is a good candidate for pre-composition. TODO: decide on full set of relations to delineate all possible roles (cargo, destination, source, conduit)
def: "Any process in which a SHREC complex is transported to, or maintained in, a specific location." [PMID:20473289]
relationship: has_participant GeneDB_Spombe:SPAC31G5.18c ! sde2
intersection_of: GO:0034629  ! cellular protein complex localization
intersection_of: localization_target_is GO:0070824 ! SHREC complex
is_obsolete: true
replaced_by: GO:0072688 ! SHREC complex localization
! replaced by pre-composed term

[Term]
id: GeneDB_Spombe:association-GeneDB_Spombe:SPCC830.08c-GO:0005783-0
name: endoplasmic reticulum located_at cell cortex
namespace: GeneDB_Spombe
comment: An example of located_at between a CC and a CC
def: "Replaced by existing pre-composed term" [PMID:20434336]
relationship: has_participant GeneDB_Spombe:SPCC830.08c ! yop1
intersection_of: GO:0005783  ! endoplasmic reticulum
intersection_of: located_at GO:0005938 ! cell cortex
is_obsolete: true
replaced_by: GO:0032541 ! cortical endoplasmic reticulum
! replaced by pre-composed term

[Term]
id: PomBase:association-PomBase:SPCC970.09-GO:0006897-0
name: endocytosis occurs_in cell division site
namespace: PomBase
comment: An example of located_at between a BP and a CC
def: "A process of endocytosis that takes place at the cell division site." [PMID:16141239, GOC:mah]
relationship: has_participant PomBase:SPCC970.09 ! sec8
intersection_of: GO:0006897  ! endocytosis
intersection_of: occurs_in GO:0032153 ! cell division site

[Term]
id: PomBase:association-PomBase:SPBC405.04c-GO:0045324-0
name: late endosome to vacuole transport during ascospore formation
namespace: PomBase
comment: An example of happens_during between two BPs
def: "A process of late endosome to vacuole transport that takes place during ascospore formation." [GOC:mah]
relationship: has_participant PomBase:SPBC405.04c ! ypt7
intersection_of: GO:0045324 ! late endosome to vacuole transport
intersection_of: happens_during GO:0030437 ! ascospore formation

[Term]
id: PomBase:association-PomBase:SPAC27D7.13c-GO:0030989-0
name: dynein-driven meiotic oscillatory nuclear movement during meiotic prophase I
namespace: PomBase
comment: An example of happens_during between two BPs, where extension BP is a cell cycle phase
def: "A process of dynein-driven meiotic oscillatory nuclear movement that takes place during prophase of meiosis I." [GOC:mah]
relationship: has_participant PomBase:SPAC27D7.13c ! ssm4
intersection_of: GO:0030989 ! dynein-driven meiotic oscillatory nuclear movement
intersection_of: happens_during GO:0007128 ! meiotic prophase I
! note: check whether GO:0030989 occurs during any other phase; the def suggests not, and if that's the case this extension can be superseded by moving GO:0030989

[Term]
id: PomBase:association-PomBase:SPCC297.03-GO:0030428-0
name: cell septum during cellular response to stress
namespace: PomBase
comment: An example of localization to a CC during a BP
def: "Gene product location at the cell septum during a cellular response to stress." [GOC:mah]
relationship: has_participant PomBase:SPCC297.03 ! ssp1
intersection_of: GO:0030428 ! cell septum
intersection_of: exists_during GO:0033554 ! cellular response to stress

[Term]
id: PomBase:association-PomBase:SPBP4H10.06c-GO:0000939-0
name: condensed chromosome inner kinetochore during mitotic metaphase
namespace: PomBase
comment: An example of localization to a CC during a BP, where BP is a cell cycle phase
def: "Gene product location at the condensed chromosome inner kinetochore during mitotic metaphase." [GOC:mah]
relationship: has_participant PomBase:SPBP4H10.06c ! cut14
intersection_of: GO:0000939 ! condensed chromosome inner kinetochore
intersection_of: exists_during GO:0000089 ! mitotic metaphase

[Term]
id: PomBase:association-PomBase:SPAC31A2.14-GO:2000158-0
name: positive regulation of ubiquitin-specific protease activity of ubp9
namespace: PomBase
comment: An example of regulation of the activity of a specific target gp
def: "A process of positive regulation of ubiquitin-specific protease activity that regulates the activity of S. pombe ubp9." [GOC:mah]
relationship: has_participant PomBase:SPAC31A2.14 ! bun107
intersection_of: GO:2000158
intersection_of: has_regulation_target PomBase:SPBC1703.12 ! ubp9
! may change relation to a new child of has_regulation_target

