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Clean up term_tracker_item values. #27794

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Apr 30, 2024
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Clean up term_tracker_item values. #27794

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829f51e
Clean up term_tracker_item values.
balhoff Apr 30, 2024
4ff0529
Add exactMatch.
balhoff Apr 30, 2024
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49 changes: 15 additions & 34 deletions src/ontology/go-edit.obo
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Original file line number Diff line number Diff line change
Expand Up @@ -39536,7 +39536,6 @@ xref: RHEA:11740
is_a: GO:0015038 ! glutathione disulfide oxidoreductase activity
is_a: GO:0016209 ! antioxidant activity
is_a: GO:0016668 ! oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
property_value: term_tracker_item "glutathione-disulfide reductase activity" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25461" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25498" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27180" xsd:anyURI
Expand Down Expand Up @@ -50476,7 +50475,6 @@ def: "Enables the transmembrane transfer of an ion by a channel that opens when
synonym: "intracellular ligand-gated ion channel activity" BROAD []
synonym: "intracellular ligand-gated monoatomic ion channel activity" EXACT []
is_a: GO:0015276 ! ligand-gated monoatomic ion channel activity
property_value: term_tracker_item "intracellular ligand-gated monoatomic ion channel activity" xsd:anyURI

[Term]
id: GO:0005219
Expand Down Expand Up @@ -104987,7 +104985,6 @@ name: obsolete regulation of cell death
namespace: biological_process
def: "OBSOLETE. Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb]
comment: The reason for obsoletion is that this term represent an assay and not a GO process.\nThe reason for obsoletion is that this represents a phenotype.\nThe reason for obsoletion is that this term was added in error.\nThe reason for obsoletion is that more specific terms were created.\nThe reason for obsoletion is that this term was an unnecessary grouping term.
property_value: term_tracker_item "" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24755" xsd:anyURI
is_obsolete: true

Expand All @@ -105005,8 +105002,8 @@ id: GO:0010943
name: NADPH pyrophosphatase activity
namespace: molecular_function
def: "Catalysis of the reaction: NADPH + H2O = NMNH + ADP." [GOC:tb, PMID:12790796, RHEA:60820]
xref: RHEA:60820 {source="skos:exactMatch"}
is_a: GO:0004551 ! dinucleotide phosphatase activity
property_value: term_tracker_item "RHEA:60820" xsd:anyURI

[Term]
id: GO:0010944
Expand Down Expand Up @@ -172631,7 +172628,6 @@ def: "A positive regulation of gene expression mechanism that allows RNA polymer
synonym: "transcriptional readthrough" EXACT []
is_a: GO:0010628 ! positive regulation of gene expression
is_a: GO:0060567 ! negative regulation of termination of DNA-templated transcription
property_value: term_tracker_item "https://pubmed.ncbi.nlm.nih.gov/30191803/" xsd:anyURI

[Term]
id: GO:0031565
Expand Down Expand Up @@ -194535,7 +194531,6 @@ def: "Any constituent part of a host cell. The host is defined as the larger of
comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
subset: gocheck_do_not_annotate
is_a: GO:0018995 ! host cellular component
property_value: term_tracker_item "GO:0033643" xsd:anyURI

[Term]
id: GO:0033644
Expand Down Expand Up @@ -204395,7 +204390,6 @@ def: "Binding to a box C/D small nucleolar RNA." [GOC:mah]
synonym: "box C/D snoRNA binding" NARROW []
synonym: "box C/D sRNA binding" NARROW []
is_a: GO:0030515 ! snoRNA binding
property_value: term_tracker_item "- [ ] box C/D RNA 5'-end processing -> box C/D sno(s)RNA 5'-end processing" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20416" xsd:anyURI

