From 4c17ef199c7011b1f339cadb4ea76f99b982ce9c Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Thu, 12 Dec 2024 16:51:26 -0800 Subject: [PATCH] automated commit replacing obsolete ontology terms --- models/5993df9e00000138.ttl | 12 ++++++----- models/5e72450500004019.ttl | 13 ++++++------ models/5fadbcf000000208.ttl | 11 +++++----- models/61f34dd300001044.ttl | 18 ++++++++--------- models/627d95ee00001405.ttl | 11 +++++----- models/62900b6400002447.ttl | 21 +++++++++---------- models/62b4ffe300003074.ttl | 13 ++++++------ models/62b4ffe300003321.ttl | 13 ++++++------ models/62e3212700001602.ttl | 13 ++++++------ models/62f58d8800006929.ttl | 11 +++++----- models/632cf60a00000169.ttl | 13 ++++++------ models/635b1e3e00002003.ttl | 23 +++++++++++---------- models/657ba49f00001866.ttl | 10 ++++++---- models/65a1f4f800000617.ttl | 12 ++++++----- models/65bc474400000671.ttl | 11 +++++----- models/6606056e00002524.ttl | 13 ++++++------ models/662af8fa00000838.ttl | 31 +++++++++++++++++------------ models/663d668500002302.ttl | 13 ++++++------ models/MGI_MGI_104556.ttl | 12 ++++++----- models/MGI_MGI_105380.ttl | 10 +++++----- models/MGI_MGI_108027.ttl | 11 ++++++---- models/MGI_MGI_109337.ttl | 13 ++++++------ models/MGI_MGI_1355321.ttl | 10 +++++++--- models/MGI_MGI_1890471.ttl | 10 +++++++--- models/MGI_MGI_1924378.ttl | 10 +++++++--- models/MGI_MGI_2676556.ttl | 10 +++++++--- models/MGI_MGI_95824.ttl | 10 +++++++--- models/MGI_MGI_98834.ttl | 17 ++++++++-------- models/R-HSA-1482801.ttl | 13 ++++++------ models/R-HSA-6791312.ttl | 12 +++++------ models/R-HSA-69563.ttl | 14 ++++++------- models/SGD_S000000065.ttl | 10 +++++++--- models/SGD_S000000406.ttl | 10 +++++++--- models/SGD_S000003081.ttl | 10 +++++++--- models/SGD_S000003169.ttl | 10 +++++++--- models/SGD_S000003220.ttl | 10 +++++++--- models/SGD_S000003709.ttl | 10 +++++++--- models/SGD_S000004526.ttl | 10 +++++++--- models/SGD_S000004802.ttl | 10 +++++++--- models/SGD_S000005256.ttl | 10 +++++++--- models/SGD_S000006223.ttl | 10 +++++++--- models/ZFIN_ZDB-GENE-990415-270.ttl | 11 ++++++---- 42 files changed, 309 insertions(+), 216 deletions(-) diff --git a/models/5993df9e00000138.ttl b/models/5993df9e00000138.ttl index 3912df469f6b..416427e9fc86 100644 --- a/models/5993df9e00000138.ttl +++ b/models/5993df9e00000138.ttl @@ -51,9 +51,10 @@ ; "gomodel:5993df9e00000138"^^ ; a ; + "Automated change 2024-12-12: GO:0033207 replaced by GO:0033842" ; "The directed migration of gonadal distal tip cells in Caenorhabditis elegans requires NGAT-1, a ß1,4-N-acetylgalactosaminyltransferase enzyme"^^ ; "https://orcid.org/0000-0002-1706-4196"^^ ; - "2017-08-20"^^ . + "2024-12-12"^^ . a , ; "https://orcid.org/0000-0002-1706-4196"^^ ; @@ -64,9 +65,10 @@ ; ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0033207 replaced by GO:0033842" ; "https://orcid.org/0000-0002-1706-4196"^^ ; - "2017-08-20"^^ . + "2024-12-12"^^ . "197"^^ ; "138"^^ ; @@ -108,10 +110,10 @@ "2017-08-20"^^ ; "PMID:28817611"^^ . - a . - a . + a . + a . a . diff --git a/models/5e72450500004019.ttl b/models/5e72450500004019.ttl index 6e30a859f992..66060f6ab185 100644 --- a/models/5e72450500004019.ttl +++ b/models/5e72450500004019.ttl @@ -91,8 +91,6 @@ a . - a . - a . a . @@ -131,6 +129,8 @@ a . + a . + a . a . @@ -162,11 +162,11 @@ ; , , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; """SARS-COV2/HOST """^^ ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . "579"^^ ; "47"^^ ; @@ -475,9 +475,10 @@ "1837"^^ ; "12"^^ ; "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2021-04-27"^^ . + "2024-12-12"^^ . "260"^^ ; "355"^^ ; diff --git a/models/5fadbcf000000208.ttl b/models/5fadbcf000000208.ttl index 109d6275287c..355f2ca56856 100644 --- a/models/5fadbcf000000208.ttl +++ b/models/5fadbcf000000208.ttl @@ -51,7 +51,7 @@ a . - a . + a . a . @@ -63,10 +63,10 @@ "http://greekc.org"^^ ; ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002407" , "Automated change 2022-04-14: replaced_by " , "Automated change 2022-04-14: replaced_by " ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002407" , "Automated change 2022-04-14: replaced_by " , "Automated change 2022-04-14: replaced_by " , "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "TP53 DNA-binding transcription factor"^^ ; "https://orcid.org/0000-0002-8534-6582"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . "271.875"^^ ; "381.25"^^ ; @@ -89,9 +89,10 @@ "75"^^ ; "http://greekc.org"^^ ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "https://orcid.org/0000-0002-8534-6582"^^ ; - "2022-05-24"^^ . + "2024-12-12"^^ . "http://greekc.org"^^ ; a , ; diff --git a/models/61f34dd300001044.ttl b/models/61f34dd300001044.ttl index afe675593874..207f35ba8d3e 100644 --- a/models/61f34dd300001044.ttl +++ b/models/61f34dd300001044.ttl @@ -163,10 +163,10 @@ "https://www.uniprot.org"^^ , "http://www.wormbase.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2024-09-26: GO:0047012 replaced by GO:0102191" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2024-09-26: GO:0047012 replaced by GO:0102191" , "Automated change 2024-12-12: GO:0102191 replaced by GO:0102175" ; "Yeast ergosterol"^^ ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0002-4187-2863"^^ ; - "2024-09-26"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -864,10 +864,10 @@ ; ; ; - a , ; - "Automated change 2024-09-26: GO:0047012 replaced by GO:0102191" ; + a , ; + "Automated change 2024-09-26: GO:0047012 replaced by GO:0102191" , "Automated change 2024-12-12: GO:0102191 replaced by GO:0102175" ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0002-4187-2863"^^ ; - "2024-09-26"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -1119,10 +1119,10 @@ ; ; ; - a , ; - "Automated change 2024-09-26: GO:0047012 replaced by GO:0102191" ; + a , ; + "Automated change 2024-09-26: GO:0047012 replaced by GO:0102191" , "Automated change 2024-12-12: GO:0102191 replaced by GO:0102175" ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0002-4187-2863"^^ ; - "2024-09-26"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -1924,7 +1924,7 @@ a . - a . + a . a . diff --git a/models/627d95ee00001405.ttl b/models/627d95ee00001405.ttl index f6e46d1cd69c..481d257c4f4f 100644 --- a/models/627d95ee00001405.ttl +++ b/models/627d95ee00001405.ttl @@ -57,10 +57,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2022-09-22: GO:0005887 replaced by GO:0005886" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2022-09-22: GO:0005887 replaced by GO:0005886" , "Automated change 2024-12-12: GO:0019049 replaced by GO:0052031" ; "Il17A