Activity for Varun Kothamachu
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Varun Kothamachu modified ticket #125
Charge
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Dear Andreas, Thank you for the term request. I am weary to use "charge" to represent the definition that you are after. Instead, I have created a new term called "fractional occupancy" SBO:0000663. I hope this works for you.
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Hi Andreas, I have now created a new term SBO:0000662 in response to your request.
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Occupancy
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Capacity
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Dear Andreas, Thank you for the term request. I have created a new term SBO:0000661 in response.
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Hi Vasundra, I have created new terms for polymerisation (SBO:0000652) and de-polymerisation (SBO:0000653). For co-transport we now have the term SBO:0000654 which is currently described for 2 substances. I am not aware of examples of co-transport being used for more than 2 substances. Could you share some examples ? Will wait for more responses on the other terms.
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Posting on behalf of Vasundra: Hi Varun and Nicolas, Polymerization/Depolymerization looks good to me. Co-transport: "simultaneous transport of two substances" : isn't "two" a bit restrictive here? There could be more than two substances co-transported, right? Could we say "of two or more substances"? Regarding the term Transfers to, the definition in the paper was: "a chemical group is transferred from a high-energy donor to a recipient, forming a covalently bonded modification." So I don't think...
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Hi Nicolas, Vasundra, I have the following definitions and proposed changes for the terms that you both have been discussing. Kindly let me know if you have any feedback on the proposed definitions before I create the terms. I will create new terms 1. Polymerization (Parent term: SBO:0000182 - conversion) A chemical reaction involving two or more molecules combining to form a larger molecule with repeated structural units. 2. De-polymerization (Parent term: SBO:0000182 - conversion) A chemical reaction...
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Hi Nicolas, I agree on moving SBO:0000376 - hydrolysis as a child term to SBO:0000178 - cleavage. Have made this change and am now closing the ticket now.
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Make "hydrolysis" a child of "conversion"
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Proposed definitions are Preferred Name: Genome-scale model Definitions: A stoichiometric model of metabolism derived from information found in the genome and used to describe the metabolic potential of an organism. It is valuable for investigations on metabolic potential of an organism using constraint-based modelling approaches. subClassOf: domain model seeAlso: http://identifiers.org/pubmed/21993642 Preferred Name: Patient-derived genome-scale model Definitions: A stoichiometric model of metabolism...
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Terms for Genome-scale and Patient-derived genome scale models
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Proposed definitions are Preferred Name: Genome-scale model Definitions: A stoichiometric model of metabolism derived from information found in the genome and used to describe the metabolic potential of an organism. It is valuable for investigations on metabolic potential of an organism using constraint-based modelling approaches. subClassOf: domain model Preferred Name: Patient-derived genome-scale model Definitions: A stoichiometric model of metabolism generated using data (example: transcriptomic)...
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Terms for Genome-scale and Patient-derived genome scale models
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SBO:0000492 - amplitude with a parent SBO:0000002 - quantitative systems description parameter was created.
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sbo terms for reaction rates
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Closing this ticket as it has been dealt with in ticket #105
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Closing this ticket as it has been dealt with in #105
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refining SBO:0000475 - "periodic light forcing function"
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ticket will be closed now due to no further comments or updates.
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transport reaction direction
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ticket will be closed now due to no further comments or updates.
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Ticket will be closed as there has been no further discussion or update to these terms.
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Sideproduct and sidesubstrate
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Ticket closed as there has been no further discussion or update to these terms.
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Reversible and irreversible reaction or process
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Reversible and irreversible reaction or process
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Created SBO:0000650 - reversible process and SBO:0000651 - irreversible process. Best, Varun
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Created terms SBO:0000650 - reversible process and SBO:0000651 - irreversible process. Best, Varun
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Created terms SBO:0000650 - reversible reaction and SBO:0000651 - irreversible reaction. Best, Varun
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Enzymatic catalysis
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Please have a look at the term for catalysis SBO:0000172. This can be useful for this purpose. Best, Varun
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SBO:0000641 created by Nick Juty.
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high and low affinity receptors
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dimer and homodimer
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Request for adding the term "growth rate" for parameter annotation
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Request for adding the term "effective catalytic enzyme rate" for parameter annotation
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Flux balance framework
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Destinguishing flux bound parameters
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pseudoreaction terms
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Request for DNA Region and RNA Region SBO Term
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SBO terms to facilitate SBML/BioPAX mappings
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SBOL participant (object) roles request
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pMg parameter
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Term request: biomass
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Dear Matthias, Thank you for your feedback via email. The term for biomass is now online and can be referred to using the id SBO:0000649. I will now close this ticket. Thank you for your support. Best, Varun
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Term request: biomass
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Term request: biomass
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Dear Matthias, Following our email conversation, we will be creating a new term for biomass under SBO:0000241. Kindly comment on the definition for the term that we are considering. biomass - A composite representation of material entities required for organismal growth. It includes macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and atomic composition (eg. nitrogen atoms). Varun
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Dear Matthias, Following our email conversation, we will be creating a new term for biomass under SBO:0000241. Before the term is madeKindly comment on the definition for the term that we are considering. biomass - A composite representation of material entities required for organismal growth. It includes macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and atomic composition (eg. nitrogen atoms). Varun
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Dear Matthias, Following our email conversation, we will be creating a new term for biomass under SBO:0000241. Kindly comment on the definition for the term that we are currently considering. biomass - A composite representation of material entities required for organismal growth. It includes macromolecular content (eg. cellular protein fraction), metabolic constitution of each fraction (eg. amino acids), and atomic composition (eg. nitrogen atoms). Varun
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Dear Matthias, Thank you for the term request. Why not use one of the terms under material entity (SBO:0000240) or functional entity (SBO:0000241) nodes for this ? Varun
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Term request: biomass
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Compound and enzyme molecular mass
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Dear Wolf, Thank you for your term request. I have now created two new terms SBO:0000647 and SBO:0000648. Regards, Varun P.S. Nick has recently completed his stint at EMBL-EBI and will no longer be curating SBO
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Compound and enzyme molecular mass
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Compound and enzyme molecular mass
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Mathml for this term has been updated and the bug has been fixed. You can now see...
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Add SBO for mass action rate law for reversible reactions, continuous scheme
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Term created by Nick Juty.
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Term created by Nick Juty.
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Term created by Nick Juty.
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Term created by Nick Juty
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pMg parameter
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Add SBO for mass action rate law for reversible reactions, continuous scheme
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Dear Stefan, As per your request, this term has now been created (SBO:0000646). We...
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