QC text |
Comments |
My suggestions
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Precondition not satisfied: epidermal growth factor receptor activity |
done 10-9-2007 |
Should be a RoMF. Should it be an is_a regulation of epidermal growth factor receptor signaling pathway?
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Precondition not satisfied: sodium:hydrogen antiporter activity |
done 10-9-2007 |
regulation of transporter activity should be an is a RoMF
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Precondition not satisfied: transcription factor activity |
done 10-9-2007, left as an is_a regulation of transcription based on the def |
part_of regulation of transcription. Is_a regulation of transcription factor activity
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Precondition not satisfied: transporter activity |
done 10-9-2007 |
should be a RoMF, regulation of transmembrane transporter activity should be an is_a of this.
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Refered to class does not exist: DNA transposition |
done 10-9-2007 |
should be 'regulation of transposition, DNA-mediated' same for children
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Refered to class does not exist: IP3 receptor activity |
done 10-9-2007 |
should be 'regulation of inositol-1,4,5-triphosphate receptor activity' RoMF there is no signaling pathway here. same for children
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Refered to class does not exist: JNK activity |
done 10-9-2007 |
should be regulation of JUN kinase activity, same for children. Should be is_a regualtion of JNK cascade
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Refered to class does not exist: L-glutamate transport |
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is all transport L-glutamate? L-glu is the biologically relevant form. From the lit search I did, it looks like D-glu can be transported by certain systems but that is not their primary purpose. It has also been used as an inhibitor or competitor for L-aa transporters. From PMID:3304825: "In a number of cell systems, D-acidic amino acids have substantial affinity for transport; D-glutamate, in a number of systems, however, appears to have little reactivity."
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Refered to class does not exist: MAPK activity |
done 10-9-2007 |
should be MAP kinase activity
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Refered to class does not exist: R7 differentiation |
done 10-9-2007 |
should be R7 cell differentiation
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Refered to class does not exist: R8 differentiation |
done 10-9-2007 |
should be R8 cell differentiation
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Refered to class does not exist: R8 spacing |
done 10-9-2007, made an is_a child of pattern specification |
perhaps this term should be R8 spacing in compund eye. Perhaps there should be a term called 'compund eye pattern formation'?
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Refered to class does not exist: RNA stability |
Made an ROBP did not change name because of complications with child terms |
Should be 'regulation of RNA catabolic process' part_of GO:0006401
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Refered to class does not exist: Type I restriction endodeoxyribonuclease activity |
done 10-9-2007 |
Should be regulation of Type I site-specific deoxyribonuclease activity
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Refered to class does not exist: Type II restriction endodeoxyribonuclease activity |
done 10-9-2007 |
Should be regulation of Type II site-specific deoxyribonuclease activity
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Refered to class does not exist: Type III restriction endodeoxyribonuclease activity |
done 10-9-2007 |
Should be regulation of Type III site-specific deoxyribonuclease activity
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Refered to class does not exist: Type IV restriction endodeoxyribonuclease activity |
done 10-9-2007, did not make a subtype of Type II ask Jim Hu |
Should be 'regulation of Type IV site-specific deoxyribonuclease activity. Should type IV be a subtype of type II ?
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Refered to class does not exist: actin filament length |
done 10-11-2007dph, also is_a reg of GO:0032956 |
Should be regulation of a biological quality GO:0032535 cellular component size
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Refered to class does not exist: adrenocorticotropic hormone secretion |
done 10-11-2007dph, made all terms univocal |
Should be adrenocorticotropin hormone secretion
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Refered to class does not exist: aggregate size |
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need new term 'regulation of aggregation during fruiting body development' this should be an is_a of it?
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Refered to class does not exist: angiotensin levels in blood |
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Should have parent 'regulation of angiotensin metabolic process'
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Refered to class does not exist: anterior neural cell fate of the neural plate |
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Check into what this term really means.
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Refered to class does not exist: antiviral response |
done 10-11-2007dph |
should be regulation of response to virus
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Refered to class does not exist: antiviral response by host |
done 10-11-2007dph |
ok subtype of regulation of response to virus
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Refered to class does not exist: antiviral response by virus |
done 10-11-2007dph |
ok subtype of regulation of response to virus
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Refered to class does not exist: apoptosis involved in mammary gland involution |
done 10-11-2007dph |
typo in parent. Should be apoptosis
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Refered to class does not exist: appetite |
done 10-11-2007dph |
Should be a RoBQ and a part_of response to nutrient levels GO:0031667?
