Closed gocentral closed 9 years ago
gocentral
commented
20 years ago Logged In: YES user_id=436423
All of the '... activity' definitions should start with 'Catalysis of ...' -- some are already OK; most just need the beginning adjusted slightly; the def for SUMO-specific protease activity (GO:0016929) should have the part about 'cysteine protease' removed because it's gene product information.
One more small picky thing: 'crater-like' should be hyphenated.
m
Original comment by: mah11
gocentral
commented
20 years ago Logged In: YES user_id=775618
Thanks for the feedback. I have removed 'cyteine protease', hyphenated crater-like and have changed all activity terms to start with "Catalysis of..." with the exception of "cyclin-dependent protein kinase regulator activity " where I cannot think of an adequate way to express it starting with "Catalysis of...". All of the other similar terms in the ontology that end with "... kinase regulator activity" are defined as "Modulates the activity of..." Suggestions welcome.
Here are the updated definitions:
term: bud scar goid: 0005621 definition: Crater-like ring of chitinous scar tissue located on the surface of the mother cell that forms after the newly emerged daughter cell separates thereby marking the site of cytokinesis. The number of bud scars that accumulate on the surface of a cell is a useful determinant of replicative age. definition_reference: PMID: 2005820 definition_reference: PMID: 14600225 definition_reference: SGD:rn
term: cyclin-dependent protein kinase regulator activity goid: 0016538 definition: Modulates the activity of a cyclin-dependent protein kinase, enzymes of the protein kinase family that are regulated through association with cyclins. definition_reference: 9442875 definition_reference: PMID: 7877684 definition_reference: SGD:rn
term: SUMO-specific protease activity goid: 0016929 definition: Catalysis of the hydrolysis of SUMO, a small ubiquitin- related modifier, from previously sumoylated substrates. definition_reference: PMID: 10094048 definition_reference: PMID: 11031248 definition_reference: PMID: 11265250 definition_reference: SGD:rn
term: SUMO ligase activity goid: 0019789 definition: Catalysis of ATP-dependent isopeptide bond formation between the carboxy terminal glycine residues of the small ubiquitin- related modifier, SUMO, and a substrate lysine residue, leading to the formation of predominately monosumoylated proteins with modified function. definition_reference: PMID: 11031248 definition_reference: PMID: 11265250 definition_reference: SGD:rsn
term: SUMO activating enzyme activity goid: 0019948 definition: Catalysis of the activation of the proteolytically processed small ubiquitin-related modifier, SUMO, through the formation of an ATP-dependent high-energy thioester bond. definition_reference: PMID: 11265250 definition_reference: PMID: 10187858 definition_reference: SGD:rsn
term: ubiquitin-like conjugating enzyme activity goid: 0008640 definition: Catalysis of the covalent attachment of ubiquitin-like proteins to lysine residues on the target protein. This function may be performed alone or in conjunction with an E3, ubiquitin-like protein ligase. definition_reference: PMID: 10806345 definition_reference: PMID: 10884686 definition_reference: SGD:rsn
term: cyclin-dependent protein kinase activity goid: 0004693 definition: Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein, where activity is dependent on the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). definition_reference: PMID: 9841670 definition_reference: PMID: 7877684 definition_reference: SGD:rsn
term: RAN protein binding goid: 0008536 definition: Interacting selectively with RAN, a conserved Ras-like GTP- binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly. definition_reference: PMID: 14726649 definition_reference: PMID: 12787777 definition_reference: SGD:rsn
term: proteasome activator activity goid: 0008538 definition: Catalysis of the activation of the proteasome, a large multisubunit complex which performs regulated ubiquitin-dependent cytosolic and nuclear proteolysis. definition_reference: PMID: 10428771 definition_reference: SGD:rsn
term: telomere capping goid: 0016233 definition: A process in which specific single-stranded telomeric DNA binding proteins interact with the ends of linear chromosomes, ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. definition_reference: PMID: 11352055 definition_reference: PMID: 11349150 definition_reference: SGD:rsn
