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Merge pull request #25669 from geneontology/issue-25659
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obsoleted term fixes #25659
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pgaudet authored Jul 4, 2023
2 parents a22b7e0 + d25f3f9 commit 80eec46
Showing 1 changed file with 45 additions and 32 deletions.
77 changes: 45 additions & 32 deletions src/ontology/go-edit.obo
Original file line number Diff line number Diff line change
Expand Up @@ -69358,16 +69358,19 @@ relationship: part_of GO:0007179 ! transforming growth factor beta receptor sign

[Term]
id: GO:0007182
name: common-partner SMAD protein phosphorylation
name: obsolete common-partner SMAD protein phosphorylation
namespace: biological_process
def: "The process of introducing a phosphate group on to a common-partner SMAD protein. A common partner SMAD protein binds to pathway-restricted SMAD proteins forming a complex that translocates to the nucleus." [GOC:dph, ISBN:3527303782]
subset: gocheck_do_not_annotate
def: "OBSOLETE. The process of introducing a phosphate group on to a common-partner SMAD protein. A common partner SMAD protein binds to pathway-restricted SMAD proteins forming a complex that translocates to the nucleus." [GOC:dph, ISBN:3527303782]
comment: This term was obsoleted because it represents a molecular function.
synonym: "co-SMAD protein phosphorylation" EXACT [GOC:rl]
synonym: "common mediator SMAD protein phosphorylation" EXACT []
synonym: "common partner SMAD protein phosphorylation" EXACT [GOC:rl]
synonym: "common-mediator SMAD protein phosphorylation" EXACT [GOC:rl]
is_a: GO:0006468 ! protein phosphorylation
relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25531" xsd:anyURI
is_obsolete: true
consider: GO:0004672
consider: GO:0060391
consider: GO:0060395

[Term]
id: GO:0007183
Expand Down Expand Up @@ -103804,12 +103807,14 @@ consider: GO:0061136

[Term]
id: GO:0010862
name: positive regulation of pathway-restricted SMAD protein phosphorylation
name: obsolete positive regulation of pathway-restricted SMAD protein phosphorylation
namespace: biological_process
def: "Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:dph, GOC:tb]
is_a: GO:0090100 ! positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0060389 ! pathway-restricted SMAD protein phosphorylation
def: "OBSOLETE. Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:dph, GOC:tb]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25531" xsd:anyURI
is_obsolete: true
consider: GO:0030295
consider: GO:0060391

[Term]
id: GO:0010863
Expand Down Expand Up @@ -147614,8 +147619,7 @@ comment: This term was made obsolete because it did not adequately describe phos
synonym: "inositol phospholipid-mediated signaling" EXACT []
synonym: "inositol phospholipid-mediated signalling" EXACT []
is_obsolete: true
consider: GO:0048016
consider: GO:0048017
consider: GO:0035556

[Term]
id: GO:0019937
Expand Down Expand Up @@ -295562,7 +295566,7 @@ synonym: "phosphatidylinositol-mediated signal transduction" EXACT [GOC:signalin
synonym: "phosphatidylinositol-mediated signalling" EXACT []
synonym: "phosphoinositide-mediated signaling" EXACT []
synonym: "phosphoinositide-mediated signalling" EXACT []
is_a: GO:0048017 ! inositol lipid-mediated signaling
is_a: GO:0035556 ! intracellular signal transduction

[Term]
id: GO:0048016
Expand All @@ -295574,13 +295578,16 @@ is_a: GO:0019932 ! second-messenger-mediated signaling

[Term]
id: GO:0048017
name: inositol lipid-mediated signaling
name: obsolete inositol lipid-mediated signaling
namespace: biological_process
def: "The series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids." [GOC:bf, GOC:ceb, PMID:16088939]
def: "OBSOLETE. The series of molecular signals in which a cell uses an inositol-containing lipid to convert a signal into a response. Inositol lipids include the phosphoinositides (phosphatidylinositol and its phosphorylated derivatives), ceramides containing inositol, and inositol glycolipids." [GOC:bf, GOC:ceb, PMID:16088939]
comment: This term was obsoleted because it did not clearly define a signal transduction pathway.
synonym: "inositol lipid-mediated signal transduction" EXACT [GOC:signaling]
synonym: "inositol lipid-mediated signalling" EXACT []
synonym: "inositol phospholipid-mediated signaling" NARROW []
is_a: GO:0035556 ! intracellular signal transduction
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25659" xsd:anyURI
is_obsolete: true
consider: GO:0035556

