diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
index cfcf760e..142f797c 100644
--- a/src/ontology/imports/chebi_import.owl
+++ b/src/ontology/imports/chebi_import.owl
@@ -15,9 +15,9 @@
xmlns:chebi4="http://purl.obolibrary.org/obo/chebi#1"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
-
- 2023-07-26
+
+
+ 2023-08-09
@@ -15833,6 +15833,12 @@
+
+
+
+
+
+
A doubly-charged N-acyl-L-alpha-amino acid anion resulting from deprotonation of both carboxy groups of N-acetyl-L-aspartic acid.
-2
C6H7NO5
@@ -26731,6 +26737,60 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ An N-acyl-D-alpha-amino acid anion resulting from deprotonation of both carboxy groups of N-acetyl-D-aspartic acid. Major microspecies at pH 7.3.
+ -2
+ C6H7NO5
+ InChI=1S/C6H9NO5/c1-3(8)7-4(6(11)12)2-5(9)10/h4H,2H2,1H3,(H,7,8)(H,9,10)(H,11,12)/p-2/t4-/m1/s1
+ OTCCIMWXFLJLIA-SCSAIBSYSA-L
+ 173.125
+ 173.03352
+ O=C([O-])[C@H](NC(=O)C)CC([O-])=O
+ PMID:36690779
+ chebi_ontology
+ N-acetyl-D-Asp
+ N-acetyl-D-aspartate
+ CHEBI:195274
+
+ N-acetyl-D-aspartate(2-)
+
+
+
+
+ PMID:36690779
+ SUBMITTER
+
+
+
+
+ N-acetyl-D-Asp
+ SUBMITTER
+
+
+
+
+ N-acetyl-D-aspartate
+ UniProt
+
+
+
+
diff --git a/src/ontology/imports/cl_import.owl b/src/ontology/imports/cl_import.owl
index 9727bf0c..4227454f 100644
--- a/src/ontology/imports/cl_import.owl
+++ b/src/ontology/imports/cl_import.owl
@@ -16,9 +16,9 @@
xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
- 2023-07-26
+ 2023-08-09
diff --git a/src/ontology/imports/go_import.owl b/src/ontology/imports/go_import.owl
index 87cdb76d..f8d637f8 100644
--- a/src/ontology/imports/go_import.owl
+++ b/src/ontology/imports/go_import.owl
@@ -12,9 +12,9 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
-
- 2023-07-26
+
+
+ 2023-08-09
@@ -50,6 +50,20 @@
+
+
+
+ IAO:0000700
+ external
+ has_ontology_root_term
+ true
+ true
+ has_ontology_root_term
+ has ontology root term
+
+
+
+
@@ -356,6 +370,18 @@
+
+
+
+
+
+
+
+
+
+
+
+
@@ -1419,41 +1445,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
- biological_process
- GO:0000904
- cell morphogenesis involved in differentiation
-
-
-
-
- The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
- GOC:go_curators
-
-
-
-
@@ -18953,13 +18944,13 @@
Catalysis of the reaction: a donor + a peroxide = an oxidized donor + 2 H2O.
https://github.com/geneontology/go-ontology/issues/23121
+ https://github.com/geneontology/go-ontology/issues/25776
GO:0016685
GO:0016686
GO:0016687
GO:0016693
EC:1.11.1.-
KEGG_REACTION:R03532
- MetaCyc:PEROXID-RXN
Reactome:R-HSA-1222346
Reactome:R-HSA-140359
Reactome:R-HSA-209815
@@ -23833,6 +23824,12 @@
+
+
+
+
+
+
The synthesis of an RNA transcript from a DNA template.
https://github.com/geneontology/go-ontology/issues/14854
https://github.com/geneontology/go-ontology/issues/16737
@@ -23900,6 +23897,7 @@
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
+ https://github.com/geneontology/go-ontology/issues/25256
GO:0032583
GO:0045449
GO:0061019
@@ -24011,6 +24009,45 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.
+ https://github.com/geneontology/go-ontology/issues/14854
+ transcription from mitochondrial promoter
+ biological_process
+ GO:0006390
+ mitochondrial transcription
+
+
+
+
+ The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.