mediated signaling pathway (Human)"^^ ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2023-11-02"^^ . + "2024-12-12"^^ . a . @@ -183,9 +183,10 @@ "17"^^ ; "390.9999694824219"^^ ; "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0019049 replaced by GO:0052031" ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2022-05-24"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -498,7 +499,7 @@ a . - a . + a . a . diff --git a/models/62900b6400002447.ttl b/models/62900b6400002447.ttl index df5b6d97f818..db91f29e6e53 100644 --- a/models/62900b6400002447.ttl +++ b/models/62900b6400002447.ttl @@ -81,8 +81,6 @@ a . - a . - a . a . @@ -159,10 +157,10 @@ "https://www.uniprot.org"^^ , "http://www.wormbase.org"^^ ; ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "Replisome (Human)"^^ ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0001-8769-177X"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . "1115"^^ ; "482.25001525878906"^^ ; @@ -217,9 +215,10 @@ "75"^^ ; "https://www.uniprot.org"^^ , "http://www.wormbase.org"^^ ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0001-8769-177X"^^ ; - "2022-06-29"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -265,9 +264,10 @@ "862.5"^^ ; "75"^^ ; "https://www.uniprot.org"^^ , "http://www.wormbase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0001-8769-177X"^^ ; - "2022-06-29"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -318,9 +318,10 @@ "468.75"^^ ; "75"^^ ; "https://www.uniprot.org"^^ , "http://www.wormbase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0002-1706-4196"^^ , "https://orcid.org/0000-0001-8769-177X"^^ ; - "2022-06-29"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; diff --git a/models/62b4ffe300003074.ttl b/models/62b4ffe300003074.ttl index 5e3249ab47d2..54a5a372846c 100644 --- a/models/62b4ffe300003074.ttl +++ b/models/62b4ffe300003074.ttl @@ -47,8 +47,6 @@ a . - a . - a . a . @@ -57,6 +55,8 @@ a . + a . + a . a . @@ -65,10 +65,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "Poxvirus-OPG029 inhibition of host TBK1 adaptor TANK (Human-Poxvirus) "^^ ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . "1256.25"^^ ; "381.25"^^ ; @@ -148,9 +148,10 @@ "862.5"^^ ; "75"^^ ; "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2022-10-12"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; diff --git a/models/62b4ffe300003321.ttl b/models/62b4ffe300003321.ttl index 1b12c02545cc..cd0659106a78 100644 --- a/models/62b4ffe300003321.ttl +++ b/models/62b4ffe300003321.ttl @@ -51,8 +51,6 @@ a . - a . - a . a . @@ -69,6 +67,8 @@ a . + a . + a . a . @@ -77,10 +77,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "Poxvirus-OPG062 inhibition of host mTOR/cGAS signaling (Human-Poxvirus) "^^ ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2024-11-14"^^ . + "2024-12-12"^^ . "301"^^ ; "304.25"^^ ; @@ -102,9 +102,10 @@ "83"^^ ; "52"^^ ; "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2022-07-05"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; diff --git a/models/62e3212700001602.ttl b/models/62e3212700001602.ttl index e55e70ee8356..41538a11c7d4 100644 --- a/models/62e3212700001602.ttl +++ b/models/62e3212700001602.ttl @@ -47,8 +47,6 @@ a . - a . - a . a . @@ -61,6 +59,8 @@ a . + a . + a . a . @@ -71,10 +71,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "FMDV-3A inhibition of host IRF3 via DDX56 (Human-Aphthovirus) "^^ ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . ; "https://www.uniprot.org"^^ ; @@ -146,9 +146,10 @@ "2022-08-10"^^ . "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2022-08-10"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; diff --git a/models/62f58d8800006929.ttl b/models/62f58d8800006929.ttl index ecd4a5eb313c..d1859df1dd91 100644 --- a/models/62f58d8800006929.ttl +++ b/models/62f58d8800006929.ttl @@ -75,16 +75,14 @@ a . - a . - "production"^^ ; "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-02-01: GO:0039503 replaced by GO:0052170" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-02-01: GO:0039503 replaced by GO:0052170" , "Automated change 2024-12-12: GO:0075528 replaced by GO:0052170" ; "Cleavage of NLRP1and GSDMD by SARS-CoV-2 protease Nsp5, leading to inhibition of GSDMD-mediated pyroptosis and concomitant initiation of GSDME-mediated pyroptosis in lung epithelial cells (Human and SARS-CoV-2)"^^ ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2024-02-01"^^ . + "2024-12-12"^^ . ; "https://www.uniprot.org"^^ ; @@ -102,9 +100,10 @@ "2022-09-15"^^ . "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0075528 replaced by GO:0052170" ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2022-09-15"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; ; diff --git a/models/632cf60a00000169.ttl b/models/632cf60a00000169.ttl index 97db456185f5..be2d9fb0d692 100644 --- a/models/632cf60a00000169.ttl +++ b/models/632cf60a00000169.ttl @@ -57,10 +57,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "HHV1-ICP0 modulation of interferon production via MORC3 degradation (Human-Herpesvirus) "^^ ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . ; "https://www.uniprot.org"^^ ; @@ -186,9 +186,10 @@ "2022-09-27"^^ . "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0039501 replaced by GO:0039502" ; "https://orcid.org/0000-0001-7646-0052"^^ ; - "2022-09-27"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -309,10 +310,10 @@ a . - a . - a . + a . + a . a . diff --git a/models/635b1e3e00002003.ttl b/models/635b1e3e00002003.ttl index 02a1f5a7669e..690deb5514c8 100644 --- a/models/635b1e3e00002003.ttl +++ b/models/635b1e3e00002003.ttl @@ -59,10 +59,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" ; + "Automated change 2023-03-16: RO:0002213 replaced by RO:0002629" , "Automated change 2023-03-16: RO:0002212 replaced by RO:0002630" , "Automated change 2024-12-12: GO:0034054 replaced by GO:0052041" ; "Inhibition of GSDMD-mediated pyroptosis by M.tuberculosis PtpB phosphatase that alters membrane phospholipid composition (Human and M.tuberculosis)"^^ ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2023-03-16"^^ . + "2024-12-12"^^ . ; "https://www.uniprot.org"^^ ; @@ -80,9 +80,10 @@ "https://www.uniprot.org"^^ ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0034054 replaced by GO:0052041" ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2022-11-09"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -135,9 +136,10 @@ "https://www.uniprot.org"^^ ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0034054 replaced by GO:0052041" ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2022-11-09"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -200,9 +202,10 @@ "https://www.uniprot.org"^^ ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0034054 replaced by GO:0052041" ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2022-11-09"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -454,14 +457,14 @@ a . - a . - a . a . a . + a . + a . a . diff --git a/models/657ba49f00001866.ttl b/models/657ba49f00001866.ttl index 799df50f9133..01a57cd35349 100644 --- a/models/657ba49f00001866.ttl +++ b/models/657ba49f00001866.ttl @@ -27,9 +27,10 @@ "http://www.yeastgenome.org"^^ ; ; a ; + "Automated change 2024-12-12: GO:1902971 replaced by GO:1902969" ; "MCM10 regulates origin unwinding"^^ ; "https://orcid.org/0000-0002-3726-7441"^^ ; - "2024-01-11"^^ . + "2024-12-12"^^ . "75"^^ ; "381.25"^^ ; @@ -48,9 +49,10 @@ "75"^^ ; "75"^^ ; "http://www.yeastgenome.