[Term]
Expand Down Expand Up @@ -228927,7 +228921,7 @@ def: "OBSOLETE. The process in which a virus effects a change in the function of
comment: This term was obsoleted because it represents a molecular function.
synonym: "modification by virus of host protein function" EXACT [GOC:bf]
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23089" xsd:anyURI
property_value: term_tracker_item "https://github.com/progeneontology/go-ontology/issues/21963" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21963" xsd:anyURI
is_obsolete: true
created_by: bf
creation_date: 2011-06-02T02:38:42Z
Expand Down Expand Up @@ -229072,7 +229066,7 @@ comment: This term was obsoleted because it represents a molecular function.
synonym: "modulation of catalytic activity of host by virus" EXACT [GOC:bf]
synonym: "regulation by virus of host catalytic activity" EXACT [GOC:bf]
synonym: "regulation of host catalytic activity by virus" EXACT [GOC:bf]
property_value: term_tracker_item "https://github.com/progeneontology/go-ontology/issues/21963" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21963" xsd:anyURI
is_obsolete: true
created_by: bf
creation_date: 2011-06-16T02:59:35Z
Expand Down Expand Up @@ -249935,7 +249929,7 @@ synonym: "phosphatidylinositol 4-phosphate phosphatase activity" EXACT []
xref: RHEA:55652
is_a: GO:0034596 ! phosphatidylinositol phosphate 4-phosphatase activity
is_a: GO:0052744 ! phosphatidylinositol monophosphate phosphatase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/compare/issue-24252?expand=1" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24252" xsd:anyURI

[Term]
id: GO:0043813
Expand Down Expand Up @@ -280366,7 +280360,6 @@ comment: This term was obsoleted because it is a molecular function represented
synonym: "induction by virus of modification of host RNA polymerase II" BROAD [GOC:bf, GOC:jl]
synonym: "virus-induced modification of host RNA polymerase II" EXACT []
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23640" xsd:anyURI
property_value: term_tracker_item "This term was obsoleted because it is a molecular function represented as a biological process." xsd:anyURI
is_obsolete: true

[Term]
Expand Down Expand Up @@ -395461,7 +395454,6 @@ synonym: "positive regulation by symbiont of host G-protein coupled receptor pro
synonym: "positive regulation by symbiont of host signal transduction mediated by G-protein alpha subunit" NARROW []
synonym: "positive regulation by symbiont of host signal transduction mediated by G-protein beta subunit" NARROW []
synonym: "positive regulation by symbiont of host signal transduction mediated by G-protein gamma subunit" NARROW []
property_value: term_tracker_item "http://amigo.geneontology.org/amigo/term/GO:0075119" xsd:anyURI
is_obsolete: true

[Term]
Expand Down Expand Up @@ -421103,7 +421095,6 @@ name: obsolete mRNA cleavage involved in mRNA processing
namespace: biological_process
def: "OBSOLETE. Cleavage of an immature mRNA transcript to produce one or more more mature mRNA transcripts, prior to translation into polypeptide." [GOC:dos]
comment: This term was obsoleted because it represents a molecular function
property_value: term_tracker_item "This term was obsoleted because it represents a molecular function" xsd:anyURI
is_obsolete: true

[Term]
Expand Down Expand Up @@ -435458,7 +435449,6 @@ def: "OBSOLETE. Catalysis of the reaction: orcinol + S-adenosyl-L-methionine = H
comment: The reason for obsoletion is that it is more specific than the specificity of any known gene product.
xref: EC:2.1.1.6
xref: MetaCyc:RXN-9017
property_value: term_tracker_item "orcinol O-methyltransferase activity" xsd:anyURI
is_obsolete: true
replaced_by: GO:0016206

Expand Down Expand Up @@ -446814,7 +446804,7 @@ namespace: cellular_component
def: "The radial spoke of each group of radial spokes, whether grouped as triplets or doublets, that is most proximal to the base of the cilium. Radial spoke 1 (RS1), similarly to radial spoke 2, is comprised of four domains: 1) a very short base anchored to the A microtubule, 2) an elongaged stalk, 3) a bifurcated neck, and 4) an orthogonal head. The base of RS1 is connected to the tail of the inner dynein arm a/d." [GOC:krc, PMID:22754630]
synonym: "RS1" RELATED [PMID:22754630]
is_a: GO:0001534 ! radial spoke
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:13:01Z

Expand All @@ -446825,7 +446815,7 @@ namespace: cellular_component
def: "The radial spoke of each group of radial spokes, whether grouped as triplets or doublets, that is immediately distal to radial spoke 1 (RS1). Radial spoke 2 (RS2), similarly to RS1, is comprised of four domains: 1) a very short base anchored to the A microtubule, 2) an elongaged stalk, 3) a bifurcated neck, and 4) an orthogonal head. The base of RS2 is connected to the tail of the inner dynein arm c." [GOC:krc, PMID:22754630]
synonym: "RS2" RELATED [PMID:22754630]
is_a: GO:0001534 ! radial spoke
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:14:02Z