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Refered to class does not exist: astral microtubule depolymerization |
created 'astral microtubule depolymerization' done 10-11-2007dph |
Should have 'astral microtubule depolymerization' as a parent via part_of. Astral microtubule depolymerization should be is_a microtubule depolymerization
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Refered to class does not exist: atrichoblast fate |
done 10-10-07 rev 5.500 TB, I agree, for neg and pos regulation terms as well. Tanya |
Should be regulation of atrichoblast fate specification
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Refered to class does not exist: axonemal microtubule depolymerization |
done 10-11-2007dph |
Should be 'negative regulation of microtubule depolymerization in axoneme'. Ok subtype of GO:0007026
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Refered to class does not exist: balance |
done 10-11-2007dph |
Maybe this term should be neuromuscular process controling balance and should be an is_a 'neuromuscular process', GO:0050905?
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Refered to class does not exist: blood vessel size |
RoBQ |
Should be a regulation of tube size.
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Refered to class does not exist: body fluids |
This relates to the 'regulation of water loss via skin' term below. Do them together. |
Should we have a term called 'fluid homeostasis' and have this be an is_a fluid homeostasis? This would then be an is_a RoBQ.
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Refered to class does not exist: body size |
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Should be regulation of growth of body. Then is is an ok subtype of GO:0040008.
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Refered to class does not exist: brain-derived neurotrophic factor receptor activity |
Made this molecular function term. Done 10/16/07dph |
Need brain-derived neurotrophic factor receptor activity in MF ontology
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Refered to class does not exist: calcium ion transport via voltage gated calcium channel |
ok children of GO:0051924 |
Make univocal with calcium ion transport via voltage-gated calcium channel
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Refered to class does not exist: cell fusion by virus |
done 10/16.07 dph |
Should be positive regulation of syncitium formation by virus?
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Refered to class does not exist: cell locomotion involved in cerebral cortex glial-mediated radial cell migration |
made all child terms univocal with GO:0021801 done 10/16/07dph |
Should be negative regulation of cell motility involved in cerebral cortex glial-mediated radial cell migration
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Refered to class does not exist: cell organization and biogenesis |
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Should be an is_a to regulation of cellular component organization and biogenesis
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Refered to class does not exist: cell proliferation in dorsal spinal cord |
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Sould be is_a regulation of cell proliferation, part_of cell proliferation in dorsal spinal cord (doen not exist)
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Refered to class does not exist: cell shape |
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Should we have a term called cell shape morphogenesis and cell size morphogenesis. Should we get rid of the word mass from the cell morphogenesis definition?
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Refered to class does not exist: cell size |
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Should we have a term called cell shape morphogenesis and cell size morphogenesis. Should we get rid of the word mass from the cell morphogenesis definition?
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Refered to class does not exist: cell volume |
Opened SF item 1815288 |
This term should be 'cell volume homeostasis'. Definition needs improvement. Annotations may need to be checked.
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Refered to class does not exist: cell-glial cell adhesion involved in cerebral cortex lamination |
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Should be a subtype of 'negative regulation of cell-glial cell adhesion involved in cerebral cortex lamination.
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Refered to class does not exist: centriole-centriole cohesion |
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Should we have a term centriole-centriole cohesion as an is_a GO:0051297? Def is:The process by which the two centrioles within a centrosome remain tightly paired.
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Refered to class does not exist: contractile ring contraction during cytokinesis |
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Should the parent term be called 'contractile ring contraction involved in cytokinesis'? Rename this term 'regulation of contractile ring contraction involved in cytokinesis'?
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Refered to class does not exist: cyclic nucleotide phosphodiesterase activity |
done 10-18-07 rev. 5.518 TB |
RoMF, Should be cyclic-nucleotide phosphodiesterase activity
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Refered to class does not exist: developmental pigmentation |
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Should be regulation of pigmentation during development
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Refered to class does not exist: endosome volume |
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"Should this term be part_of 'endosome organization and biogenesis' and is_a 'regulation of cellular component size'? Should the term be ""regulation of endosome size'?"
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Refered to class does not exist: enzyme activity |
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Should be regulation of catalytic activity RoMF
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Refered to class does not exist: enzyme activity in other organism during symbiotic interaction |
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Should be negative regulation of catalytic activity in other organism during symbiotic interaction. Is_a negative regulation of catalytic activity. Should we change all these terms to be univocal?
