Difference between revisions of "Part 3"

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|Refered to class does not exist: cell size||done 11-28-07 rev. 5.573 dph/tb|| Should regulation of cell size be an is_a child of regulation of cell morphogenesis? YES.  
 
|Refered to class does not exist: cell size||done 11-28-07 rev. 5.573 dph/tb|| Should regulation of cell size be an is_a child of regulation of cell morphogenesis? YES.  
 
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|Refered to class does not exist: cell volume||pos and neg regulation terms still need to be sorted out, Opened SF item 1815288||Made this term 'cell volume homeostasis'.  
+
|Refered to class does not exist: cell volume||done 11-29-07 dph/tb ||Made this term 'cell volume homeostasis'. Documented in SF item 1815288 which has been closed.
 
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|-
 
|Refered to class does not exist: cell-glial cell adhesion involved in cerebral cortex lamination||done 11/05/07 tb/dph rev. 5.537||Should be a subtype of 'negative regulation of cell-cell adhesion.
 
|Refered to class does not exist: cell-glial cell adhesion involved in cerebral cortex lamination||done 11/05/07 tb/dph rev. 5.537||Should be a subtype of 'negative regulation of cell-cell adhesion.
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|Refered to class does not exist: smoothened activity||done 11-28-07 rev. 5.572 dph/tb, ok subtype of GO:0008589||Decided not to add a molecular function 'smoothened activity' as this was too specific a term. Made 'regulation of receptor activity', moved three other terms as well as this one under here.
 
|Refered to class does not exist: smoothened activity||done 11-28-07 rev. 5.572 dph/tb, ok subtype of GO:0008589||Decided not to add a molecular function 'smoothened activity' as this was too specific a term. Made 'regulation of receptor activity', moved three other terms as well as this one under here.
 
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|Refered to class does not exist: survival gene product activity||Made this a type of regulation of gene expression based on its def and the one for gene expression.Changed name. done 11-27-2007 TB/DPH||Sounds like this should be a 'regulation of gene expression'.
+
|Refered to class does not exist: survival gene product activity||done 11-27-2007 TB/DPH Made this a type of regulation of gene expression based on its def and the one for gene expression.Changed name. ||Sounds like this should be a 'regulation of gene expression'.
 
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|Refered to class does not exist: synapse structure||done 11-9-07 rev. 5.542 dph/tb, renamed as 'regulation of synapse organization and biogenesis'||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? No.
 
|Refered to class does not exist: synapse structure||done 11-9-07 rev. 5.542 dph/tb, renamed as 'regulation of synapse organization and biogenesis'||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? No.