[Term]
id: PomBase:association-PomBase:SPAC1002.08c-GO:0006357-0
name: regulation of transcription of srk1 from RNA polymerase II promoter
namespace: PomBase
comment: An example of transcriptional regulation of a specific gene
def: "A process of regulation of transcription from RNA polymerase II promoter that regulates transcription of S. pombe srk1." [GOC:mah]
relationship: has_participant PomBase:SPAC1002.08c ! mtf1
intersection_of: GO:0006357
intersection_of: has_regulation_target PomBase:SPCC1322.08 ! srk1
! may change relation to a new child of has_regulation_target

[Term]
id: GeneDB_Spombe:association-GeneDB_Spombe:SPAC4G8.13c-GO:0005634-0
name: regulation of transcription of srk1 from RNA polymerase II promoter
namespace: GeneDB_Spombe
comment: An example of localization to CC in presence of a chemical
def: "Localization of S. pombe Prz1 to the nucleus in the presence of calcium ions." [GOC:mah]
relationship: has_participant GeneDB_Spombe:SPAC4G8.13c ! prz1
intersection_of: GO:0005634 ! nucleus
intersection_of: in_presence_of CHEBI:29108 ! calcium(2+)
! Note that this is completely made up for the purpose of illustrating how in_presence_of could be used with a GO annotation

[Term]
id: PomBase:association-PomBase:SPBC19C7.10-GO:0045141-0
name: meiotic telomere clustering requiring localization to nuclear inner membrane
comment: An example of a gene product involved in a process only when it is located at a CC
def: "A process of meiotic telomere clustering that required gene product localization to the nuclear inner membrane." [GOC:mah]
relationship: has_participant PomBase:SPBC19C7.10 ! bqt4
intersection_of: GO:0045141 ! meiotic telomere clustering
intersection_of: requires_localization GO:0005637 ! nuclear inner membrane

[Term]
id: PomBase:association-PomBase:SPAC24B11.11c-GO:0004674-0
name: protein serine/threonine kinase activity requiring direct regulation by Mob1
comment: An example of a gene product executing a MF only in the presence of a direct regulator
def: "A protein serine/threonine kinase activity executed only in the presence of the regulator Mob1." [GOC:mah]
relationship: has_participant PomBase:SPAC24B11.11c ! sid2
intersection_of: GO:0004674 ! protein serine/threonine kinase activity
intersection_of: requires_direct_regulator PomBase:SPBC428.13c ! mob1

[Term]
id: PomBase:association-PomBase:SPBC15D4.02-GO:0030702-0
name: chromatin silencing at regional centromere outer repeat region
comment: An example of a BP that occurs at a specific sequence within a chromosome
def: "A process of chromatin silencing that occurs at the regional centromere outer repeat region." [GOC:mah]
relationship: has_participant PomBase:SPBC15D4.02 ! SPBC15D4.02
intersection_of: GO:0030702 ! chromatin silencing at centromere
intersection_of: occurs_at SO:0001799 ! regional_centromere_outer_repeat_region

[Term]
id: PomBase:association-PomBase:SPAC24B11.06c-GO:0004707-0
name: MAP kinase activity acting on Srk1
comment: An example of MF with a gene product substrate
def: "A MAP kinase activity that phosphorylates Srk1." [GOC:mah]
relationship: has_participant PomBase:SPAC24B11.06c ! sty1
intersection_of: GO:0004707 ! MAP kinase activity
intersection_of: has_substrate PomBase:SPCC1322.08 ! srk1

[Term]
id: PomBase:association-PomBase:SPAC2F7.03c-GO:0034613-0
name: cellular protein localization of Rga4
comment: An example of localization of a gene product
def: "A process of cellular protein localization that localizes Rga4." [GOC:mah]
relationship: has_participant PomBase:SPAC2F7.03c ! pom1
intersection_of: GO:0034613 ! cellular protein localization
intersection_of: localizes PomBase:SPBC28E12.03 ! rga4

[Term]
id: PomBase:association-PomBase:SPAC31A2.11c-GO:0001202-0
name: copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity binding to CuRE
comment: An example of MF with a sequence feature substrate
def: "A copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity that binds DNA at a copper-response element." [GOC:mah]
relationship: has_participant PomBase:SPAC31A2.11c ! cuf1
intersection_of: GO:0001202 ! copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity
intersection_of: has_substrate PomBase:SO:0001844 ! CuRE

[Term]
id: PomBase:association-PomBase:SPAC664.01c-GO:0004707-0
name: nucleosomal histone binding activity binding to K-10 methylated histone H3.1
comment: An example of MF with a specific modified protein substrate
def: "A nucleosomal histone binding activity that binds to histone 3.1 that has its initiator methionine removed and has been methylated on Lys 10." [GOC:mah]
relationship: has_participant PomBase:SPAC664.01c ! swi6
intersection_of: GO:0031493 ! nucleosomal histone binding
intersection_of: has_substrate PR:000027578 ! histone H3.1, initiator methionine removed methylated 1 (Schizosaccharomyces pombe)