Expand All @@ -446836,7 +446826,7 @@ namespace: cellular_component
def: "Radial spoke 3 (RS3), when present, is the most distal of each group of radial spokes, whether grouped as triplets or doublets. RS3 has significantly different morphology and protein composition than RS1 and RS2 and also extends at a slant from the microtubule doublet, rather than perpendicularly like RS1 and RS2. In some organisms (e.g. Chlamydomonas and Sarcophaga bullata), RS3 is represented only as a stump attached to the A-microtubule lacking the rest of the stalk structure and entirely lacking the head structure." [GOC:krc, ISBN:0124325653, PMID:22754630, PMID:25694453, PMID:9450971]
synonym: "RS3" RELATED [PMID:22754630]
is_a: GO:0001534 ! radial spoke
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:15:03Z

Expand All @@ -446848,7 +446838,7 @@ def: "The portion of the radial spoke 1 that is orthogonal to the elongated stal
synonym: "radial spokehead 1" EXACT []
intersection_of: GO:0001535 ! radial spoke head
intersection_of: part_of GO:0120333 ! radial spoke 1
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:16:04Z

Expand All @@ -446860,7 +446850,7 @@ def: "The portion of the radial spoke 2 that is orthogonal to the elongated stal
synonym: "radial spokehead 2" EXACT []
intersection_of: GO:0001535 ! radial spoke head
intersection_of: part_of GO:0120334 ! radial spoke 2
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:17:05Z

Expand All @@ -446872,7 +446862,7 @@ def: "The portion of the radial spoke 3 that is orthogonal to the elongated stal
synonym: "radial spokehead 3" EXACT []
intersection_of: GO:0001535 ! radial spoke head
intersection_of: part_of GO:0120335 ! radial spoke 3
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:18:06Z

Expand All @@ -446883,7 +446873,7 @@ namespace: cellular_component
def: "The short portion of the radial spoke that is directly anchored to the A microtubule of an axonemal microtubule doublet." [GOC:krc, PMID:22754630, PMID:25694453]
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0001534 ! radial spoke
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:19:07Z

Expand All @@ -446894,7 +446884,7 @@ namespace: cellular_component
def: "The short portion of the radial spoke 1 (RS1) that is directly anchored to the A microtubule of an axonemal microtubule doublet." [GOC:krc, PMID:22754630, PMID:25694453]
intersection_of: GO:0120339 ! radial spoke base
intersection_of: part_of GO:0120333 ! radial spoke 1
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:20:08Z

Expand All @@ -446905,7 +446895,7 @@ namespace: cellular_component
def: "The short portion of the radial spoke 2 (RS2) that is directly anchored to the A microtubule of an axonemal microtubule doublet." [GOC:krc, PMID:22754630, PMID:25694453]
intersection_of: GO:0120339 ! radial spoke base
intersection_of: part_of GO:0120334 ! radial spoke 2
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:21:09Z

Expand All @@ -446916,7 +446906,7 @@ namespace: cellular_component
def: "The short portion of the radial spoke 3 (RS3 )that is directly anchored to the A microtubule of an axonemal microtubule doublet." [GOC:krc, PMID:22754630, PMID:25694453]
intersection_of: GO:0120339 ! radial spoke base
intersection_of: part_of GO:0120335 ! radial spoke 3
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:22:10Z

Expand All @@ -446927,7 +446917,7 @@ namespace: cellular_component
def: "The radial spoke neck is a complex that connects the spoke stalk to the head." [GOC:krc, PMID:22754630]
is_a: GO:0032991 ! protein-containing complex
relationship: part_of GO:0001534 ! radial spoke
property_value: term_tracker_item "#25320" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25320" xsd:anyURI
created_by: krc
creation_date: 2023-04-26T22:23:11Z

