Activity for Systems Biology Ontology
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Anonymous created ticket #147
Term request: recombination
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Jonathan Karr posted a comment on ticket #138
Added to SBO
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New modeling framework for particle-based discrete spatial simulation
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New terms for hybrid frameworks
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Added to SBO
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population-based discrete non-spatial simulation
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Added to SBO
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population-based discrete spatial simulation
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Added to SBO
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New term for deterministic non-spatial continuous framework
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Added to SBO
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New term for stochastic non-spatial continuous framework
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Added to SBO
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New term for deterministic non-spatial continuous framework
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Added to SBO
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stochastic non-spatial continuous framework
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Added to SBO
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New modeling framework for particle-based discrete spatial simulation
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Added to SBO
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Summary of tickets 137-145
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Added to SBO
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Anonymous posted a comment on ticket #139
Revised request: (a) name: hybrid framework parent: SBO_0000004 description: Modelling approach which combines multiple canonical modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and ordinary differential equations....
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Revised request: (a) name: hybrid framework parent: SBO_0000004 description: Modelling approach which combines multiple canonical modeling frameworks. For example, a hybrid model could consider both continuous (represented by real values) and discrete (represented by integers) participants. Hybrid models are executed with hybrid simulation algorithms. For example, a hybrid continuous-discrete model may be simulation using a combination of stochastic simulation and ordinary differential equations....
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Summary of tickets 137-145
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stochastic non-spatial continuous framework
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New term for deterministic non-spatial continuous framework
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Anonymous created ticket #143
New term for stochastic non-spatial continuous framework
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Anonymous created ticket #142
New term for deterministic non-spatial continuous framework
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Anonymous created ticket #141
population-based discrete spatial simulation
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Anonymous created ticket #140
population-based discrete non-spatial simulation
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Anonymous created ticket #139
New terms for hybrid frameworks
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New modeling framework for particle-based discrete spatial simulation
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New modeling framework for particle-based discrete spatial simulation
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Krishna Tiwari modified ticket #136
Apparent kcat values
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New SBO entry created for forward and reverse catalytic rates.
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Anonymous created ticket #136
Apparent kcat values
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SBO:0000672 term created for Spontaneous reaction.
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spontaneous reaction
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Andreas Dräger created ticket #135
spontaneous reaction
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Term for non-enzymatic catalysts
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New term created for Non-enzymatic Catalysts (SBO:0000671) under catalyst.
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non-enzymatic catalysts term (SBO:0000671) created under catalyst as child
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Eike Pertuch created ticket #134
Term for non-enzymatic catalysts
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Protein chain length
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Yield
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Feedback regulation
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Request ontology "Inactivation"
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http://wwwdev.ebi.ac.uk/sbo/main/search?query=SBO%3A0000665
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added in SBO term with id SBO:0000665
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Request ontology "Inactivation"
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Anonymous created ticket #132
Yield
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Anonymous created ticket #131
Protein chain length
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Anonymous created ticket #130
self-regulation
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Anonymous created ticket #129
Logistic Growth
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Nicolas Le Novère modified ticket #128
Object role for SBO:Containment
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Anonymous created ticket #128
Object role for SBO:Containment
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We will also need mutant and wild type.
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Terms for describing of higher-level entities
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It might be so, but "charge" is universally used in chemistry and biochemistry, including in FBA models, for the electric charge. It would be incredibly confusing to use the term for another meaning.
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Nicolas Rodriguez modified ticket #125
Charge
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Anonymous posted a comment on ticket #125
The definition of charge in this form can be found in the textbook by Palsson (2011) "Systems Biology: Simulation of Dynamic Network States," p. 27, eq. 2.17: charge = occupancy / capacity. There you can also find explanation about the energy charge, the catabolic and anabolic redox charges, and many more. It would be nice if aggregate variables in biological models could be annotated using the exact same term that is used in relevant textbooks.
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Anonymous created ticket #126
Request ontology "Inactivation"
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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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Support for activation and inhibition in population-based models
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In short, the "capacity" can be describe as the total amount that can be contained or produced by a specific entity.
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Charge
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Occupancy
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Capacity
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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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[adding Vasundra to the discussion. I think the initial mail only went to SF] On 20/01/18 23:49, Varun Kothamachu wrote: 3. Co-transport (Parent term: SBO:0000185 - transport reaction) A biochemical process involving the simultaneous transport of two substances across a membrane via a protein or protein complex. I will change SBO:0000185 - transport reaction to SBO:0000185: translocation reaction (Parent term: SBO:0000167 - biochemical or transport reaction) and create child terms to translocation...
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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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Make "hydrolysis" a child of "conversion"
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Thank you Vasundra. Many of those terms are already in SBO, but some would indeed be welcome additions. SBO terms are nouns, not verbs. I think the difference comes from the fact that despite its name, Reactome is not a reaction database but a physical entityffunction database (initialy gene product - its original name was the "Genome Knowledge Base"). So the terms characterise a gene product or a chemical compound. But we can draw equivalences. TRANSFORMS TO ? seems to be SBO:0000167 - biochemical...
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Vasundra Toure created ticket #121
Terms request for Event/Reaction representation in Reactome
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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