Revision as of 22:08, 29 November 2007

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 done 11-1-07 dph/tb rev. 5.534 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 done Made an ROBQ 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 done 11-1-07 rev.5.534 dph/tb need new term 'regulation of aggregation during sorocarp development' this should be an is_a of it? added new term as parent and also made RoBQ
Refered to class does not exist: angiotensin levels in blood done 11-1-07 rev. 5.534 dph/tb Should have parent 'regulation of angiotensin metabolic process', added this term as parent
Refered to class does not exist: anterior neural cell fate of the neural plate done 11/02/07 rev. 5.536 tb/dph This term refers to the negtive regulation of cell fate commitment. We added the appropriate parents to the ontology and then made this term an is_a child of those and cleaned up what appeared to be a cut and paste error in the def. 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 done 10-11-2007dph created '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 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 RoBQ Should be a regulation of tube size.
Refered to class does not exist: body fluids done 11-2-07 rev. 5.536 tb/dph We made this term a ROBQ and changed the name to reflect the levels as is in the def. We rearranged some of the terms underneath and opened a SF item SF:1824802 to get input for some of the other terms that seemed problematic under this parent. 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 done 11-2-07 rev. 5.536 tb/dph made it 'multicellular organism growth' to be univocal. 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 done 10/16/07dph Made this molecular function term. Need brain-derived neurotrophic factor receptor activity in MF ontology
Refered to class does not exist: calcium ion transport via voltage gated calcium channel done 11-2-07 rev. 5.536 tb/dph ok children of GO:0051924, made all terms univocal 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 done 10/16/07dph made all child terms univocal with GO:0021801 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 done 11/02/07 tb/dph rev. 5.536 Should be positive regulation of cellular component organization and biogenesis. Fix synonyms so that the 'cell' ones are related not exact.
Refered to class does not exist: cell proliferation in dorsal spinal cord done 11/05/07 tb/dph rev. 5.537 Added parent. Got rid of the word 'the' in the forebrain term. Should be is_a regulation of cell proliferation, part_of cell proliferation in dorsal spinal cord (does not exist)
Refered to class does not exist: cell shape done 11-28-07 rev. 5.573 dph/tb Got rid of the word 'mass and volume' in the cell morphogenesis def and in the other term defs that have the word 'mass and volume' in them. replaced with 'size'.
Refered to class does not exist: cell size done 11-28-07 rev. 5.573 dph/tb Should regulation of cell size be an is_a child of regulation of cell morphogenesis? YES.
Refered to class does not exist: cell volume done 11-29-07 dph/tb Made this term 'cell volume homeostasis'. Documented in SF item 1815288 which has been closed.
Refered to class does not exist: cell-glial cell adhesion involved in cerebral cortex lamination done 11/05/07 tb/dph rev. 5.537 Should be a subtype of 'negative regulation of cell-cell adhesion.
Refered to class does not exist: centriole-centriole cohesion done 11/05/07 tb/dph rev. 5.537 Made this term a regulation of cytoskeleton org and bio based on cc. Created parent term. 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 done 11/05/07 tb/dph rev. 5.537 Rearranged all terms in this node as suggested, just in case we need to add more regulates terms later. 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 done 11/05/07 tb/dph rev. 5.537 moved this term to be under the correct parent. "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 done 11/05/07 tb/dph rev. 5.537 created parent term. 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 done 11/06/07 tb/dph rev. 5.538 Added the 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 done 11/06/07 tb/dph rev. 5.538 Should we have male and female mating behavior as parts of 'mating behavior'? Female receptivity would be a type of female mating behavior. Did this. Also made a link between 'behavioral interaction between organisms' and 'behavior'.
Refered to class does not exist: female receptivity, post-mating done 11/06/07 tb/dph rev. 5.538 Should we have male and female mating behavior as parts of 'mating behavior'? Added these as part_of mating behavior since this term is an interaction between two organisms! Is_a parent for both terms is reproductive behavior in a multicellular organism. Female receptivity (another new term) 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 done 11/06/07 tb/dph rev. 5.538 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. Looking at this again, I don't think so. From the definition of this term and its children, this term should be merged with its parent. I think if it specified frizzled-1 then it could regulate Wnt receptor signaling pathway through beta-catenin. (We merged reg. of frizzled signaling pathway with 'reg of Wnt receptor signaling pathway' to be conservative and make sure than any annotations to this term were still valid. The other option, which was to rename this as frizzled-1, specifically, left open the possibility of annotations getting corrupted.)
Refered to class does not exist: frizzled-2 signaling pathway done 11/06/07 tb/dph rev. 5.538 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.Looking at this again, I don't think so. I think this refers to the old frizzled-2 pathway term which has a name change to Wnt receptor signaling pathway, calcium modulating pathway. It is already a child of this and will need some work on the def. (This was easy. Made this univocal with 'Wnt receptor signaling pathway, calcium modulating pathway'.)
Refered to class does not exist: gene expression, epigenetic done 11-16-07 rev. 5.554 dph/tb, added parent term 'gene expression' and 'reg. of gene expression' as parents See SF item 1418820 for complete proposal.