term: mitotic sister chromatid cohesion goid: 0007064 definition: The physical attachment between sister chromatids that is established during S phase of the mitotic cycle at discrete sites along the entire chromosome, maintained until the metaphase-anaphase transition, and dissolved when sisters separate to opposite poles. This cohesion cycle is critical for high fidelity chromosome transmission. definition_reference: PMID: 11389843 definition_reference: PMID: 10827941 definition_reference: SGD:rsn
term: mitotic checkpoint goid: 0007093 definition: A signal transduction based surveillance mechanism that ensures accurate chromosome segregation by preventing premature passage through and exit from mitosis. Events that are monitored include the formation of a correctly assembled spindle, the position of the spindle pole (centrosome) and the orientation of the spindle. definition_reference: PMID: 12360190 definition_reference: SGD:rsn
term: mitotic spindle checkpoint goid: 0007094 definition: A signal transduction based surveillance mechanism that ensures the fidelity of cell division by preventing the premature advance of cells from metaphase to anaphase prior to the successful attachment of kinetochores to spindle microtubules (spindle assembly). definition_reference: PMID: 12360190 definition_reference: SGD:rsn
term: DNA replication checkpoint goid: 0000076 definition: A signal transduction based surveillance mechanism that prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome. definition_reference: PMID: 12537518 definition_reference: PMID: 11728327 definition_reference: SGD:rsn
term: MAP kinase phosphatase activity goid: 0017017 definition: Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein, where activity is dependent on the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). definition_reference: PMID: 12184814 definition_reference: SGD:rsn
Original comment by: rnash
gocentral
commented
20 years ago Logged In: YES user_id=616548
Hi Rob,
These look great to me. I'm just wondering whether the bud scar definition shouldn't make some reference to the type of organism it appears in, something like "Crater-like ring of chitinous scar tissue, seen in budding fungi,..." ?
Maria
Original comment by: mariacostanzo
gocentral
commented
20 years ago Logged In: YES user_id=775618
Thanks for looking at these Maria. I will clarify the bud scar def., as you suggested so that it is clear that it refers to fungi.
Cheers, Rob
Original comment by: rnash
gocentral
commented
20 years ago Logged In: YES user_id=439222
Hi Rob
I'm chiming in way late, but I just have a couple of picky things. So, if you are already committing terms, no biggy! See comments below in "".
-Chandra
term: bud scar definition: Crater-like ring of chitinous scar tissue located on the surface of the mother cell that forms after the newly emerged daughter cell separates thereby marking the site of cytokinesis "and septation". The number of bud scars that accumulate on the surface of a cell is a useful determinant of replicative age.
term: cyclin-dependent protein kinase regulator activity
definition: Modulates the activity of a cyclin-dependent protein kinase, enzymes of the protein kinase family that are regulated through association with cyclins "and other proteins".
(otherwise, to me it sounds like only cyclins can be annotated with this term)
term: mitotic checkpoint goid: 0007093 definition: A signal transduction-based (added hyphen) surveillance mechanism that ensures accurate chromosome segregation by preventing "entry into, " passage through, and exit from mitosis. Events that "may be" monitored include the formation of a correctly assembled spindle, the position of the spindle pole (centrosome), the orientation of the spindle, "and cellular morphogenesis".
(I assumed this is a generic, parent term for all checkpoints that prevent aberrant mitoses. Sorry if I got it wrong! BTW, that last bit refers to yeast, of course!)
Original comment by: clt4
gocentral
commented
20 years ago Original comment by: rbalakri
Hi all,
Here are some proposed definitions for existing terms that are currently undefined. We plan to commit these definitions by the April 15th. So, please provide feedback before that.
