Part 3

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QC text Comments My suggestions
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?
Precondition not satisfied: sodium:hydrogen antiporter activity done 10-9-2007 regulation of transporter activity should be an is a RoMF
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
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.
Refered to class does not exist: DNA transposition done 10-9-2007 should be 'regulation of transposition, DNA-mediated' same for children
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
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
Refered to class does not exist: L-glutamate transport is all transport L-glutamate?
Refered to class does not exist: MAPK activity done 10-9-2007 should be MAP kinase activity
Refered to class does not exist: R7 differentiation done 10-9-2007 should be R7 cell differentiation
Refered to class does not exist: R8 differentiation done 10-9-2007 should be R8 cell differentiation
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'?
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
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
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
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
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 ?
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
Refered to class does not exist: adrenocorticotropic hormone secretion done 10-11-2007dph, made all terms univocal Should be adrenocorticotropin hormone secretion
Refered to class does not exist: aggregate size need new term 'regulation of aggregation during fruiting body development' this should be an is_a of it?
Refered to class does not exist: angiotensin levels in blood Should have parent 'regulation of angiotensin metabolic process'
Refered to class does not exist: anterior neural cell fate of the neural plate Check into what this term really means.
Refered to class does not exist: antiviral response done 10-11-2007dph should be regulation of response to virus
Refered to class does not exist: antiviral response by host done 10-11-2007dph ok subtype of regulation of response to virus
Refered to class does not exist: antiviral response by virus done 10-11-2007dph ok subtype of regulation of response to virus
Refered to class does not exist: apoptosis involved in mammary gland involution done 10-11-2007dph typo in parent. Should be apoptosis
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?
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
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
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
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?
Refered to class does not exist: blood vessel size RoBQ Should be a regulation of tube size.
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.
Refered to class does not exist: body size Should be regulation of growth of body. Then is is an ok subtype of GO:0040008.
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
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
Refered to class does not exist: cell fusion by virus done 10/16.07 dph Should be positive regulation of syncitium formation by virus?
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
Refered to class does not exist: cell organization and biogenesis Should be an is_a to regulation of cellular component organization and biogenesis
Refered to class does not exist: cell proliferation in dorsal spinal cord Sould be is_a regulation of cell proliferation, part_of cell proliferation in dorsal spinal cord (doen not exist)
Refered to class does not exist: cell shape 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?
Refered to class does not exist: cell size 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?
Refered to class does not exist: cell volume Are cell volume and cell size the same?
Refered to class does not exist: cell-glial cell adhesion involved in cerebral cortex lamination Should be a subtype of 'negative regulation of cell-glial cell adhesion involved in cerebral cortex lamination.
Refered to class does not exist: centriole-centriole cohesion 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.
Refered to class does not exist: contractile ring contraction during cytokinesis Should the parent term be called 'contractile ring contraction involved in cytokinesis'? Rename this term 'regulation of contractile ring contraction involved in cytokinesis'?
Refered to class does not exist: cyclic nucleotide phosphodiesterase activity RoMF Should be cyclic-nucleotide phosphodiesterase activity
Refered to class does not exist: developmental pigmentation Should be regulation of pigmentation during development
Refered to class does not exist: endosome volume "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'?"
Refered to class does not exist: enzyme activity Should be regulation of catalytic activity RoMF
Refered to class does not exist: enzyme activity in other organism during symbiotic interaction 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?
Refered to class does not exist: exit from mitosis 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.
Refered to class does not exist: exocyst localization during endocytosis Should have a term 'regulation of exocyst localization' part_of 'exocyst loaclization'. This term would be a legitimate subtype of the new term.
Refered to class does not exist: female receptivity Should we have male and female mating behavior as parts of 'mating behavior'? Female receptivity would be a type of female mating behavior.
Refered to class does not exist: female receptivity, post-mating Should we have male and female mating behavior as parts of 'mating behavior'? Female receptivity would be a type of female mating behavior.
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)
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'.
Refered to class does not exist: frizzled signaling pathway 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.
Refered to class does not exist: frizzled-2 signaling pathway 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.
Refered to class does not exist: gene expression, epigenetic Should be a RoBQ
Refered to class does not exist: heart contraction rate by epinephrine-norepinephrine Should be related to cardiac chronotrophy. Need positive and negative children, then these terms should be their children.
Refered to class does not exist: heart contraction rate in baroreceptor response to decreased blood pressure Should be related to cardiac chronotrophy. Need positive and negative children, then these terms should be their children.
Refered to class does not exist: heart contraction rate in baroreceptor response to increased blood pressure Should be related to cardiac chronotrophy. Need positive and negative children, then these terms should be their children.