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Refered to class does not exist: exit from mitosis |
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Should we have a term 'exit from mitosis' as a part_of 'M phase of mitotic cell cycle', GO:0000087 and is_a 'cell cycle process', GO:0022402? Def:The cell cycle process where a cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place. The tanscription terms and this regulation term would be children of this.
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Refered to class does not exist: exocyst localization during endocytosis |
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Should have a term 'regulation of exocyst localization' part_of 'exocyst loaclization'. This term would be a legitimate subtype of the new term.
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Refered to class does not exist: female receptivity |
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Should we have male and female mating behavior as parts of 'mating behavior'? Female receptivity would be a type of female mating behavior.
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Refered to class does not exist: female receptivity, post-mating |
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Should we have male and female mating behavior as parts of 'mating behavior'? Female receptivity would be a type of female mating behavior.
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Refered to class does not exist: floral meristem size |
done 10-10-07 rev. 5.500 TB, I agree. Make 'regulation of FM growth' the primary term name, FM size as synonym. |
Should be 'regulation of floral meristem growth'. Should add 'floral meristem growth' as an is_a meristem growth. Regulates should be part_of this term. (You mean the regulation term should have a 'regulates' relationship to 'floral meristem growth', right? -TB)
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Refered to class does not exist: floral organ number |
done 10-10-07 rev. 5.500 TB |
Change term name to 'specification of floral organ number'.
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Refered to class does not exist: frizzled signaling pathway |
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Do we need a type of WNT receptor signaling pathway called 'WNT receptor signalling pathway through frizzled'? Then this term would be 'regulation of 'WNT receptor signalling pathway through frizzled' and be given a part_of relationship.
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Refered to class does not exist: frizzled-2 signaling pathway |
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Do we need a type of WNT receptor signaling pathway called 'WNT receptor signalling pathway through frizzled'-2? Then this term would be 'regulation of 'WNT receptor signalling pathway through frizzled-2' and be given a part_of relationship.
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Refered to class does not exist: gene expression, epigenetic |
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Should be a RoBQ
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Refered to class does not exist: heart contraction rate by epinephrine-norepinephrine |
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Should be related to cardiac chronotrophy. Need positive and negative children, then these terms should be their children.
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Refered to class does not exist: heart contraction rate in baroreceptor response to decreased blood pressure |
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Should be related to cardiac chronotrophy. Need positive and negative children, then these terms should be their children.
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Refered to class does not exist: heart contraction rate in baroreceptor response to increased blood pressure |
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Should be related to cardiac chronotrophy. Need positive and negative children, then these terms should be their children.
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Refered to class does not exist: histone H3-K36 methylation |
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Need 'histone H3-K36 methylation' for this term to be a part_of.
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Refered to class does not exist: inflorescence meristem size |
done 10-10-07 rev. 5.500 TB, added new term as suggested |
Should be 'regulation of inflorescence meristem growth'. Should add 'inflorescence meristem growth' as an is_a meristem growth. Regulates should be part_of this term.
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Refered to class does not exist: ion transporter activity |
done 10-17-07 rev.5.515 TB |
Should be 'regulation of ion transmembrane transporter activity'. RoMF
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Refered to class does not exist: light-activated channel activity |
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Should we have a MF that is 'light-activated channel activity'? Is_a GO:0015075. def: Catalysis of the transfer of an ion from one side of a membrane to the other in response to a light stimulus.
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Refered to class does not exist: long-term neuronal synaptic plasticity |
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Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't realate to this.
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Refered to class does not exist: mRNA stability |
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Should be 'regulation of mRNA catabolic process' and be a part_of GO:0006402
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Refered to class does not exist: mRNA translation, snRNA-mediated |
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Should be 'regulation of translation, sn RNA mediated'.
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Refered to class does not exist: membrane potential |
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Should be RoBQ, is it part_of cellular ion homeostasis?
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Refered to class does not exist: meristem size |
done 10-10-07 rev. 5.500 TB,I agree. Make 'regulation of m growth' the primary term name, M size as synonym. done 10-10-07 rev 5.499 TB |
Should be regulation of meristem growth
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Refered to class does not exist: mesenchymal cell proliferation |
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Should have 'mesenchymal cell proliferation' is_a 'cell proliferation', GO:0008283. Or maybe an ok subtype of GO:0042127?
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Refered to class does not exist: metalloenzyme activity |
RoMF |
Note that we do not specify a metalloenzyme activity in the MF ontology.