+ GOC:jl
+ PMID:23632312
+
+
+
+
@@ -24103,9 +24140,7 @@
-
-
@@ -26755,7 +26790,7 @@
- A mitotic cell cycle checkpoint that delays mitotic sister chromatid separation and consequently the mitotic metaphase/anaphase transition until the spindle is correctly assembled and chromosomes are attached to the spindle. Spindle assembly checkpoint signalling begins with the activated Mph family kinase, and results in the inhibition of the Anaphase Promoting Complex and its activator Sleepy/Cdc20 by the mitotic checkpoint complex (MCC).
+ A mitotic cell cycle checkpoint that delays mitotic sister chromatid separation and consequently the mitotic metaphase/anaphase transition until the spindle is correctly assembled and chromosomes are attached to the spindle. Spindle assembly checkpoint signaling begins with the activated Mph family kinase, and results in the inhibition of the Anaphase Promoting Complex and its activator Sleepy/Cdc20 by the mitotic checkpoint complex (MCC).
https://github.com/geneontology/go-ontology/issues/19810
https://github.com/geneontology/go-ontology/issues/20935
https://github.com/geneontology/go-ontology/issues/24179
@@ -26788,7 +26823,7 @@
- A mitotic cell cycle checkpoint that delays mitotic sister chromatid separation and consequently the mitotic metaphase/anaphase transition until the spindle is correctly assembled and chromosomes are attached to the spindle. Spindle assembly checkpoint signalling begins with the activated Mph family kinase, and results in the inhibition of the Anaphase Promoting Complex and its activator Sleepy/Cdc20 by the mitotic checkpoint complex (MCC).
+ A mitotic cell cycle checkpoint that delays mitotic sister chromatid separation and consequently the mitotic metaphase/anaphase transition until the spindle is correctly assembled and chromosomes are attached to the spindle. Spindle assembly checkpoint signaling begins with the activated Mph family kinase, and results in the inhibition of the Anaphase Promoting Complex and its activator Sleepy/Cdc20 by the mitotic checkpoint complex (MCC).
GOC:mtg_cell_cycle
PMID:12360190
@@ -29770,11 +29805,13 @@
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
+ https://github.com/geneontology/go-ontology/issues/24680
biological_process
accidental cell death
necrosis
GO:0008219
- This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
+
+ This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms.
cell death
@@ -30309,7 +30346,7 @@
- Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) -> ADP + phosphate + Na+(out); by a phosphorylative mechanism.
+ Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) = ADP + phosphate + Na+(out); by a phosphorylative mechanism.
https://github.com/geneontology/go-ontology/issues/21796
Na(+)-exporting ATPase activity
Na(+)-transporting ATPase activity
@@ -30332,7 +30369,7 @@
- Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) -> ADP + phosphate + Na+(out); by a phosphorylative mechanism.
+ Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na+(in) = ADP + phosphate + Na+(out); by a phosphorylative mechanism.
PMID:9224683
@@ -30844,9 +30881,11 @@
+
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
- http://amigo.geneontology.org/amigo/term/GO:0070589
+ https://github.com/geneontology/go-ontology/issues/15249
+ https://github.com/geneontology/go-ontology/issues/25418
GO:0043284
biopolymer biosynthetic process
macromolecule anabolism
@@ -33040,7 +33079,7 @@
- Any signalling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
+ Any signaling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
regulation of mitotic entry
biological_process
GO:0010389
@@ -33049,7 +33088,7 @@
- Any signalling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
+ Any signaling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
GOC:mtg_cell_cycle
PMID:17329565
@@ -33231,9 +33270,10 @@
-
- The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
+
+ The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.
https://github.com/geneontology/go-ontology/issues/22557
+ https://github.com/geneontology/go-ontology/issues/25419
Wikipedia:Gene_expression
biological_process
GO:0010467
@@ -33243,7 +33283,7 @@
- The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
+ The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes.