Refered to class does not exist: histone H3-K36 methylation Need 'histone H3-K36 methylation' for this term to be a part_of.
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.
Refered to class does not exist: ion transporter activity Should be 'regulation of ion transmembrane transporter activity'. RoMF
Refered to class does not exist: light-activated channel activity 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.
Refered to class does not exist: long-term neuronal synaptic plasticity Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't realate to this.
Refered to class does not exist: mRNA stability Should be 'regulation of mRNA catabolic process' and be a part_of GO:0006402
Refered to class does not exist: mRNA translation, snRNA-mediated Should be 'regulation of translation, sn RNA mediated'.
Refered to class does not exist: membrane potential Should be RoBQ, is it part_of cellular ion homeostasis?
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
Refered to class does not exist: mesenchymal cell proliferation Should have 'mesenchymal cell proliferation' is_a 'cell proliferation', GO:0008283. Or maybe an ok subtype of GO:0042127?
Refered to class does not exist: metalloenzyme activity RoMF Note that we do not specify a metalloenzyme activity in the MF ontology.
Refered to class does not exist: mitochondrial membrane permeability Should be RoBQ and a part_of mitochondrial membrane organization and biobgenesis.
Refered to class does not exist: monophenol oxygenase activity Should be 'regulation of monophenol monooxygenase activity'.
Refered to class does not exist: nerve growth factor receptor activity Should be RoMF and we should have 'nerve growth factor receptor activity' as a legit MF.
Refered to class does not exist: neuronal synaptic plasticity Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't realate to this.
Refered to class does not exist: neuronal synaptic plasticity in response to neurotrophin Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't realate to this.
Refered to class does not exist: nitrogen metabolic process Should be 'regulation of nitrogen compound metabolic process'.
Refered to class does not exist: organ number done 10-10-07 rev. 5.500 TB, Change term name to 'specification of organ number'.
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'.
Refered to class does not exist: organismal metabolic process Should be 'regulation of multicellular organismal metabolic process'.
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)
Refered to class does not exist: peptidyl-serine phosphorylation of STAT protein Should be a subtype of GO:0033135.
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
Refered to class does not exist: posture Maybe this term should be neuromuscular process controling posture and should be an is_a 'neuromuscular process', GO:0050905?
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.
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.
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.
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?
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?
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?
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?
Refered to class does not exist: protease activity in other organism during symbiotic interaction Should be a negative regulation of peptidase activity
Refered to class does not exist: protein activity, epigenetic Should this be 'regulation of molecular function, epigenetic'? Should we remove it as a RoBP?
Refered to class does not exist: protein biosynthetic process Should be changed to regulation of translation??
Refered to class does not exist: protein function in other organism during symbiotic interaction Should be 'negative regulation of molecular function in other…'? Should this be a RoMF.
Refered to class does not exist: protein heterodimerization done 10-12-07 TB rev. 5.508 Should be 'regulation of protein heterodimerization activity', RoMF
Refered to class does not exist: protein homodimerization done 10-12-07 TB rev. 5.508 Should be 'regulation of protein homodimerization activity', RoMF
Refered to class does not exist: protein modification done 10-12-07 TB rev. 5.508 Should be 'regulation of protein modification process'.
Refered to class does not exist: protein stability RoBQ?
Refered to class does not exist: receptor mediated endocytosis done 10-12-07 TB rev. 5.508 should be receptor-mediated endocytosis
Refered to class does not exist: release of sequestered calcium ion into cytoplasm Should be 'release of sequestered calcium ion into cytosol'.
Refered to class does not exist: resting membrane potential Should be RoBQ, is it part_of cellular ion homeostasis?
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'.
Refered to class does not exist: rhodopsin gene activity Should this eventually be 'regulation of rhodopsin gene expression'?
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)
Refered to class does not exist: salivary gland determination done 10-11-07 rev. 5.505 TB Should be 'salivary gland boundary specification'.
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?
Refered to class does not exist: smoothened activity Should have a molecular function 'smoothened activity' is_a GO:0004888. 'regulation of smoothened activity' should be a RoMF of this MF. 'regulation of smoothened activity' is an ok subtype of GO:0008589.
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'.
Refered to class does not exist: synapse structure 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?
Refered to class does not exist: synapse structure and activity Isn't this the same as synaptic plasticity?
Refered to class does not exist: synaptic activity 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?
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?
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'.
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
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)
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)
Refered to class does not exist: viral life cycle done 10-10-07 rev 5.499 TB Should be 'viral reproduction'.
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.
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'.
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.
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