Refered to class does not exist: heart contraction rate by epinephrine-norepinephrine done 11/7/2007 tb/dph. rev.5.540 Changed cardiac chronotropy to heart rate to make univocal. Worked on univocity of all these terms as well as force terms. Should be related to cardiac chronotropy. 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 done 11/7/2007 tb/dph. rev.5.540 Changed cardiac chronotropy to heart rate to make univocal. Worked on univocity of all these terms as well as force terms. Should be related to cardiac chronotropy. 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 done 11/7/2007 tb/dph. rev.5.540 Changed cardiac chronotropy to heart rate to make univocal. Worked on univocity of all these terms as well as force terms. 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 done 11/7/07 rev.5.540 Made this term. Also cleaned up TPVs for the regulates term since not all of these channels are involved in rhodopsin and transport calcium. There are anion ones in plants and potassium ones in animals. 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 done 11-9-07 rev. 5.542 dph/tb Made is_a 'regulation of synaptic plasticity'. Need to sort this out is it RoBQ? We also have terms referring to synaptic structural plasticity that don't relate to this.
Refered to class does not exist: mRNA stability done, made RoBQ Should be 'regulation of mRNA catabolic process' and be a part_of GO:0006402
Refered to class does not exist: mRNA translation, snRNA-mediated done 11-9-07 rev. 5.542 dph/tb ok subtype of 'regulation of translation' Should be 'regulation of translation, sn RNA mediated'. Made univocal.
Refered to class does not exist: membrane potential done 11-9-07 rev. 5.542 dph/tb Made RoBQ, via is_a 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 done 11-14-07 rev 5.546 dph/tb, created mesenchymal cell proliferation and its regulates child. 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 done 11-14-07 rev 5.546 dph/tb, Did not make the MF, kept this a a RoMF. Note that we do not specify a metalloenzyme activity in the MF ontology.
Refered to class does not exist: mitochondrial membrane permeability done 11-15-07 rev 5.546 dph/tb, Made an ROBQ. Retained the is_a to mitochondrial membrane organization and biogenesis based on the def of the parent. Talk with Chris about this. Should be RoBQ and a part_of mitochondrial membrane organization and biogenesis.
Refered to class does not exist: monophenol oxygenase activity done 11-15-07 rev 5.546 tb/dph, Found a paper where they used this name to describe the enzyme. Made an RoMF and made all terms univocal. Should be 'regulation of monophenol monooxygenase activity'.apparently there may also be monophenol dioxygenases, should we update the defs to also say monooxygenase then?
Refered to class does not exist: nerve growth factor receptor activity done 11-15-07 rev 5.546 tb/dph 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 done 11-9-07 rev. 5.542 dph/tb, as part of fixing the other 'synapse' related terms 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 done 11-9-07 rev. 5.542 dph/tb, as part of fixing the other 'synapse' related terms 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 done 11-28-07 dph/tb Renamed as 'hydrogen ion homeostasis', retained 'regulation of pH' name as an exact synonym. Made 'cellular hydrogen ion homeostasis' an is_a child of this term.
Refered to class does not exist: peptidyl-serine phosphorylation of STAT protein done 11-15-07 rev 5.546 tb/dph Should be a subtype of GO:0033135.
Refered to class does not exist: petal number done 10-10-07 rev. 5.500 TB, 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 done 11-15-07 rev. 5.552 dph/tb Renamed this term to be neuromuscular process controling posture and made is_a 'neuromuscular process', GO:0050905
Refered to class does not exist: progression through S phase Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 Made GO:0051726 part_of cell cycle. left this as subtype, but still have questions. 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 done 11-15-07 rev 5.546 dph/tb, made all protease/peptidase terms univocal. Should be a negative regulation of peptidase activity
Refered to class does not exist: protein activity, epigenetic done 11-15-07 rev. 5.552 dph/tb Renamed as 'regulation of molecular function, epigenetic'. Should we remove it as a RoBP? No, will be both RoBP and RoMF.
Refered to class does not exist: protein biosynthetic process done 11-15-07 rev. 5.552 dph/tb Changed to regulation of translation.
Refered to class does not exist: protein function in other organism during symbiotic interaction done 11-15-07 rev. 5.552 dph/tb, made all 'protein function' terms univocal as 'molecular function' Renamed as 'negative regulation of molecular function in other…'. Made 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 done 11-15-07 rev. 5.552 dph/tb RoBQ? Yes.
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 done 11-15-07 rev. 5.552 dph/tb, ok subchild of 'cellular ion homeostasis' Is RoBQ. Is it part_of cellular ion homeostasis? No, this term is an ok 'is_a' child.
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 done 11-16-07 rev. 5.554 and 5.555 dph/tb Made 'regulation of rhodopsin gene expression' (made + and - children univocal as well) and a child of 'regulation of 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 done 11-9-07 rev. 5.542 dph/tb, as part of fixing the other 'synapse' related terms, ok subtype of GO:0050804 Should regulation of synapse structure and activity be an is_a child of regulation of synaptic transmission? No. Is_a RoBQ. Changing synapse structure may not necessarily affect synaptic transmission.
Refered to class does not exist: smoothened activity done 11-28-07 rev. 5.572 dph/tb, ok subtype of GO:0008589 Decided not to add a molecular function 'smoothened activity' as this was too specific a term. Made 'regulation of receptor activity', moved three other terms as well as this one under here.
Refered to class does not exist: survival gene product activity done 11-27-2007 TB/DPH Made this a type of regulation of gene expression based on its def and the one for gene expression.Changed name. Sounds like this should be a 'regulation of gene expression'.
Refered to class does not exist: synapse structure done 11-9-07 rev. 5.542 dph/tb, renamed as 'regulation of synapse organization and biogenesis' 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? No.
Refered to class does not exist: synapse structure and activity done 11-9-07 rev. 5.542 dph/tb, as part of fixing the other 'synapse' related terms Isn't this the same as synaptic plasticity? No. Regulation of synaptic plasticity is a child of this term. Synaptic plasticity, by definition, is in response to something.
Refered to class does not exist: synaptic activity done 11-9-07 rev. 5.542 dph/tb, as part of fixing the other 'synapse' related terms 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 done 11-9-07 rev. 5.542 dph/tb, as part of fixing the other 'synapse' related terms, 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 done 11-28-07 dph/tb Should this be 'regulation of viral protein metabolic process in host cell'? NO. Made is_a chemical homeostasis.
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

11-16-09 110/125 total items done