Regulation Worksheet - Part 3: Difference between revisions
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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'. | |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|| | |Refered to class does not exist: pH||||Rename as 'hydrogen ion homeostasis', retain this name as an exact synonym. RoBQ,Make 'cellular hydrogen ion homeostasis' an is_a child of this. Make an exact synonym for that term, 'regulation of cellular pH'. | ||
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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. |
Revision as of 16:46, 28 October 2007
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? |
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? 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." | |
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 sorocarp 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 | done 10-24-07 rev. 5.524 TB (should this still be part of 'circulation'
?)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 | Opened SF item 1815288 | This term should be 'cell volume homeostasis'. Definition needs improvement. Annotations may need to be checked. |
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 | done 10-18-07 rev. 5.518 TB | RoMF, Should be cyclic-nucleotide phosphodiesterase activity |
Refered to class does not exist: developmental pigmentation | done 10-22-07 rev. 5.521 TB | 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 | done 10-22-07 rev. 5.521 TB | Should be regulation of catalytic activity RoMF |
Refered to class does not exist: enzyme activity in other organism during symbiotic interaction | done 10-22-07 rev. 5.521 TB | 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? Yes, made all these terms univocal, catalytic activity, not enzyme activity. |
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 | done 10-24-07 rev.5.524 TB | 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 | done 10-17-07 rev.5.515 TB | 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 | apparently there may also be monophenol dioxygenases, should we update the defs to also say monooxygenase then? | 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 | done 10-16-07 rev. 5.513 TB | 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 | done 10-16-07 rev. 5.513 TB | Should be 'regulation of multicellular organismal metabolic process'. |
Refered to class does not exist: pH | Rename as 'hydrogen ion homeostasis', retain this name as an exact synonym. RoBQ,Make 'cellular hydrogen ion homeostasis' an is_a child of this. Make an exact synonym for that term, 'regulation of cellular pH'. | |
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 | done 10-17-07 rev.5.515 TB | 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 | ok subtype of GO:0008589 | Decided not to add a molecular function 'smoothened activity' as this was too specific a term. |
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 |