GOC:txnOH-2018
PMID:25934543
PMID:31580950
@@ -33265,7 +33305,7 @@
-
+
@@ -33535,7 +33575,7 @@
-
+
@@ -33572,9 +33612,9 @@
-
+
@@ -33610,9 +33650,9 @@
-
+
@@ -34242,7 +34282,7 @@
-
+
@@ -34279,7 +34319,7 @@
-
+
@@ -35648,42 +35688,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
- biological_process
- GO:0010769
- regulation of cell morphogenesis involved in differentiation
-
-
-
-
- Any process that modulates the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
- GOC:dph
- GOC:tb
-
-
-
-
@@ -35693,23 +35697,24 @@
-
+
-
+
-
+
Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
+ https://github.com/geneontology/go-ontology/issues/24299
biological_process
GO:0010770
- positive regulation of cell morphogenesis involved in differentiation
+ positive regulation of cell morphogenesis
@@ -35730,23 +35735,24 @@
-
+
-
+
-
+
Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
+ https://github.com/geneontology/go-ontology/issues/24299
biological_process
GO:0010771
- negative regulation of cell morphogenesis involved in differentiation
+ negative regulation of cell morphogenesis
@@ -37031,7 +37037,7 @@
- Any signalling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
+ Any signaling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
tb
2009-06-01T10:16:34Z
GO:0031662
@@ -37044,7 +37050,7 @@
- Any signalling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
+ Any signaling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
GOC:dph
GOC:mtg_cell_cycle
GOC:tb
@@ -37081,7 +37087,7 @@
- Any signalling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
+ Any signaling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
tb
2009-06-01T10:18:29Z
negative regulation of mitotic entry
@@ -37092,7 +37098,7 @@
- Any signalling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
+ Any signaling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the mitotic cell cycle.
GOC:mtg_cell_cycle
@@ -42048,45 +42054,6 @@
-
-
-
-
- Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
- EC:1.5.-.-
- oxidoreductase activity, acting on the CH-NH group of donors, other acceptors
- molecular_function
- GO:0016645
- oxidoreductase activity, acting on the CH-NH group of donors
-
-
-
-
- Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
- GOC:ai
-
-
-
-
-
-
-
-
- Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces oxygen.
- EC:1.5.3.-
- molecular_function
- GO:0016647
- oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor
-
-
-
-
- Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces oxygen.
- GOC:jl
-
-
-
-
@@ -42859,23 +42826,13 @@
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
+ https://github.com/geneontology/go-ontology/issues/25755
GO:0003869
GO:0016302
EC:3.1.3.-
- MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN
Reactome:R-HSA-4419986
Reactome:R-HSA-9636457
phosphoric monoester hydrolase activity
- 4-nitrophenylphosphatase activity
- 4-nitrophenylphosphate phosphohydrolase activity
- K-pNPPase activity
- NPPase activity
- PNPPase activity
- ecto-p-nitrophenyl phosphatase activity
- nitrophenyl phosphatase activity
- p-nitrophenylphosphatase activity
- p-nitrophenylphosphate phosphohydrolase activity
- para-nitrophenyl phosphatase activity
molecular_function
phosphatase
GO:0016791
@@ -43574,9 +43531,7 @@
-
-
@@ -47661,6 +47616,7 @@
+
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cell projection organisation
@@ -52044,6 +52000,7 @@
+
@@ -52087,6 +52044,7 @@
+
@@ -52141,6 +52099,7 @@
+
@@ -52489,6 +52448,7 @@
Catalysis of the reaction: peptidyl L-proline + 2-oxoglutarate + O2 = peptidyl trans-4-hydroxy-L-proline + succinate + CO2.
prolyl 4-hydroxylase
+ RHEA:63484
Reactome:R-HSA-1234165
Reactome:R-HSA-1234166
Reactome:R-HSA-1234173
@@ -66480,6 +66440,7 @@
ATPase activity, coupled to movement of substances
P-P-bond-hydrolysis-driven transmembrane transporter activity
P-P-bond-hydrolysis-driven transporter
+ EC:7.2.2.-
Reactome:R-HSA-1467457
Reactome:R-HSA-2161506
Reactome:R-HSA-2161538
@@ -70906,7 +70867,6 @@
-
@@ -70951,7 +70911,6 @@
-
@@ -70996,7 +70955,6 @@
-
@@ -77672,9 +77630,7 @@
-
-
@@ -86336,7 +86292,7 @@
-
+
@@ -95078,7 +95034,6 @@
-
Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
apoptosis of neuronal cells
apoptosis of neurons
@@ -96414,19 +96369,20 @@
-
- Catalysis of the reaction: L-proline + O2 + H2O = L-delta1-pyrroline-5-carboxylate + H2O2.