Thanks
Rob
term: bud scar goid: 0005621 definition: Crater like ring of chitinous scar tissue located on the surface of the mother cell that forms after the newly emerged daughter cell separates thereby marking the site of cytokinesis. The number of bud scars that accumulate on the surface of a cell is a useful determinant of replicative age. definition_reference: PMID: 2005820 definition_reference: PMID: 14600225 definition_reference: SGD:rn
term: cyclin-dependent protein kinase regulator activity goid: 0016538 definition: Modulates the activity of a cyclin-dependent protein kinase, enzymes of the protein kinase family that are regulated through association with cyclins. definition_reference: 9442875 definition_reference: PMID: 7877684 definition_reference: SGD:rn
term: SUMO-specific protease activity goid: 0016929 definition: Cysteine protease that catalyses the hydrolysis of SUMO, a small ubiquitin-related modifier, from previously sumoylated substrates. definition_reference: PMID: 10094048 definition_reference: PMID: 11031248 definition_reference: PMID: 11265250 definition_reference: SGD:rn
term: SUMO ligase activity goid: 0019789 definition: Catalyses ATP-dependent isopeptide bond formation between the carboxy terminal glycine residues of the small ubiquitin-related modifier, SUMO, and a substrate lysine residue, leading to the formation of predominately monosumoylated proteins with modified function. definition_reference: PMID: 11031248 definition_reference: PMID: 11265250 definition_reference: SGD:rsn
term: SUMO activating enzyme activity goid: 0019948 definition: Catalyses the activation of the proteolytically processed small ubiquitin-related modifier, SUMO, through the formation of an ATP-dependent high-energy thioester bond. definition_reference: PMID: 11265250 definition_reference: PMID: 10187858 definition_reference: SGD:rsn
term: ubiquitin-like conjugating enzyme activity goid: 0008640 definition: Catalyses the covalent attachment of ubiquitin-like proteins to lysine residues on the target protein. This function may be performed alone or in conjunction with an E3, ubiquitin- like protein ligase. definition_reference: PMID: 10806345 definition_reference: PMID: 10884686 definition_reference: SGD:rsn
term: cyclin-dependent protein kinase activity goid: 0004693 definition: Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein, where activity is dependent on the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). definition_reference: PMID: 9841670 definition_reference: PMID: 7877684 definition_reference: SGD:rsn
term: RAN protein binding goid: 0008536 definition: Interacting selectively with RAN, a conserved Ras-like GTP-binding protein, implicated in nucleocytoplasmic transport, cell cycle progression, spindle assembly, nuclear organization and nuclear envelope (NE) assembly. definition_reference: PMID: 14726649 definition_reference: PMID: 12787777 definition_reference: SGD:rsn
term: proteasome activator activity goid: 0008538 definition: Increases the activity of the proteasome, a large multisubunit complex which performs regulated ubiquitin- dependent cytosolic and nuclear proteolysis. definition_reference: PMID: 10428771 definition_reference: SGD:rsn
term: telomere capping goid: 0016233 definition: A process in which specific single-stranded telomeric DNA binding proteins interact with the ends of linear chromosomes, ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. definition_reference: PMID: 11352055 definition_reference: PMID: 11349150 definition_reference: SGD:rsn
term: mitotic sister chromatid cohesion goid: 0007064 definition: The physical attachment between sister chromatids that is established during S phase of the mitotic cycle at discrete sites along the entire chromosome, maintained until the metaphase-anaphase transition, and dissolved when sisters separate to opposite poles. This cohesion cycle is critical for high fidelity chromosome transmission. definition_reference: PMID: 11389843 definition_reference: PMID: 10827941 definition_reference: SGD:rsn
term: mitotic checkpoint goid: 0007093 definition: A signal transduction based surveillance mechanism that ensures accurate chromosome segregation by preventing premature passage through and exit from mitosis. Events that are monitored include the formation of a correctly assembled spindle, the position of the spindle pole (centrosome) and the orientation of the spindle. definition_reference: PMID: 12360190 definition_reference: SGD:rsn
term: mitotic spindle checkpoint goid: 0007094 definition: A signal transduction based surveillance mechanism that ensures the fidelity of cell division by preventing the premature advance of cells from metaphase to anaphase prior to the successful attachment of kinetochores to spindle microtubules (spindle assembly). definition_reference: PMID: 12360190 definition_reference: SGD:rsn
term: DNA replication checkpoint goid: 0000076 definition: A signal transduction based surveillance mechanism that prevents the initiation of mitosis until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome. definition_reference: PMID: 12537518 definition_reference: PMID: 11728327 definition_reference: SGD:rsn
term: MAP kinase phosphatase activity goid: 0017017 definition: Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein, where activity is dependent on the binding of a regulatory cyclin subunit and full activity requires stimulatory phosphorylation by a CDK-activating kinase (CAK). definition_reference: PMID: 12184814 definition_reference: SGD:rsn
Reported by: rnash
Original Ticket: "geneontology/ontology-requests/1632":https://sourceforge.net/p/geneontology/ontology-requests/1632