Regulation Worksheet - Part 3: Difference between revisions
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|Refered to class does not exist: nitrogen metabolic process||||Should be 'regulation of nitrogen compound metabolic process'. | |Refered to class does not exist: nitrogen metabolic process||||Should be 'regulation of nitrogen compound metabolic process'. | ||
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|Refered to class does not exist: organ number||||Change term name to 'regionalization specifying organ number'? | |Refered to class does not exist: organ number||I don't like the proposed term name but I don't know what to use as an alternative. Let's talk. TB||Change term name to 'regionalization specifying organ number'? | ||
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|Refered to class does not exist: organ size||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: organ size||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||||Should be 'regulation of multicellular organismal metabolic process'. | |Refered to class does not exist: organismal metabolic process||||Should be 'regulation of multicellular organismal metabolic process'. | ||
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|Refered to class does not exist: pH||RoBQ||Should have a parent, 'hydrogen ion homeostasis'? | |Refered to class does not exist: pH||RoBQ||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||||Should be a subtype of GO:0033135. | |Refered to class does not exist: peptidyl-serine phosphorylation of STAT protein||||Should be a subtype of GO:0033135. | ||
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|Refered to class does not exist: petal number||||Change term name to 'regionalization specifying petal number'? | |Refered to class does not exist: petal number||I don't like the proposed term name but I don't know what to use as an alternative. Let's talk. TB||Change term name to 'regionalization specifying petal number'? | ||
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|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: posture||||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: rhodopsin gene activity||||Should this eventually be 'regulation of rhodopsin gene expression'? | |Refered to class does not exist: rhodopsin gene activity||||Should this eventually be 'regulation of rhodopsin gene expression'? | ||
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|Refered to class does not exist: root meristem size||||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. | |Refered to class does not exist: root meristem size||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||||Should be 'salivary gland boundary specification'. | |Refered to class does not exist: salivary gland determination||||Should be 'salivary gland boundary specification'. | ||
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|Refered to class does not exist: telomeric recombination at telomere||ok subtype of GO:0045910||Should be 'regulation of DNA recombination at telomere'. | |Refered to class does not exist: telomeric recombination at telomere||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||||should be regulation of trichoblast fate specification | |Refered to class does not exist: trichoblast fate||Yup. I agree. TB||should be regulation of trichoblast fate specification | ||
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|Refered to class does not exist: ubiquitin ligase activity||||Should be regulation of ubiquitin-protein ligase activity and be a RoMF | |Refered to class does not exist: ubiquitin ligase activity||||Should be regulation of ubiquitin-protein ligase activity and be a RoMF | ||
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|Refered to class does not exist: vegetative meristem size||||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. | |Refered to class does not exist: vegetative meristem size||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||||Should be 'viral reproduction'. | |Refered to class does not exist: viral life cycle||||Should be 'viral reproduction'. |
Revision as of 19:30, 7 September 2007
QC text | Comments | My suggestions |
---|---|---|
Precondition not satisfied: epidermal growth factor receptor activity | 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 | regulation of transporter activity should be an is a RoMF | |
Precondition not satisfied: transcription factor activity | part_of regulation of transcription. Is_a regulation of transcription factor activity | |
Precondition not satisfied: transporter activity | should be a RoMF, regulation of transmembrane transporter activity should be an is_a of this. | |
Refered to class does not exist: DNA transposition | should be 'regulation of transposition, DNA-mediated' same for children | |
Refered to class does not exist: IP3 receptor activity | 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 | 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 | should be MAP kinase activity | |
Refered to class does not exist: R7 differentiation | should be R7 cell differentiation | |
Refered to class does not exist: R8 differentiation | should be R8 cell differentiation | |
Refered to class does not exist: R8 spacing | 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 | Should be 'regulation of RNA catabolic process' part_of GO:0006401 | |
Refered to class does not exist: Type I restriction endodeoxyribonuclease activity | Should be regulation of Type I site-specific deoxyribonuclease activity | |
Refered to class does not exist: Type II restriction endodeoxyribonuclease activity | Should be regulation of Type II site-specific deoxyribonuclease activity | |
Refered to class does not exist: Type III restriction endodeoxyribonuclease activity | Should be regulation of Type III site-specific deoxyribonuclease activity | |
Refered to class does not exist: Type IV restriction endodeoxyribonuclease activity | 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 | Should be regulation of a biological quality GO:0032535 cellular component size | |
Refered to class does not exist: adrenocorticotropic hormone secretion | 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 | should be regulation of response to virus | |
Refered to class does not exist: antiviral response by host | ok subtype of regulation of response to virus | |
Refered to class does not exist: antiviral response by virus | ok subtype of regulation of response to virus | |
Refered to class does not exist: apoptosis involved in mammary gland involution | typo in parent. Should be apoptosis | |
Refered to class does not exist: appetite | Should be a RoBQ and a part_of response to nutrient levels GO:0031667? | |
Refered to class does not exist: astral microtubule depolymerization | 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 | 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 | Should be 'negative regulation of microtubule depolymerization in axoneme'. Ok subtype of GO:0007026 | |
Refered to class does not exist: balance | 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 | 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 | 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 | 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 | 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 | 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 | I don't like the proposed term name but I don't know what to use as an alternative. Let's talk. TB | Change term name to 'regionalization specifying 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 | 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 | I agree. Make 'regulation of m growth' the primary term name, M size as synonym. | 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 | I don't like the proposed term name but I don't know what to use as an alternative. Let's talk. TB | Change term name to 'regionalization specifying organ number'? |
Refered to class does not exist: organ size | 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 | 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 | I don't like the proposed term name but I don't know what to use as an alternative. Let's talk. TB | Change term name to 'regionalization specifying 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 | Should be 'regulation of protein heterodimerization activity', RoMF | |
Refered to class does not exist: protein homodimerization | Should be 'regulation of protein homodimerization activity', RoMF | |
Refered to class does not exist: protein modification | 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 | 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 | 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 | 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 | 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 | ok subtype of GO:0045910 | Should be 'regulation of DNA recombination at telomere'. |
Refered to class does not exist: trichoblast fate | Yup. I agree. TB | should be regulation of trichoblast fate specification |
Refered to class does not exist: ubiquitin ligase activity | Should be regulation of ubiquitin-protein ligase activity and be a RoMF | |
Refered to class does not exist: vegetative meristem size | 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 | Should be 'viral reproduction'. | |
Refered to class does not exist: viral protein levels in host cell | 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 | Should be 'virion penetration into host cell'. | |
Refered to class does not exist: water loss via skin | 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 | Should be positive regulation of transcription of target genes involved in unfolded protein response |