- MetaCyc:RXN-821
- RHEA:26124
+ OBSOLETE. Catalysis of the reaction: L-proline + O2 + H2O = L-delta1-pyrroline-5-carboxylate + H2O2.
+ https://github.com/geneontology/go-announcements/issues/552
+ GO:0004657
molecular_function
GO:0051699
- proline oxidase activity
+ This term was obsoleted because it represents the same molecular function as proline dehydrogenase activity ; GO:0051699.
+ obsolete proline oxidase activity
+ true
- Catalysis of the reaction: L-proline + O2 + H2O = L-delta1-pyrroline-5-carboxylate + H2O2.
- MetaCyc:RXN-821
+ OBSOLETE. Catalysis of the reaction: L-proline + O2 + H2O = L-delta1-pyrroline-5-carboxylate + H2O2.
+ GOC:curators
@@ -107520,7 +107476,7 @@
- Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another via the reaction X-SCP + Y = Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.
+ Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another molecule, usually another protein, via the reaction X-SCP + Y = Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.
dph
2014-11-06T13:15:27Z
E2
@@ -107532,7 +107488,7 @@
- Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another via the reaction X-SCP + Y = Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.
+ Isoenergetic transfer of a ubiquitin-like protein (ULP) from one protein to another molecule, usually another protein, via the reaction X-SCP + Y = Y-SCP + X, where both the X-SCP and Y-SCP linkages are thioester bonds between the C-terminal amino acid of SCP and a sulfhydryl side group of a cysteine residue.
GOC:dph
@@ -111538,43 +111494,6 @@
-
-
-
-
- The process of cell death in a neuron.
- mah
- 2009-11-03T02:37:17Z
- neuron cell death
- neuronal cell death
- biological_process
- GO:0070997
- This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide or use of neuron-specific markers) show that neuron death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the neuron death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'), and the cell type captured as an annotation extension; or the term GO:0051402 'neuron apoptotic process' may be considered, if appropriate.
- neuron death
-
-
-
-
- The process of cell death in a neuron.
- GOC:BHF
- GOC:mah
-
-
-
-
- neuron cell death
- GOC:mah
- GOC:rl
-
-
-
-
- neuronal cell death
- GOC:mah
-
-
-
-
@@ -119411,12 +119330,6 @@
-
-
-
-
-
-
@@ -119425,6 +119338,7 @@
The process in which the migration of a neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues.
https://github.com/geneontology/go-ontology/issues/19809
+ https://github.com/geneontology/go-ontology/issues/25417
pr
2013-07-08T13:32:37Z
neuron process guidance
@@ -120993,7 +120907,7 @@
- The portion of the cytoskeleton that lies within a dendritic spine. The actin component of this cytoskeleton is involved in spine head remodeling in response to postsynaptic signalling.
+ The portion of the cytoskeleton that lies within a dendritic spine. The actin component of this cytoskeleton is involved in spine head remodeling in response to postsynaptic signaling.
cellular_component
GO:0098836
cytoskeleton of dendritic spine
@@ -121001,7 +120915,7 @@
- The portion of the cytoskeleton that lies within a dendritic spine. The actin component of this cytoskeleton is involved in spine head remodeling in response to postsynaptic signalling.
+ The portion of the cytoskeleton that lies within a dendritic spine. The actin component of this cytoskeleton is involved in spine head remodeling in response to postsynaptic signaling.
PMID:24854120
@@ -122020,8 +121934,8 @@
+
-
@@ -122035,8 +121949,8 @@
The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol.
+ postsynaptic process involved in chemical synaptic transmission
biological_process
- postsynaptic process involved in chemical synaptic transmission
GO:0099565
chemical synaptic transmission, postsynaptic
@@ -122049,7 +121963,7 @@
-
+
postsynaptic process involved in chemical synaptic transmission
@@ -130779,332 +130693,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Any process that modulates the frequency, rate or extent of neuron death.
