Binding Terms minutes June 09: Difference between revisions
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Peter: a catalyst or transporter has to bind its substrate | Peter: a catalyst or transporter has to bind its substrate | ||
Jim: if not much is known about a protein then it is good to be able to annotate to binding | Jim: if not much is known about a protein then it is good to be able to annotate to binding | ||
Petra: For a ras exchange factor it is useful to be able to specify the specific ras protein substrate rather than create gene specific exchange factor terms. | Petra: For a ras exchange factor it is useful to be able to specify the specific ras protein substrate rather than create gene specific exchange factor terms. | ||
Ben: agrees that substrate binding should be used if there is no known function. | Ben: agrees that substrate binding should be used if there is no known function. | ||
Peter: there is an option that the ontology could be modified so that a catalyst 'has_part' to a binding term. | Peter: there is an option that the ontology could be modified so that a catalyst 'has_part' to a binding term. | ||
Jim: During the study of thymidine biosynthesis in yeast the enzymes involved were identified due to their binding of thymidine before any catalytic activity was shown. There are likely to be many more 'binding' experiments like this, for example in chemical screening, where the binding is confirmed but the gene function is unknown. | Jim: During the study of thymidine biosynthesis in yeast the enzymes involved were identified due to their binding of thymidine before any catalytic activity was shown. There are likely to be many more 'binding' experiments like this, for example in chemical screening, where the binding is confirmed but the gene function is unknown. | ||
Peter: need to consider costs involved in continuing the practice of annotating to binding terms. | Peter: need to consider costs involved in continuing the practice of annotating to binding terms. | ||
Debbie: is clutter in ontology a problem? | Debbie: is clutter in ontology a problem? | ||
Judy: Clutter is not a problem, we have to decide how to proceed without the concerns about finances and then decide if our proposal is financially viable, if need be. | Judy: Clutter is not a problem, we have to decide how to proceed without the concerns about finances and then decide if our proposal is financially viable, if need be. | ||
Ranjana:are we going to create very specific substrate terms? | Ranjana:are we going to create very specific substrate terms? | ||
Alex: annotation should be to the level curator is comfortable with. | Alex: annotation should be to the level curator is comfortable with. | ||
Notes To be continued Monday, please add/edit as required | Notes To be continued Monday, please add/edit as required | ||
Revision as of 04:12, 12 June 2009
Present
please sign up Peter, Ben, Jim, Pascale, Judy, Susan, Ranjana, Ruth, Donghui, Petra, Harold, Alex, Rachael, Yasmin,
Minutes
Peter: a catalyst or transporter has to bind its substrate
Jim: if not much is known about a protein then it is good to be able to annotate to binding
Petra: For a ras exchange factor it is useful to be able to specify the specific ras protein substrate rather than create gene specific exchange factor terms.
Ben: agrees that substrate binding should be used if there is no known function.
Peter: there is an option that the ontology could be modified so that a catalyst 'has_part' to a binding term.
Jim: During the study of thymidine biosynthesis in yeast the enzymes involved were identified due to their binding of thymidine before any catalytic activity was shown. There are likely to be many more 'binding' experiments like this, for example in chemical screening, where the binding is confirmed but the gene function is unknown.
Peter: need to consider costs involved in continuing the practice of annotating to binding terms.
Debbie: is clutter in ontology a problem?
Judy: Clutter is not a problem, we have to decide how to proceed without the concerns about finances and then decide if our proposal is financially viable, if need be.
Ranjana:are we going to create very specific substrate terms?
Alex: annotation should be to the level curator is comfortable with.
Notes To be continued Monday, please add/edit as required
Action Items
sorry I am leave today, will add notes from meeting on Monday, although please add information if you want to - Ruth