[Term]
id: GO:0048018
Expand Down Expand Up @@ -342603,16 +342610,19 @@ is_a: GO:0035805 ! egg coat

[Term]
id: GO:0060389
name: pathway-restricted SMAD protein phosphorylation
name: obsolete pathway-restricted SMAD protein phosphorylation
namespace: biological_process
def: "The process of introducing a phosphate group on to a pathway restricted SMAD protein. A pathway restricted SMAD protein is an effector protein that acts directly downstream of the transforming growth factor family receptor." [GOC:dph, ISBN:3527303782]
subset: gocheck_do_not_annotate
def: "OBSOLETE. The process of introducing a phosphate group on to a pathway restricted SMAD protein. A pathway restricted SMAD protein is an effector protein that acts directly downstream of the transforming growth factor family receptor." [GOC:dph, ISBN:3527303782]
comment: This term was obsoleted because it represents a molecular function.
synonym: "pathway restricted SMAD protein phosphorylation" EXACT [GOC:rl]
synonym: "R-SMAD protein phosphorylation" EXACT [GOC:rl]
synonym: "receptor regulated SMAD protein phosphorylation" EXACT [GOC:rl]
synonym: "receptor-regulated SMAD protein phosphorylation" EXACT [GOC:rl]
is_a: GO:0006468 ! protein phosphorylation
relationship: part_of GO:0007178 ! transmembrane receptor protein serine/threonine kinase signaling pathway
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25531" xsd:anyURI
is_obsolete: true
consider: GO:0004672
consider: GO:0060391
consider: GO:0060395

[Term]
id: GO:0060390
Expand Down Expand Up @@ -342649,21 +342659,25 @@ relationship: negatively_regulates GO:0007178 {http://purl.obolibrary.org/obo/IA

[Term]
id: GO:0060393
name: regulation of pathway-restricted SMAD protein phosphorylation
name: obsolete regulation of pathway-restricted SMAD protein phosphorylation
namespace: biological_process
def: "Any process that modulates the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:BHF, GOC:dph, GOC:tb]
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0060389 ! pathway-restricted SMAD protein phosphorylation
relationship: regulates GO:0060389 ! pathway-restricted SMAD protein phosphorylation
def: "OBSOLETE. Any process that modulates the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:BHF, GOC:dph, GOC:tb]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25531" xsd:anyURI
is_obsolete: true
consider: GO:0019887
consider: GO:0060390

[Term]
id: GO:0060394
name: negative regulation of pathway-restricted SMAD protein phosphorylation
name: obsolete negative regulation of pathway-restricted SMAD protein phosphorylation
namespace: biological_process
def: "Any process that decreases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:BHF, GOC:dph, GOC:tb]
is_a: GO:0090101 ! negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0060389 ! pathway-restricted SMAD protein phosphorylation
def: "OBSOLETE. Any process that decreases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways." [GOC:BHF, GOC:dph, GOC:tb]
comment: This term was obsoleted because it represents a molecular function.
property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/25531" xsd:anyURI
is_obsolete: true
consider: GO:0004860
consider: GO:0060392

[Term]
id: GO:0060395
Expand Down Expand Up @@ -422364,7 +422378,6 @@ synonym: "TGFbeta dimer" EXACT []
is_a: GO:0032991 ! protein-containing complex
relationship: capable_of GO:0005160 ! transforming growth factor beta receptor binding
relationship: capable_of_part_of GO:0007179 ! transforming growth factor beta receptor signaling pathway
relationship: capable_of_part_of GO:0010862 ! positive regulation of pathway-restricted SMAD protein phosphorylation
relationship: part_of GO:0062023 ! collagen-containing extracellular matrix

[Term]
Expand Down

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