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:1902971 replaced by GO:1902969" ; "https://orcid.org/0000-0002-3726-7441"^^ ; - "2024-01-11"^^ . + "2024-12-12"^^ . "http://www.yeastgenome.org"^^ ; a , ; @@ -64,7 +66,7 @@ "2024-01-10"^^ ; "PMID:38109526"^^ . - a . + a . a . diff --git a/models/65a1f4f800000617.ttl b/models/65a1f4f800000617.ttl index ae66c9855225..f236f387208b 100644 --- a/models/65a1f4f800000617.ttl +++ b/models/65a1f4f800000617.ttl @@ -96,9 +96,10 @@ ; ; a ; + "Automated change 2024-12-12: GO:0046538 replaced by GO:0004619" ; "Canonical glycolysis (Dmel)"^^ ; "https://orcid.org/0000-0002-3358-4423"^^ , "https://orcid.org/0000-0003-2759-266X"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . a . @@ -118,10 +119,10 @@ a . - a . - a . + a . + a . a . @@ -491,9 +492,10 @@ ; ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0046538 replaced by GO:0004619" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; a , ; diff --git a/models/65bc474400000671.ttl b/models/65bc474400000671.ttl index c1c0c72ba904..e859aa425e19 100644 --- a/models/65bc474400000671.ttl +++ b/models/65bc474400000671.ttl @@ -132,10 +132,10 @@ ; ; a ; - "Copy the glycolysis pathway"^^ ; + "Copy the glycolysis pathway"^^ , "Automated change 2024-12-12: GO:0046538 replaced by GO:0004619" ; "Gluconeogenesis (from pyruvate to glucose 6-phosphate) (Dmel)"^^ ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . ; "http://flybase.org"^^ ; @@ -308,9 +308,10 @@ ; ; ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0046538 replaced by GO:0004619" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; a , ; @@ -1024,7 +1025,7 @@ a . - a . + a . a . diff --git a/models/6606056e00002524.ttl b/models/6606056e00002524.ttl index 965c945a5a7f..c43af0cdedfd 100644 --- a/models/6606056e00002524.ttl +++ b/models/6606056e00002524.ttl @@ -35,6 +35,8 @@ a . + a . + a . a . @@ -59,10 +61,10 @@ "https://www.uniprot.org"^^ ; , ; a ; - "Automated change 2024-05-09: GO:0047844 replaced by GO:0004126"^^ ; + "Automated change 2024-05-09: GO:0047844 replaced by GO:0004126"^^ , "Automated change 2024-12-12: GO:0075528 replaced by GO:0052170" ; "HIV-1 Vif protein hijacks a cullin-5-RING E3 ubiquitin-protein ligase to mediate ubiquitination and degradation of APOBEC3G (Human)."^^ ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2024-05-16"^^ . + "2024-12-12"^^ . ; "https://www.uniprot.org"^^ ; @@ -86,9 +88,10 @@ "2024-04-11"^^ . "https://www.uniprot.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0075528 replaced by GO:0052170" ; "https://orcid.org/0000-0001-7299-6685"^^ ; - "2024-04-11"^^ . + "2024-12-12"^^ . "https://www.uniprot.org"^^ ; a , ; @@ -386,8 +389,6 @@ a . - a . - a . a . diff --git a/models/662af8fa00000838.ttl b/models/662af8fa00000838.ttl index 4f81ad173957..b5ba45edd762 100644 --- a/models/662af8fa00000838.ttl +++ b/models/662af8fa00000838.ttl @@ -92,10 +92,10 @@ ; ; a ; - "Replaced enzyme inhibitor activity with small molecule sensor activity "^^ ; + "Replaced enzyme inhibitor activity with small molecule sensor activity "^^ , "Automated change 2024-12-12: GO:0141199 replaced by GO:0061729" ; "GDP-mannose biosynthetic process from glucose (Dmel)"^^ ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; a , ; @@ -192,9 +192,10 @@ "2024-04-29"^^ . "http://flybase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0141199 replaced by GO:0061729" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; a , ; @@ -214,9 +215,10 @@ "FB:FBrf0033426 | PMID:109448"^^ . "http://flybase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0141199 replaced by GO:0061729" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . ; "http://flybase.org"^^ ; @@ -234,9 +236,10 @@ "2024-04-29"^^ . "http://flybase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0141199 replaced by GO:0061729" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; a , ; @@ -250,9 +253,10 @@ "FB:FBrf0033426 | PMID:109448"^^ . "http://flybase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0141199 replaced by GO:0061729" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; ; @@ -290,9 +294,10 @@ "2024-11-11"^^ . "http://flybase.org"^^ ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0141199 replaced by GO:0061729" ; "https://orcid.org/0000-0002-3358-4423"^^ ; - "2024-11-11"^^ . + "2024-12-12"^^ . "http://flybase.org"^^ ; a , ; @@ -342,7 +347,7 @@ a . - a . + a . a . diff --git a/models/663d668500002302.ttl b/models/663d668500002302.ttl index 363d5d39ab1f..afa65a3fc0c8 100644 --- a/models/663d668500002302.ttl +++ b/models/663d668500002302.ttl @@ -65,10 +65,10 @@ a . - a . - a . + a . + a . a . @@ -99,10 +99,10 @@ "http://www.pombase.org"^^ ; ; a ; - "To do, add other input chemicals and activities"^^ ; + "To do, add other input chemicals and activities"^^ , "Automated change 2024-12-12: GO:0046538 replaced by GO:0004619" ; "canonical glycolysis (GO:0061621)"^^ ; "https://orcid.org/0000-0001-6330-7526"^^ ; - "2024-06-18"^^ . + "2024-12-12"^^ . ; "http://www.pombase.org"^^ ; @@ -681,9 +681,10 @@ ; ; , ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0046538 replaced by GO:0004619" ; "https://orcid.org/0000-0001-6330-7526"^^ ; - "2024-05-25"^^ . + "2024-12-12"^^ . "http://www.pombase.org"^^ ; a , ; diff --git a/models/MGI_MGI_104556.ttl b/models/MGI_MGI_104556.ttl index 39867c1a5614..0889dfcdb5fe 100644 --- a/models/MGI_MGI_104556.ttl +++ b/models/MGI_MGI_104556.ttl @@ -97,12 +97,12 @@ a . - a . - a . a . + a . + a . a . @@ -136,9 +136,10 @@ "2003-08-21" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "Cdkn1a (MGI:MGI:104556)" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0002-9796-7693" , "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-7476-6306"^^ , "https://orcid.org/0000-0001-9990-8331" ; - "2023-09-08"^^ . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2011-01-20" ; @@ -575,9 +576,10 @@ "http://informatics.jax.org" ; "2016-06-02" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0002-9796-7693" ; - "2023-09-08"^^ . + "2024-12-12"^^ . "MGI:MGI:1933751" ; "http://informatics.jax.org" ; diff --git a/models/MGI_MGI_105380.ttl b/models/MGI_MGI_105380.ttl index c31791fcb52a..ee415fac3f16 100644 --- a/models/MGI_MGI_105380.ttl +++ b/models/MGI_MGI_105380.ttl @@ -52,9 +52,10 @@ "2002-02-22" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "Mcm2 (MGI:MGI:105380)" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0002-9796-7693" , "https://orcid.org/0000-0001-7476-6306" , "https://orcid.org/0000-0003-2689-5511"^^ ; - "2024-11-18"^^ . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2003-10-07" ; @@ -224,9 +225,10 @@ "http://informatics.jax.org" ; "2002-02-22" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0003-2689-5511" ; - "2002-02-22" . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2010-11-17" ; @@ -360,8 +362,6 @@ a . - a . - a . a . diff --git a/models/MGI_MGI_108027.ttl b/models/MGI_MGI_108027.ttl index 1eb209e41c30..ebbf9f2c8285 100644 --- a/models/MGI_MGI_108027.ttl +++ b/models/MGI_MGI_108027.ttl @@ -23,6 +23,8 @@ a . + a . + a . "production" ; @@ -32,10 +34,10 @@ "2006-02-09" ; "2022-03-28" ; a ; - "Automated change 2024-10-10: GO:0044242 replaced by GO:0016042" ; + "Automated change 2024-10-10: GO:0044242 replaced by GO:0016042" , "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" ; "Ptprv (MGI:MGI:108027)" ; "https://orcid.org/0000-0002-9796-7693" , "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-7476-6306" ; - "2024-10-10"^^ . + "2024-12-12"^^ . "MGI:MGI:3039948" ; "http://informatics.jax.org" ; @@ -505,9 +507,10 @@ ; "2006-02-09" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" ; "https://orcid.org/0000-0001-7476-6306" ; - "2006-02-09" . + "2024-12-12"^^ . ; ; diff --git a/models/MGI_MGI_109337.ttl b/models/MGI_MGI_109337.ttl index 525ca8113cbd..0d33d9a819ce 100644 --- a/models/MGI_MGI_109337.ttl +++ b/models/MGI_MGI_109337.ttl @@ -93,12 +93,12 @@ a . - a . - a . a . + a . + a . a . @@ -118,10 +118,10 @@ "2001-11-09" ; "2022-03-28" ; a ; - "Automated change 2022-12-15: GO:0008022 replaced by GO:0005515" ; + "Automated change 2022-12-15: GO:0008022 replaced by GO:0005515" , "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "Brca2 (MGI:MGI:109337)" ; "https://orcid.org/0000-0002-9796-7693" , "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-7476-6306" , "https://orcid.org/0000-0003-3394-9805"^^ ; - "2022-12-15"^^ . + "2024-12-12"^^ . "MGI:MGI:2653914" ; "http://informatics.jax.org" ; @@ -1540,9 +1540,10 @@ "http://informatics.jax.org" ; "2007-07-23" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-7476-6306" ; - "2022-12-01"^^ . + "2024-12-12"^^ . "MGI:MGI:1930615" ; "http://informatics.jax.org" ; diff --git a/models/MGI_MGI_1355321.ttl b/models/MGI_MGI_1355321.ttl index 6c8b298228df..6dd47e302186 100644 --- a/models/MGI_MGI_1355321.ttl +++ b/models/MGI_MGI_1355321.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://informatics.jax.org" ; ; @@ -26,9 +28,10 @@ "2007-03-14" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "Chek2 (MGI:MGI:1355321)" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0001-7476-6306" , "https://orcid.org/0000-0001-9990-8331" ; - "2016-06-02" . + "2024-12-12"^^ . ; ; @@ -423,9 +426,10 @@ "http://informatics.jax.org" ; "2016-06-02" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "https://orcid.org/0000-0003-3394-9805" ; - "2016-06-02" . + "2024-12-12"^^ . "UniProtKB:O96017" ; "http://informatics.jax.org" ; diff --git a/models/MGI_MGI_1890471.ttl b/models/MGI_MGI_1890471.ttl index 3965cfb1a2ae..43ff4c32e08e 100644 --- a/models/MGI_MGI_1890471.ttl +++ b/models/MGI_MGI_1890471.ttl @@ -17,6 +17,8 @@ a . + a . + "production" ; "http://informatics.jax.org" ; ; @@ -24,9 +26,10 @@ "2014-09-24" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:1902163 replaced by GO:0043518" ; "Pcbp4 (MGI:MGI:1890471)" ; "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-5501-853X" ; - "2016-03-04" . + "2024-12-12"^^ . ; ; @@ -163,9 +166,10 @@ "http://informatics.jax.org" ; "2016-03-04" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:1902163 replaced by GO:0043518" ; "https://orcid.org/0000-0003-2689-5511" ; - "2016-03-04" . + "2024-12-12"^^ . a . diff --git a/models/MGI_MGI_1924378.ttl b/models/MGI_MGI_1924378.ttl index 49b4c884d3a9..5683e63f2ec2 100644 --- a/models/MGI_MGI_1924378.ttl +++ b/models/MGI_MGI_1924378.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://informatics.jax.org" ; ; @@ -26,9 +28,10 @@ "2014-06-16" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:1900170 replaced by GO:2000323" ; "Crebrf (MGI:MGI:1924378)" ; "https://orcid.org/0000-0001-7476-6306" ; - "2014-06-16" . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2014-06-16" ; @@ -40,9 +43,10 @@ "http://informatics.jax.org" ; "2014-06-16" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:1900170 replaced by GO:2000323" ; "https://orcid.org/0000-0001-7476-6306" ; - "2014-06-16" . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2014-06-16" ; diff --git a/models/MGI_MGI_2676556.ttl b/models/MGI_MGI_2676556.ttl index cbb75b59b678..cf7fc2cb38b0 100644 --- a/models/MGI_MGI_2676556.ttl +++ b/models/MGI_MGI_2676556.ttl @@ -24,9 +24,10 @@ "2012-03-13" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:1900169 replaced by GO:2000322" ; "Akap13 (MGI:MGI:2676556)" ; "https://orcid.org/0000-0003-2689-5511" ; - "2012-03-13" . + "2024-12-12"^^ . ; ; @@ -40,9 +41,10 @@ "http://informatics.jax.org" ; "2012-03-13" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:1900169 replaced by GO:2000322" ; "https://orcid.org/0000-0003-2689-5511" ; - "2012-03-13" . + "2024-12-12"^^ . "MGI:MGI:5308769" ; "http://informatics.jax.org" ; @@ -67,6 +69,8 @@ "https://orcid.org/0000-0003-2689-5511" ; "2012-03-13" . + a . + a . a . diff --git a/models/MGI_MGI_95824.ttl b/models/MGI_MGI_95824.ttl index 4b612d69e4f1..67b95d8f2b86 100644 --- a/models/MGI_MGI_95824.ttl +++ b/models/MGI_MGI_95824.ttl @@ -27,6 +27,8 @@ a . + a . + "production" ; "http://informatics.jax.org" ; ; @@ -34,9 +36,10 @@ "2001-10-30" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:1900170 replaced by GO:2000323" ; "Nr3c1 (MGI:MGI:95824)" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0002-9796-7693" , "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-7476-6306" , "https://orcid.org/0000-0001-5501-853X" ; - "2019-07-17" . + "2024-12-12"^^ . "MGI:MGI:1857745" ; "http://informatics.jax.org" ; @@ -1092,9 +1095,10 @@ "http://informatics.jax.org" ; "2014-05-20" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:1900170 replaced by GO:2000323" ; "https://orcid.org/0000-0003-2689-5511" ; - "2014-05-20" . + "2024-12-12"^^ . "MGI:MGI:97762" ; "http://informatics.jax.org" ; diff --git a/models/MGI_MGI_98834.ttl b/models/MGI_MGI_98834.ttl index ddbb142171a8..c1cc326e0f97 100644 --- a/models/MGI_MGI_98834.ttl +++ b/models/MGI_MGI_98834.ttl @@ -223,8 +223,6 @@ a . - a . - a . a . @@ -264,9 +262,10 @@ "2002-07-26" ; "2022-03-28" ; a ; + "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" , "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "Trp53 (MGI:MGI:98834)" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0002-9796-7693" , "https://orcid.org/0000-0003-2689-5511" , "https://orcid.org/0000-0001-5501-853X" , "https://orcid.org/0000-0001-7476-6306"^^ , "https://orcid.org/0000-0001-9990-8331" , "https://orcid.org/0000-0002-1706-4196"^^ ; - "2023-10-27"^^ . + "2024-12-12"^^ . "6452.043572940123"^^ ; "2196.1940444673014"^^ ; @@ -5160,9 +5159,10 @@ ; "2010-07-06" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" ; "https://orcid.org/0000-0002-9796-7693" ; - "2023-10-23"^^ . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2004-03-19" ; @@ -8421,9 +8421,10 @@ "http://informatics.jax.org" ; "2016-06-02" ; "2022-03-28" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "https://orcid.org/0000-0003-3394-9805" , "https://orcid.org/0000-0002-9796-7693" ; - "2023-10-23"^^ . + "2024-12-12"^^ . "http://informatics.jax.org" ; "2006-02-09" ; @@ -9479,8 +9480,6 @@ a . - a . - a . a . diff --git a/models/R-HSA-1482801.ttl b/models/R-HSA-1482801.ttl index 5430e9ca4dca..7021e63a7af0 100644 --- a/models/R-HSA-1482801.ttl +++ b/models/R-HSA-1482801.ttl @@ -67,6 +67,8 @@ a . + a . + a . a . @@ -1403,10 +1405,10 @@ "https://reactome.org" ; ; a ; - "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" , "Imported from Reactome: https://reactome.org/content/detail/R-HSA-1482801" ; + "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" , "Imported from Reactome: https://reactome.org/content/detail/R-HSA-1482801" , "Automated change 2024-12-12: GO:0052739 replaced by GO:0008970" ; "Acyl chain remodelling of PS - imported from: Reactome" ; "GOC:reactome_curators" ; - "2023-06-21" . + "2024-12-12"^^ . "https://reactome.org" ; "R-HSA-1482801" ; @@ -1504,12 +1506,13 @@ , ; , ; "Reactome:R-HSA-8869425" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0052739 replaced by GO:0008970" ; "PLA1A hydrolyses PS to 2-acyl LPS" ; ; "org.biopax.paxtools.model.level3.BiochemicalReaction" ; "GOC:reactome_curators" ; - "2023-06-21" . + "2024-12-12"^^ . "https://reactome.org" ; a , ; @@ -1561,8 +1564,6 @@ "GOC:reactome_curators" ; "2023-06-21" . - a . - a . a . diff --git a/models/R-HSA-6791312.ttl b/models/R-HSA-6791312.ttl index 37431596ecd5..8aba44df9e34 100644 --- a/models/R-HSA-6791312.ttl +++ b/models/R-HSA-6791312.ttl @@ -11,26 +11,26 @@ a . - a . + a . "https://reactome.org" ; "R-HSA-6791312" ; ; - a , ; - "Under a variety of stress conditions, TP53 (p53), stabilized by stress-induced phosphorylation at least on S15 and S20 serine residues, can induce the transcription of genes involved in cell cycle arrest. Cell cycle arrest provides cells an opportunity to repair the damage before division, thus preventing the transmission of genetic errors to daughter cells. In addition, it allows cells to attempt a recovery from the damage and survive, preventing premature cell death.

TP53 controls transcription of genes involved in both G1 and G2 cell cycle arrest. The most prominent TP53 target involved in G1 arrest is the inhibitor of cyclin-dependent kinases CDKN1A (p21). CDKN1A is one of the earliest genes induced by TP53 (El-Deiry et al. 1993). CDKN1A binds and inactivates CDK2 in complex with cyclin A (CCNA) or E (CCNE), thus preventing G1/S transition (Harper et al. 1993). Nevertheless, under prolonged stress, the cell destiny may be diverted towards an apoptotic outcome. For instance, in case of an irreversible damage, TP53 can induce transcription of an RNA binding protein PCBP4, which can bind and destabilize CDKN1A mRNA, thus alleviating G1 arrest and directing the affected cell towards G2 arrest and, possibly, apoptosis (Zhu and Chen 2000, Scoumanne et al. 2011). Expression of E2F7 is directly induced by TP53. E2F7 contributes to G1 cell cycle arrest by repressing transcription of E2F1, a transcription factor that promotes expression of many genes needed for G1/S transition (Aksoy et al. 2012, Carvajal et al. 2012). ARID3A is a direct transcriptional target of TP53 (Ma et al. 2003) that may promote G1 arrest by cooperating with TP53 in induction of CDKN1A transcription (Lestari et al. 2012). However, ARID3A may also promote G1/S transition by stimulating transcriptional activity of E2F1 (Suzuki et al. 1998, Peeper et al. 2002).

TP53 contributes to the establishment of G2 arrest by inducing transcription of GADD45A and SFN, and by inhibiting transcription of CDC25C. TP53 induces GADD45A transcription in cooperation with chromatin modifying enzymes EP300, PRMT1 and CARM1 (An et al. 2004). GADD45A binds Aurora kinase A (AURKA), inhibiting its catalytic activity and preventing AURKA-mediated G2/M transition (Shao et al. 2006, Sanchez et al. 2010). GADD45A also forms a complex with PCNA. PCNA is involved in both normal and repair DNA synthesis. The effect of GADD45 interaction with PCNA, if any, on S phase progression, G2 arrest and DNA repair is not known (Smith et al. 1994, Hall et al. 1995, Sanchez et al. 2010, Kim et al. 2013). SFN (14-3-3-sigma) is induced by TP53 (Hermeking et al. 1997) and contributes to G2 arrest by binding to the complex of CDK1 and CCNB1 (cyclin B1) and preventing its translocation to the nucleus. Phosphorylation of a number of nuclear proteins by the complex of CDK1 and CCNB1 is needed for G2/M transition (Chan et al. 1999). While promoting G2 arrest, SFN can simultaneously inhibit apoptosis by binding to BAX and preventing its translocation to mitochondria, a step involved in cytochrome C release (Samuel et al. 2001). TP53 binds the promoter of the CDC25C gene in cooperation with the transcriptional repressor E2F4 and represses CDC25C transcription, thus maintaining G2 arrest (St Clair et al. 2004, Benson et al. 2014).

