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The following extension of the MITE Standard JSON Schema is proposed: Extending the Data Standard to explicitly add one or more co-factors that are involved in the reaction. This addition would be on a reaction-level as a list of controlled terms. More details will be added at a later date. |
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I propose the following changes to the MITE Standard JSON Schema: Add explicit non-substrates to MITE entries MotivationMachine leaning application on enzyme substrate or reaction predictions often lack explicit, experimentally verified negative data (i.e. no reaction on this substrate). Currently, such applications create their negative data by e.g. random sampling of the chemical space, assuming that reactions are unlikely to occur on a random reactant/substrate. This assumption may not be valid in case of very promiscuous enzymes (e.g. JamD). By allowing MITE to store a list of experimentally verified non-substrates, this would not only support machine learning applications, but also allow to store this information, which is otherwise not available in a machine-readable format. Possible implementation
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This thread organizes all public communication with regard to the MITE Data Standard Schema.
Please add your proposals for changes of the MITE Schema to this thread. The MITE Governing Body (defined in GOVERNANCE) will meet regularly to review proposals and decide on changes based on majority vote. The decision will also be posted in this thread.
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