Expand Down Expand Up @@ -462899,7 +462889,6 @@ def: "Binds to and increases the activity of cyclic nucleotide phosphodiesterase
intersection_of: GO:0140677 ! molecular function activator activity
intersection_of: directly_positively_regulates GO:0004112 ! cyclic-nucleotide phosphodiesterase activity
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24706" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/new?assignees=&labels=&template=custom.md&title=" xsd:anyURI
created_by: ew
creation_date: 2023-01-24T19:49:38Z

Expand Down Expand Up @@ -463531,7 +463520,6 @@ synonym: "cotranscriptional 3' processing of RNA polymerase II mRNA transcripts"
synonym: "mRNA polyadenylation" RELATED []
is_a: GO:0031124 ! mRNA 3'-end processing
is_a: GO:0180012 ! co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway
property_value: term_tracker_item "" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24921" xsd:anyURI
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27004" xsd:anyURI
created_by: vw
Expand Down Expand Up @@ -487635,7 +487623,6 @@ synonym: "up-regulation of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "up-regulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie]
synonym: "upregulation of SREBP cleavage" EXACT [GOC:TermGenie]
synonym: "upregulation of sterol regulatory element binding protein cleavage" EXACT [GOC:TermGenie]
property_value: term_tracker_item "This term was obsoleted because it represents a molecular function." xsd:anyURI
is_obsolete: true
created_by: bf
creation_date: 2012-08-21T16:43:40Z
Expand Down Expand Up @@ -499216,7 +499203,6 @@ def: "OBSOLETE. Any process that modulates the frequency, rate or extent of hist
comment: This term was obsoleted because it represents a molecular function.
synonym: "regulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
property_value: term_tracker_item "H3-K18 acetylation" xsd:anyURI
is_obsolete: true
consider: GO:0043993
created_by: jl
Expand All @@ -499242,7 +499228,6 @@ synonym: "up-regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3-K18 acetylation" EXACT [GOC:TermGenie]
synonym: "upregulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
property_value: term_tracker_item "H3-K18 acetylation" xsd:anyURI
is_obsolete: true
consider: GO:0043993
created_by: jl
Expand All @@ -499268,7 +499253,6 @@ synonym: "inhibition of histone H3-K18 acetylation" NARROW [GOC:TermGenie]
synonym: "inhibition of histone H3K18 acetylation" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone H3 acetylation at K18" EXACT [GOC:TermGenie]
synonym: "negative regulation of histone H3K18 acetylation" EXACT [GOC:TermGenie]
property_value: term_tracker_item "H3-K18 acetylation" xsd:anyURI
is_obsolete: true
created_by: jl
creation_date: 2013-03-28T20:19:39Z
Expand Down Expand Up @@ -509811,7 +509795,6 @@ synonym: "pentose catabolic process to butanol" EXACT [GOC:tt]
synonym: "pentose catabolism to butan-1-ol" EXACT [GOC:TermGenie]
synonym: "pentose degradation to butan-1-ol" EXACT [GOC:TermGenie]
synonym: "solventogenesis" BROAD [GOC:tt]
property_value: term_tracker_item "pentose catabolic process to butan-1-ol" xsd:anyURI
is_obsolete: true
created_by: tb
creation_date: 2014-02-19T18:28:47Z
Expand All @@ -509829,7 +509812,6 @@ synonym: "pentose catabolic process to isopropyl alcohol" EXACT [GOC:tt]
synonym: "pentose catabolism to propan-2-ol" EXACT [GOC:TermGenie]
synonym: "pentose degradation to propan-2-ol" EXACT [GOC:TermGenie]
synonym: "solventogenesis" BROAD [GOC:tt]
property_value: term_tracker_item "pentose catabolic process to propan-2-ol" xsd:anyURI
is_obsolete: true
created_by: tb
creation_date: 2014-02-19T18:28:57Z
Expand Down Expand Up @@ -524217,7 +524199,6 @@ name: obsolete establishment of mitotic actomyosin contractile ring localization
namespace: biological_process
def: "OBSOLETE. Any establishment of actomyosin contractile ring localization that is involved in mitotic cell cycle." [GO_REF:0000060, GOC:mtg_cell_cycle, GOC:TermGenie]
comment: The reason for obsoletion is that the term is represented in another branch (merge)
property_value: term_tracker_item "establishment of mitotic actomyosin contractile ring localization" xsd:anyURI
is_obsolete: true
replaced_by: GO:1902408
created_by: vw
Expand Down
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