- rph
- 2012-08-02T09:57:41Z
- regulation of neuron cell death
- regulation of neuronal cell death
- biological_process
- GO:1901214
- regulation of neuron death
-
-
-
-
- Any process that modulates the frequency, rate or extent of neuron death.
- GOC:TermGenie
- GOC:rph
-
-
-
-
- regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
- rph
- 2012-08-02T09:58:07Z
- down regulation of neuron cell death
- down regulation of neuron death
- down regulation of neuronal cell death
- down-regulation of neuron cell death
- down-regulation of neuron death
- down-regulation of neuronal cell death
- downregulation of neuron cell death
- downregulation of neuron death
- downregulation of neuronal cell death
- negative regulation of neuron cell death
- negative regulation of neuronal cell death
- inhibition of neuron cell death
- inhibition of neuron death
- inhibition of neuronal cell death
- biological_process
- GO:1901215
- negative regulation of neuron death
-
-
-
-
- Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
- GOC:TermGenie
- GOC:rph
-
-
-
-
- down regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- down regulation of neuron death
- GOC:TermGenie
-
-
-
-
- down regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- down-regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- down-regulation of neuron death
- GOC:TermGenie
-
-
-
-
- down-regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- downregulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- downregulation of neuron death
- GOC:TermGenie
-
-
-
-
- downregulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- negative regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- negative regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- inhibition of neuron cell death
- GOC:TermGenie
-
-
-
-
- inhibition of neuron death
- GOC:TermGenie
-
-
-
-
- inhibition of neuronal cell death
- GOC:TermGenie
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Any process that activates or increases the frequency, rate or extent of neuron death.
- rph
- 2012-08-02T09:58:15Z
- positive regulation of neuron cell death
- positive regulation of neuronal cell death
- up regulation of neuron cell death
- up regulation of neuron death
- up regulation of neuronal cell death
- up-regulation of neuron cell death
- up-regulation of neuron death
- up-regulation of neuronal cell death
- upregulation of neuron cell death
- upregulation of neuron death
- upregulation of neuronal cell death
- activation of neuron cell death
- activation of neuron death
- activation of neuronal cell death
- biological_process
- GO:1901216
- positive regulation of neuron death
-
-
-
-
- Any process that activates or increases the frequency, rate or extent of neuron death.
- GOC:TermGenie
- GOC:rph
-
-
-
-
- positive regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- positive regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- up regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- up regulation of neuron death
- GOC:TermGenie
-
-
-
-
- up regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- up-regulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- up-regulation of neuron death
- GOC:TermGenie
-
-
-
-
- up-regulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- upregulation of neuron cell death
- GOC:TermGenie
-
-
-
-
- upregulation of neuron death
- GOC:TermGenie
-
-
-
-
- upregulation of neuronal cell death
- GOC:TermGenie
-
-
-
-
- activation of neuron cell death
- GOC:TermGenie
-
-
-
-
- activation of neuron death
- GOC:TermGenie
-
-
-
-
- activation of neuronal cell death
- GOC:TermGenie
-
-
-
-
@@ -142418,7 +142006,6 @@
-
@@ -142628,7 +142215,6 @@
-
@@ -143566,7 +143152,7 @@
- Any signalling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
+ Any signaling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
jl
2014-03-05T15:38:15Z
biological_process
@@ -143576,7 +143162,7 @@
- Any signalling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
+ Any signaling pathway that modulates the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
GOC:TermGenie
GOC:jl
GO_REF:0000058
@@ -143606,7 +143192,7 @@
- Any signalling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
+ Any signaling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
jl
2014-03-05T15:38:21Z
down regulation of cell cycle G2/M phase transition
@@ -143620,7 +143206,7 @@
- Any signalling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
+ Any signaling pathway that decreases or inhibits the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
GOC:TermGenie
GOC:jl
GO_REF:0000058
@@ -143674,7 +143260,7 @@
- Any signalling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
+ Any signaling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
jl
2014-03-05T15:38:27Z
up regulation of cell cycle G2/M phase transition
@@ -143688,7 +143274,7 @@
- Any signalling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
+ Any signaling pathway that activates or increases the activity of a cell cycle cyclin-dependent protein kinase to modulate the switch from G2 phase to M phase of the cell cycle.