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Refered to class does not exist: mitochondrial membrane permeability |
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Should be RoBQ and a part_of mitochondrial membrane organization and biobgenesis.
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Refered to class does not exist: monophenol oxygenase activity |
apparently there may also be monophenol dioxygenases, should we update the defs to also say monooxygenase then? |
Should be 'regulation of monophenol monooxygenase activity'.
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Refered to class does not exist: nerve growth factor receptor activity |
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Should be RoMF and we should have 'nerve growth factor receptor activity' as a legit MF.
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Refered to class does not exist: neuronal synaptic plasticity |
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Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't realate to this.
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Refered to class does not exist: neuronal synaptic plasticity in response to neurotrophin |
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Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't realate to this.
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Refered to class does not exist: nitrogen metabolic process |
done 10-16-07 rev. 5.513 TB |
Should be 'regulation of nitrogen compound metabolic process'.
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Refered to class does not exist: organ number |
done 10-10-07 rev. 5.500 TB, |
Change term name to 'specification of organ number'.
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Refered to class does not exist: organ size |
done 10-10-07 rev. 5.500 TB, I agree. Make 'regulation of organ growth' the primary term name, organ size as synonym. |
Should be 'regulation of organ growth'.
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Refered to class does not exist: organismal metabolic process |
done 10-16-07 rev. 5.513 TB |
Should be 'regulation of multicellular organismal metabolic process'.
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Refered to class does not exist: pH |
RoBQ, There is no 'hydrogen ion homeostasis' per se, only 'cellular hydrogen ion homeostasis'. Do we want the generic one or will the 'cellular' one do? |
Should have a parent, 'hydrogen ion homeostasis'? (I like this. TB)
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Refered to class does not exist: peptidyl-serine phosphorylation of STAT protein |
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Should be a subtype of GO:0033135.
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Refered to class does not exist: petal number |
mostly done 10-10-07 rev. 5.500 TB, all done 10-11-07 rev. 5.505 TB |
Change term name to 'specification of petal number'. for +/- regulation, did specification of increased/decreased petal number
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Refered to class does not exist: posture |
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Maybe this term should be neuromuscular process controling posture and should be an is_a 'neuromuscular process', GO:0050905?
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Refered to class does not exist: progression through S phase |
ok subtype of GO:0051726 |
But, GO:0051726 'regulation of cell cycle' should be made a part_of cell cycle.
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Refered to class does not exist: progression through cell cycle |
ok subtype of GO:0051726 |
But, GO:0051726 'regulation of cell cycle' should be made a part_of cell cycle.
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Refered to class does not exist: progression through embryonic mitotic cell cycle |
ok subtype of GO:0051726 |
But, GO:0051726 'regulation of cell cycle' should be made a part_of cell cycle.
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Refered to class does not exist: progression through meiotic cell cycle |
ok subtype of GO:0051726 |
Do we need to fill in parents, regulation of meiotic cell cycle etc?
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Refered to class does not exist: progression through mitotic cell cycle |
ok subtype of GO:0051726 |
Do we need to fill in parents, regulation of meiotic cell cycle etc?
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Refered to class does not exist: progression through preblastoderm mitotic cell cycle |
ok subtype of GO:0051726 |
Do we need to fill in parents, regulation of meiotic cell cycle etc?
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Refered to class does not exist: progression through syncytial blastoderm mitotic cell cycle |
ok subtype of GO:0051726 |
Do we need to fill in parents, regulation of meiotic cell cycle etc?
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Refered to class does not exist: protease activity in other organism during symbiotic interaction |
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Should be a negative regulation of peptidase activity
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Refered to class does not exist: protein activity, epigenetic |
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Should this be 'regulation of molecular function, epigenetic'? Should we remove it as a RoBP?
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Refered to class does not exist: protein biosynthetic process |
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Should be changed to regulation of translation??
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Refered to class does not exist: protein function in other organism during symbiotic interaction |
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Should be 'negative regulation of molecular function in other…'? Should this be a RoMF.
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Refered to class does not exist: protein heterodimerization |
done 10-12-07 TB rev. 5.508 |
Should be 'regulation of protein heterodimerization activity', RoMF
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Refered to class does not exist: protein homodimerization |
done 10-12-07 TB rev. 5.508 |
Should be 'regulation of protein homodimerization activity', RoMF
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Refered to class does not exist: protein modification |
done 10-12-07 TB rev. 5.508 |
Should be 'regulation of protein modification process'.