Several direct transcriptional targets of TP53 are involved in cell cycle arrest but their mechanism of action is still unknown. BTG2 is induced by TP53, leading to cessation of cellular proliferation (Rouault et al. 1996, Duriez et al. 2002). BTG2 binds to the CCR4-NOT complex and promotes mRNA deadenylation activity of this complex. Interaction between BTG2 and CCR4-NOT is needed for the antiproliferative activity of BTG2, but the underlying mechanism has not been elucidated (Rouault et al. 1998, Mauxion et al. 2008, Horiuchi et al. 2009, Doidge et al. 2012, Ezzeddine et al. 2012). Two polo-like kinases, PLK2 and PLK3, are direct transcriptional targets of TP53. TP53-mediated induction of PLK2 may be important for prevention of mitotic catastrophe after spindle damage (Burns et al. 2003). PLK2 is involved in the regulation of centrosome duplication through phosphorylation of centrosome-related proteins CENPJ (Chang et al. 2010) and NPM1 (Krause and Hoffmann 2010). PLK2 is frequently transcriptionally silenced through promoter methylation in B-cell malignancies (Syed et al. 2006). Induction of PLK3 transcription by TP53 (Jen and Cheung 2005) may be important for coordination of M phase events through PLK3-mediated nuclear accumulation of CDC25C (Bahassi et al. 2004). RGCC is induced by TP53 and implicated in cell cycle regulation, possibly through its association with PLK1 (Saigusa et al. 2007). PLAGL1 (ZAC1) is a zinc finger protein directly transcriptionally induced by TP53 (Rozenfeld-Granot et al. 2002). PLAGL1 expression is frequently lost in cancer (Varrault et al. 1998) and PLAGL1 has been implicated in both cell cycle arrest and apoptosis (Spengler et al. 1997), but its mechanism of action remains unknown.

The zinc finger transcription factor ZNF385A (HZF) is a direct transcriptional target of TP53 that can form a complex with TP53 and facilitate TP53-mediated induction of CDKN1A and SFN (14-3-3 sigma) transcription (Das et al. 2007).

For a review of the role of TP53 in cell cycle arrest and cell cycle transcriptional targets of TP53, please refer to Riley et al. 2008, Murray-Zmijewski et al. 2008, Bieging et al. 2014, Kruiswijk et al. 2015." ; + a , ; + "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" , "Under a variety of stress conditions, TP53 (p53), stabilized by stress-induced phosphorylation at least on S15 and S20 serine residues, can induce the transcription of genes involved in cell cycle arrest. Cell cycle arrest provides cells an opportunity to repair the damage before division, thus preventing the transmission of genetic errors to daughter cells. In addition, it allows cells to attempt a recovery from the damage and survive, preventing premature cell death.

TP53 controls transcription of genes involved in both G1 and G2 cell cycle arrest. The most prominent TP53 target involved in G1 arrest is the inhibitor of cyclin-dependent kinases CDKN1A (p21). CDKN1A is one of the earliest genes induced by TP53 (El-Deiry et al. 1993). CDKN1A binds and inactivates CDK2 in complex with cyclin A (CCNA) or E (CCNE), thus preventing G1/S transition (Harper et al. 1993). Nevertheless, under prolonged stress, the cell destiny may be diverted towards an apoptotic outcome. For instance, in case of an irreversible damage, TP53 can induce transcription of an RNA binding protein PCBP4, which can bind and destabilize CDKN1A mRNA, thus alleviating G1 arrest and directing the affected cell towards G2 arrest and, possibly, apoptosis (Zhu and Chen 2000, Scoumanne et al. 2011). Expression of E2F7 is directly induced by TP53. E2F7 contributes to G1 cell cycle arrest by repressing transcription of E2F1, a transcription factor that promotes expression of many genes needed for G1/S transition (Aksoy et al. 2012, Carvajal et al. 2012). ARID3A is a direct transcriptional target of TP53 (Ma et al. 2003) that may promote G1 arrest by cooperating with TP53 in induction of CDKN1A transcription (Lestari et al. 2012). However, ARID3A may also promote G1/S transition by stimulating transcriptional activity of E2F1 (Suzuki et al. 1998, Peeper et al. 2002).

TP53 contributes to the establishment of G2 arrest by inducing transcription of GADD45A and SFN, and by inhibiting transcription of CDC25C. TP53 induces GADD45A transcription in cooperation with chromatin modifying enzymes EP300, PRMT1 and CARM1 (An et al. 2004). GADD45A binds Aurora kinase A (AURKA), inhibiting its catalytic activity and preventing AURKA-mediated G2/M transition (Shao et al. 2006, Sanchez et al. 2010). GADD45A also forms a complex with PCNA. PCNA is involved in both normal and repair DNA synthesis. The effect of GADD45 interaction with PCNA, if any, on S phase progression, G2 arrest and DNA repair is not known (Smith et al. 1994, Hall et al. 1995, Sanchez et al. 2010, Kim et al. 2013). SFN (14-3-3-sigma) is induced by TP53 (Hermeking et al. 1997) and contributes to G2 arrest by binding to the complex of CDK1 and CCNB1 (cyclin B1) and preventing its translocation to the nucleus. Phosphorylation of a number of nuclear proteins by the complex of CDK1 and CCNB1 is needed for G2/M transition (Chan et al. 1999). While promoting G2 arrest, SFN can simultaneously inhibit apoptosis by binding to BAX and preventing its translocation to mitochondria, a step involved in cytochrome C release (Samuel et al. 2001). TP53 binds the promoter of the CDC25C gene in cooperation with the transcriptional repressor E2F4 and represses CDC25C transcription, thus maintaining G2 arrest (St Clair et al. 2004, Benson et al. 2014).

Several direct transcriptional targets of TP53 are involved in cell cycle arrest but their mechanism of action is still unknown. BTG2 is induced by TP53, leading to cessation of cellular proliferation (Rouault et al. 1996, Duriez et al. 2002). BTG2 binds to the CCR4-NOT complex and promotes mRNA deadenylation activity of this complex. Interaction between BTG2 and CCR4-NOT is needed for the antiproliferative activity of BTG2, but the underlying mechanism has not been elucidated (Rouault et al. 1998, Mauxion et al. 2008, Horiuchi et al. 2009, Doidge et al. 2012, Ezzeddine et al. 2012). Two polo-like kinases, PLK2 and PLK3, are direct transcriptional targets of TP53. TP53-mediated induction of PLK2 may be important for prevention of mitotic catastrophe after spindle damage (Burns et al. 2003). PLK2 is involved in the regulation of centrosome duplication through phosphorylation of centrosome-related proteins CENPJ (Chang et al. 2010) and NPM1 (Krause and Hoffmann 2010). PLK2 is frequently transcriptionally silenced through promoter methylation in B-cell malignancies (Syed et al. 2006). Induction of PLK3 transcription by TP53 (Jen and Cheung 2005) may be important for coordination of M phase events through PLK3-mediated nuclear accumulation of CDC25C (Bahassi et al. 2004). RGCC is induced by TP53 and implicated in cell cycle regulation, possibly through its association with PLK1 (Saigusa et al. 2007). PLAGL1 (ZAC1) is a zinc finger protein directly transcriptionally induced by TP53 (Rozenfeld-Granot et al. 2002). PLAGL1 expression is frequently lost in cancer (Varrault et al. 1998) and PLAGL1 has been implicated in both cell cycle arrest and apoptosis (Spengler et al. 1997), but its mechanism of action remains unknown.