GOC:TermGenie
GOC:jl
GO_REF:0000058
@@ -146649,6 +146235,144 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Any process that modulates the frequency, rate or extent of transcription occuring in the mitochondrion.
+ al
+ 2014-06-09T11:53:14Z
+ regulation of transcription from mitochondrial promoter
+ biological_process
+ GO:1903108
+ regulation of mitochondrial transcription
+
+
+
+
+ Any process that modulates the frequency, rate or extent of transcription occuring in the mitochondrion.
+ GOC:TermGenie
+ GO_REF:0000058
+ PMID:21357609
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Any process that activates or increases the frequency, rate or extent of transcription occuring in the mitochondrion.
+ al
+ 2014-06-09T11:53:20Z
+ positive regulation of transcription from mitochondrial promoter
+ up regulation of mitochondrial transcription
+ up regulation of transcription from mitochondrial promoter
+ up-regulation of mitochondrial transcription
+ up-regulation of transcription from mitochondrial promoter
+ upregulation of mitochondrial transcription
+ upregulation of transcription from mitochondrial promoter
+ activation of mitochondrial transcription
+ activation of transcription from mitochondrial promoter
+ biological_process
+ GO:1903109
+ positive regulation of mitochondrial transcription
+
+
+
+
+ Any process that activates or increases the frequency, rate or extent of transcription occuring in the mitochondrion.
+ GOC:TermGenie
+ GO_REF:0000058
+ PMID:21357609
+
+
+
+
+ up regulation of mitochondrial transcription
+ GOC:TermGenie
+
+
+
+
+ up regulation of transcription from mitochondrial promoter
+ GOC:TermGenie
+
+
+
+
+ up-regulation of mitochondrial transcription
+ GOC:TermGenie
+
+
+
+
+ up-regulation of transcription from mitochondrial promoter
+ GOC:TermGenie
+
+
+
+
+ upregulation of mitochondrial transcription
+ GOC:TermGenie
+
+
+
+
+ upregulation of transcription from mitochondrial promoter
+ GOC:TermGenie
+
+
+
+
+ activation of mitochondrial transcription
+ GOC:TermGenie
+
+
+
+
+ activation of transcription from mitochondrial promoter
+ GOC:TermGenie
+
+
+
+
@@ -168467,94 +168191,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- Any cell surface receptor signaling pathway that is involved in cell-cell signaling.
- dos
- 2016-04-06T16:59:57Z
- cell surface receptor linked signal transduction involved in cell-cell signaling
- cell surface receptor linked signal transduction involved in cell-cell signalling
- cell surface receptor linked signaling pathway involved in cell-cell signaling
- cell surface receptor linked signaling pathway involved in cell-cell signalling
- cell surface receptor linked signalling pathway involved in cell-cell signaling
- cell surface receptor linked signalling pathway involved in cell-cell signalling
- cell surface receptor signaling pathway involved in cell-cell signalling
- biological_process
- GO:1905114
- cell surface receptor signaling pathway involved in cell-cell signaling
-
-
-
-
- Any cell surface receptor signaling pathway that is involved in cell-cell signaling.