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Refered to class does not exist: protein stability |
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RoBQ?
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Refered to class does not exist: receptor mediated endocytosis |
done 10-12-07 TB rev. 5.508 |
should be receptor-mediated endocytosis
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Refered to class does not exist: release of sequestered calcium ion into cytoplasm |
done 10-17-07 rev.5.515 TB |
Should be 'release of sequestered calcium ion into cytosol'.
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Refered to class does not exist: resting membrane potential |
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Should be RoBQ, is it part_of cellular ion homeostasis?
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Refered to class does not exist: retinal programmed cell death |
done 10-12-07 TB rev. 5.508 |
Should be 'retinal cell programmed cell death'.
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Refered to class does not exist: rhodopsin gene activity |
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Should this eventually be 'regulation of rhodopsin gene expression'?
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Refered to class does not exist: root meristem size |
done 10-10-07 rev.5.499 TB, added new term as suggested, I agree. Make 'regulation of RM growth' the primary term name, RM size as synonym. TB |
Should be 'regulation of root meristem growth'. Should add 'root meristem growth' as an is_a meristem growth. Regulates should be part_of this term. (Again, are you sure this shouldn't be a 'regulates' relationship? Maybe I missed something from our discussion earlier today. TB)
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Refered to class does not exist: salivary gland determination |
done 10-11-07 rev. 5.505 TB |
Should be 'salivary gland boundary specification'.
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Refered to class does not exist: short-term neuronal synaptic plasticity |
ok subtype of GO:0050804 |
Should regulation of synapse structure and activity be an is_a child of regulation of synaptic transmission?
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Refered to class does not exist: smoothened activity |
ok subtype of GO:0008589 |
Decided not to add a molecular function 'smoothened activity' as this was too specific a term.
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Refered to class does not exist: survival gene product activity |
ok subtype of GO:0043066 |
Sounds like this should be a 'regulation of gene expression'.
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Refered to class does not exist: synapse structure |
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Should 'regulation of synapse structure' and 'regulation of synapse activity' be is a children of 'regulation of synaptic plasticity and then should we rearrange the children?
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Refered to class does not exist: synapse structure and activity |
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Isn't this the same as synaptic plasticity?
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Refered to class does not exist: synaptic activity |
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Should 'regulation of synapse structure' and 'regulation of synapse activity' be is a children of 'regulation of synaptic plasticity and then should we rearrange the children?
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Refered to class does not exist: synaptic plasticity |
ok subtype of GO:0050804. |
Should regulation of synapse structure and activity be an is_a child of regulation of synaptic transmission?
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Refered to class does not exist: telomeric recombination at telomere |
done 10-11-07 rev. 5.505 TB, ok subtype of GO:0045910 |
Should be 'regulation of DNA recombination at telomere'.
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Refered to class does not exist: trichoblast fate |
done 10-10-07 rev.5.500 TB, Yup. I agree. TB |
should be regulation of trichoblast fate specification
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Refered to class does not exist: ubiquitin ligase activity |
done 10-10-07 rev.5.500 TB |
Should be regulation of ubiquitin-protein ligase activity and be a RoMF (it is a RoMF via transitivity over current parentage)
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Refered to class does not exist: vegetative meristem size |
done 10-10-07 rev 5.499 TB, same comment as for other meristem size terms |
Should be 'regulation of vegitative meristem growth'. Should add 'vegitative meristem growth' as an is_a meristem growth. Regulates should be part_of this term. (Again, are you sure this shouldn't be a 'regulates' relationship? Maybe I missed something from our discussion earlier today. TB)
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Refered to class does not exist: viral life cycle |
done 10-10-07 rev 5.499 TB |
Should be 'viral reproduction'.
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Refered to class does not exist: viral protein levels in host cell |
discuss |
Should this be 'regulation of viral protein metabolic process in host cell'? The this would be an ok subtype of GO:0051246.
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Refered to class does not exist: virion penetration into host |
done 10-10-07 rev 5.499 TB |
Should be 'virion penetration into host cell'.
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Refered to class does not exist: water loss via skin |
discuss, RoBQ |
Should the definition of 'water homeostasis' be restricted to an organism? Currently its parents suggest that, but its def does not.
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Refered to class does not exist: unfolded protein response, positive regulation of target gene transcription |
done 10-10-07 rev 5.499 TB |
Should be positive regulation of transcription of target genes involved in unfolded protein response
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