The zinc finger transcription factor ZNF385A (HZF) is a direct transcriptional target of TP53 that can form a complex with TP53 and facilitate TP53-mediated induction of CDKN1A and SFN (14-3-3 sigma) transcription (Das et al. 2007).

For a review of the role of TP53 in cell cycle arrest and cell cycle transcriptional targets of TP53, please refer to Riley et al. 2008, Murray-Zmijewski et al. 2008, Bieging et al. 2014, Kruiswijk et al. 2015." ; "TP53 Regulates Transcription of Cell Cycle Genes" ; "org.biopax.paxtools.model.level3.Pathway" ; "GOC:reactome_curators" , "Authored: Orlic-Milacic, Marija, 2015-10-14" , "Edited: Orlic-Milacic, Marija, 2015-10-14" , "Reviewed: Inga, Alberto, 2016-02-04" , "Reviewed: Zaccara, Sara, 2016-02-04" ; - "2023-06-21" . + "2024-12-12"^^ . "development" ; "https://reactome.org" ; ; a ; - "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" , "Imported from Reactome: https://reactome.org/content/detail/R-HSA-6791312" ; + "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" , "Imported from Reactome: https://reactome.org/content/detail/R-HSA-6791312" , "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" ; "TP53 Regulates Transcription of Cell Cycle Genes - imported from: Reactome" ; "GOC:reactome_curators" ; - "2023-06-21" . + "2024-12-12"^^ . a . diff --git a/models/R-HSA-69563.ttl b/models/R-HSA-69563.ttl index f76eb458a12d..ceca9833a506 100644 --- a/models/R-HSA-69563.ttl +++ b/models/R-HSA-69563.ttl @@ -847,20 +847,20 @@ "https://reactome.org" ; ; a ; - "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" , "Imported from Reactome: https://reactome.org/content/detail/R-HSA-69563" ; + "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" , "Imported from Reactome: https://reactome.org/content/detail/R-HSA-69563" , "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" ; "p53-Dependent G1 DNA Damage Response - imported from: Reactome" ; "GOC:reactome_curators" ; - "2023-06-21" . + "2024-12-12"^^ . "https://reactome.org" ; "R-HSA-69563" ; ; - a , ; - "Most of the damage-induced modifications of p53 are dependent on the ATM kinase. The first link between ATM and p53 was predicted based on the earlier studies that showed that AT cells exhibit a reduced and delayed induction of p53 following exposure to IR (Kastan et al, 1992 and Khanna and Lavin, 1993).

Under normal conditions, p53 is a short-lived protein. The MDM2 protein, usually interacts with p53 (Haupt et al, 1997 and Kubbutat et al, 1997), and by virtue of its E3 ubiquitin ligase activity, shuttles p53 to the cytoplasm and mediates its degradation by the ubiquitin-proteasome machinery. Upon detection of DNA damage, the ATM kinase mediates the phosphorylation of the Mdm2 protein to block its interaction with p53. Also, phosphorylation of p53 at multiple loci, by the ATM kinase and by other kinases activated by the ATM kinase, stabilizes and activates the p53 protein.

The p53 protein activates the transcription of cyclin-dependent kinase inhibitor, p21. p21 inactivates the CyclinE:Cdk2 complexes, and prevent entry of the cell into S phase, leading to G1 arrest. Under severe conditions, the cell may undergo apoptosis." ; + a , ; + "Automated change 2024-12-12: GO:0006977 replaced by GO:0030330" , "Most of the damage-induced modifications of p53 are dependent on the ATM kinase. The first link between ATM and p53 was predicted based on the earlier studies that showed that AT cells exhibit a reduced and delayed induction of p53 following exposure to IR (Kastan et al, 1992 and Khanna and Lavin, 1993).

Under normal conditions, p53 is a short-lived protein. The MDM2 protein, usually interacts with p53 (Haupt et al, 1997 and Kubbutat et al, 1997), and by virtue of its E3 ubiquitin ligase activity, shuttles p53 to the cytoplasm and mediates its degradation by the ubiquitin-proteasome machinery. Upon detection of DNA damage, the ATM kinase mediates the phosphorylation of the Mdm2 protein to block its interaction with p53. Also, phosphorylation of p53 at multiple loci, by the ATM kinase and by other kinases activated by the ATM kinase, stabilizes and activates the p53 protein.

The p53 protein activates the transcription of cyclin-dependent kinase inhibitor, p21. p21 inactivates the CyclinE:Cdk2 complexes, and prevent entry of the cell into S phase, leading to G1 arrest. Under severe conditions, the cell may undergo apoptosis." ; "p53-Dependent G1 DNA Damage Response" ; "org.biopax.paxtools.model.level3.Pathway" ; "GOC:reactome_curators" , "Reviewed: Manfredi, James J" ; - "2023-06-21" . + "2024-12-12"^^ . "https://reactome.org" ; a , ; @@ -882,8 +882,6 @@ "GOC:reactome_curators" ; "2023-06-21" . - a . - a . a . @@ -920,6 +918,8 @@ a . + a . + a . a . diff --git a/models/SGD_S000000065.ttl b/models/SGD_S000000065.ttl index cbb29a88ce08..3965120af314 100644 --- a/models/SGD_S000000065.ttl +++ b/models/SGD_S000000065.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "RFA1 (SGD:S000000065)" ; "https://orcid.org/0000-0002-3726-7441" , "GOC:Julie_Park" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0003-3166-4638" ; - "2022-04-20" . + "2024-12-12"^^ . ; "http://www.yeastgenome.org" ; @@ -759,9 +762,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "GOC:Julie_Park" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; diff --git a/models/SGD_S000000406.ttl b/models/SGD_S000000406.ttl index 9e9803bfa9c4..e3833339ae10 100644 --- a/models/SGD_S000000406.ttl +++ b/models/SGD_S000000406.ttl @@ -21,6 +21,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -28,9 +30,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "MCM7 (SGD:S000000406)" ; "https://orcid.org/0000-0002-3726-7441" , "https://orcid.org/0000-0002-8379-6600" , "GOC:Julie_Park" , "https://orcid.org/0000-0001-8850-9925" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0001-9043-693X" , "https://orcid.org/0000-0002-7301-8055" , "https://orcid.org/0000-0003-3166-4638" ; - "2022-04-20" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; @@ -747,9 +750,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0001-5472-917X" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; diff --git a/models/SGD_S000003081.ttl b/models/SGD_S000003081.ttl index a8afc61b01ea..364d0cbdd1cc 100644 --- a/models/SGD_S000003081.ttl +++ b/models/SGD_S000003081.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "SLD3 (SGD:S000003081)" ; "https://orcid.org/0000-0002-3726-7441" , "https://orcid.org/0000-0001-8850-9925" , "https://orcid.org/0000-0002-7010-0264" , "https://orcid.org/0000-0003-3166-4638" ; - "2020-10-23" . + "2024-12-12"^^ . ; "http://www.yeastgenome.org" ; @@ -233,9 +236,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0002-7010-0264" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; ; diff --git a/models/SGD_S000003169.ttl b/models/SGD_S000003169.ttl index 873dfc8fdcce..7fc9c0c4a75d 100644 --- a/models/SGD_S000003169.ttl +++ b/models/SGD_S000003169.ttl @@ -21,6 +21,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -28,9 +30,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "MCM6 (SGD:S000003169)" ; "https://orcid.org/0000-0002-3726-7441" , "https://orcid.org/0000-0002-8379-6600" , "https://orcid.org/0000-0001-8850-9925" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0001-9043-693X" , "https://orcid.org/0000-0002-7301-8055" ; - "2022-04-20" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; @@ -399,9 +402,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0001-5472-917X" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; diff --git a/models/SGD_S000003220.ttl b/models/SGD_S000003220.ttl index 094edf444bc9..99e7999e79b9 100644 --- a/models/SGD_S000003220.ttl +++ b/models/SGD_S000003220.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "HFM1 (SGD:S000003220)" ; "https://orcid.org/0000-0002-1775-4998" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0001-9043-693X" ; - "2022-04-20" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2022-04-20" ; @@ -181,9 +184,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0001-9043-693X" ; - "2013-08-07" . + "2024-12-12"^^ . ; "http://www.yeastgenome.org" ; diff --git a/models/SGD_S000003709.ttl b/models/SGD_S000003709.ttl index 382ea7ae572c..66ef8d0f78a9 100644 --- a/models/SGD_S000003709.ttl +++ b/models/SGD_S000003709.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "RFA3 (SGD:S000003709)" ; "GOC:Julie_Park" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0003-3166-4638" ; - "2014-02-12" . + "2024-12-12"^^ . "SGD:S000000065" ; "http://www.yeastgenome.org" ; @@ -646,9 +649,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "GOC:Julie_Park" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; diff --git a/models/SGD_S000004526.ttl b/models/SGD_S000004526.ttl index e68d503246f6..b8ba4b549a26 100644 --- a/models/SGD_S000004526.ttl +++ b/models/SGD_S000004526.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "PIF1 (SGD:S000004526)" ; "https://orcid.org/0000-0002-3726-7441" , "GOC:Julie_Park" , "https://orcid.org/0000-0002-1775-4998" , "https://orcid.org/0000-0002-7010-0264" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0001-9043-693X" , "https://orcid.org/0000-0003-2468-9933" , "https://orcid.org/0000-0003-3166-4638" , "https://orcid.org/0000-0003-2678-2824" ; - "2019-12-19" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-10-11" ; @@ -107,9 +110,10 @@ "http://www.yeastgenome.org" ; "2019-12-19" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0003-2678-2824" ; - "2019-12-19" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2014-04-04" ; diff --git a/models/SGD_S000004802.ttl b/models/SGD_S000004802.ttl index 0b8068620acd..0ac950882a59 100644 --- a/models/SGD_S000004802.ttl +++ b/models/SGD_S000004802.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "SGS1 (SGD:S000004802)" ; "https://orcid.org/0000-0002-3726-7441" , "GOC:Julie_Park" , "https://orcid.org/0000-0001-8850-9925" , "https://orcid.org/0000-0002-1775-4998" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0001-5501-853X" , "https://orcid.org/0000-0001-9043-693X" , "https://orcid.org/0000-0001-6749-615X" , "https://orcid.org/0000-0003-3166-4638" ; - "2022-04-20" . + "2024-12-12"^^ . ; "http://www.yeastgenome.org" ; @@ -211,9 +214,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0001-9043-693X" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; diff --git a/models/SGD_S000005256.ttl b/models/SGD_S000005256.ttl index eecd8702843a..965875c04076 100644 --- a/models/SGD_S000005256.ttl +++ b/models/SGD_S000005256.ttl @@ -19,6 +19,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -26,9 +28,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "RFA2 (SGD:S000005256)" ; "GOC:Julie_Park" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0003-3166-4638" ; - "2014-02-12" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-08-07" ; @@ -316,9 +319,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "GOC:Julie_Park" ; - "2013-08-07" . + "2024-12-12"^^ . ; "http://www.yeastgenome.org" ; diff --git a/models/SGD_S000006223.ttl b/models/SGD_S000006223.ttl index b87baba332d2..d5bb136011c6 100644 --- a/models/SGD_S000006223.ttl +++ b/models/SGD_S000006223.ttl @@ -21,6 +21,8 @@ a . + a . + "production" ; "http://www.yeastgenome.org" ; ; @@ -28,9 +30,10 @@ "2013-08-07" ; "2024-02-01" ; a ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "MCM4 (SGD:S000006223)" ; "https://orcid.org/0000-0002-3726-7441" , "https://orcid.org/0000-0002-8379-6600" , "https://orcid.org/0000-0001-8850-9925" , "https://orcid.org/0000-0001-5472-917X" , "https://orcid.org/0000-0001-9043-693X" , "https://orcid.org/0000-0002-7301-8055" , "https://orcid.org/0000-0003-3166-4638" ; - "2022-04-20" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-10-10" ; @@ -123,9 +126,10 @@ "http://www.yeastgenome.org" ; "2013-08-07" ; "2024-02-01" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006268 replaced by GO:0006260" ; "https://orcid.org/0000-0001-5472-917X" ; - "2013-08-07" . + "2024-12-12"^^ . "http://www.yeastgenome.org" ; "2013-10-07" ; diff --git a/models/ZFIN_ZDB-GENE-990415-270.ttl b/models/ZFIN_ZDB-GENE-990415-270.ttl index 6774085ad6fc..ce082762c2b0 100644 --- a/models/ZFIN_ZDB-GENE-990415-270.ttl +++ b/models/ZFIN_ZDB-GENE-990415-270.ttl @@ -17,15 +17,17 @@ a . + a . + "production" ; "http://zfin.org" ; ; ; a ; - "Automated change 2024-10-10: GO:0043280 replaced by GO:2001056" ; + "Automated change 2024-10-10: GO:0043280 replaced by GO:2001056" , "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "tp53 (ZFIN:ZDB-GENE-990415-270)" ; "GOC:zfin_curators" ; - "2024-10-10"^^ . + "2024-12-12"^^ . "ZFIN:ZDB-GENE-040625-147" ; "http://zfin.org" ; @@ -731,9 +733,10 @@ "PMID:15630097" . "http://zfin.org" ; - a , ; + a , ; + "Automated change 2024-12-12: GO:0006978 replaced by GO:0030330" ; "GOC:zfin_curators" ; - "2005-05-02" . + "2024-12-12"^^ . "ZFIN:ZDB-MRPHLNO-050725-1,ZFIN:ZDB-MRPHLNO-070126-7" ; "http://zfin.org" ;