- GOC:TermGenie
- GO_REF:0000060
- ISBN:0-7167-3051-0
-
-
-
-
- cell surface receptor linked signal transduction involved in cell-cell signaling
- GOC:TermGenie
-
-
-
-
- cell surface receptor linked signal transduction involved in cell-cell signalling
- GOC:TermGenie
-
-
-
-
- cell surface receptor linked signaling pathway involved in cell-cell signaling
- GOC:TermGenie
-
-
-
-
- cell surface receptor linked signaling pathway involved in cell-cell signalling
- GOC:TermGenie
-
-
-
-
- cell surface receptor linked signalling pathway involved in cell-cell signaling
- GOC:TermGenie
-
-
-
-
- cell surface receptor linked signalling pathway involved in cell-cell signalling
- GOC:TermGenie
-
-
-
-
- cell surface receptor signaling pathway involved in cell-cell signalling
- GOC:TermGenie
-
-
-
-
@@ -177700,7 +177336,6 @@
-
@@ -177767,7 +177402,6 @@
-
@@ -180161,7 +179795,6 @@
-
@@ -182977,7 +182610,6 @@
-
diff --git a/src/ontology/imports/mpath_import.owl b/src/ontology/imports/mpath_import.owl
index e9ae0bc3..bf1889e3 100644
--- a/src/ontology/imports/mpath_import.owl
+++ b/src/ontology/imports/mpath_import.owl
@@ -10,9 +10,9 @@
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
- 2023-07-26
+ 2023-08-09
diff --git a/src/ontology/imports/nbo_import.owl b/src/ontology/imports/nbo_import.owl
index 612c9bd6..cc7f9ac3 100644
--- a/src/ontology/imports/nbo_import.owl
+++ b/src/ontology/imports/nbo_import.owl
@@ -11,9 +11,9 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
- 2023-07-25
+ 2023-08-09
diff --git a/src/ontology/imports/pato_import.owl b/src/ontology/imports/pato_import.owl
index 0d0baba4..7078142c 100644
--- a/src/ontology/imports/pato_import.owl
+++ b/src/ontology/imports/pato_import.owl
@@ -12,9 +12,9 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
- 2023-07-26
+ 2023-08-09
diff --git a/src/ontology/imports/pr_import.owl b/src/ontology/imports/pr_import.owl
index 380a4363..b57c523a 100644
--- a/src/ontology/imports/pr_import.owl
+++ b/src/ontology/imports/pr_import.owl
@@ -13,9 +13,9 @@
xmlns:vocab="https://w3id.org/semapv/vocab/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
- 2023-07-26
+ 2023-08-09
diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl
index e42fb7da..89ef8217 100644
--- a/src/ontology/imports/ro_import.owl
+++ b/src/ontology/imports/ro_import.owl
@@ -18,9 +18,9 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
-
+
- 2023-07-26
+ 2023-08-09
diff --git a/src/ontology/imports/uberon_import.owl b/src/ontology/imports/uberon_import.owl
index c95b9437..9d0554ba 100644
--- a/src/ontology/imports/uberon_import.owl
+++ b/src/ontology/imports/uberon_import.owl
@@ -37,7 +37,7 @@
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"
xmlns:caloha-reqs-vetted="http://purl.obolibrary.org/obo/caloha-reqs-vetted#">
-
+
@@ -98,7 +98,7 @@
aggregates AAO from 13:04:2012
aggregates TAO from 09:08:2012
aggregates VSAO from 16:07:2012
- 2023-07-26
+ 2023-08-09
diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl
index 13bbd6c7..66b72532 100644
--- a/src/patterns/definitions.owl
+++ b/src/patterns/definitions.owl
@@ -7,8 +7,8 @@ Prefix(rdfs:=)
Ontology(
-
-Annotation(owl:versionInfo "2023-07-26")
+
+Annotation(owl:versionInfo "2023-08-09")
Declaration(Class())
Declaration(Class())
@@ -2293,6 +2293,9 @@ Declaration(Class())
Declaration(Class())
Declaration(Class())
Declaration(Class())
+Declaration(Class())
+Declaration(Class())
+Declaration(Class())
Declaration(Class())
Declaration(Class())
Declaration(Class())
@@ -4490,10460 +4493,10472 @@ Declaration(ObjectProperty())
# Classes
############################
-# Class: (abnormal adipose tissue morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal abdominal fat pad morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (big ears)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (small ears)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal inner ear morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal pars superior vestibularis morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal malleus morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal tympanic ring morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal cochlea morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal inner ear vestibule morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal otic capsule morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal organ of Corti morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal sulcus ampullaris morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal middle ear morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal bone marrow cavity morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal neurocranium morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal interparietal bone morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal supraoccipital bone morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal basioccipital bone morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal exoccipital bone morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal fontanelle morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal vomer bone morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: (abnormal ethmoid bone morphology)
+# Class: ()
EquivalentClasses( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))))
-# Class: