Using a model like this it's more explicit what the data means but still abstract enough to be used in a general way. There are many ontologies and vocabularies providing. To make more known about the JSON data it could be represented as something like this: [ The Smart Data Models Program does not define canonically and uniquely the terms used in the data models. This universal schema should tell the specifics of the attributes of the JSON object, like data types, if a value in JSON could be null and formatting details.įor any general interpreter the date of birth will not be considered as a date but as a string. The idea is, a JSON object is given and needs to be transformed to a more universal JSON.
Molecular Systems Biology 2021(17):e10427.I'm currently working on a universal way of modelling JSON and am looking for existing implementations or research on the idea and am unable to find the correct information, maybe because I don't know what the thing I'm trying to do is called. Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. If you use yeast species GEMs, please cite this latest paper: You could also report an issue at if you have any question or idea about the content in this repo. Data modeling is a process for building more comprehensive and flexible databases by emphasizing fundamental relationships over existing or traditional business. well as the ability to generate diagrams and models from existing. GEM Category: species Utilisation: experimental data reconstruction, multi-omics integrative analysis, in silico strain design, model template, evolution analysis Field: metabolic-network reconstruction Type of Model: reconstruction, curated Model Source: YeastMetabolicNetwork Omic Source: genomics Taxonomy: subphylum Saccharomycotina Metabolic System: general metabolism Strain: budding yeast species Ĭontributions are always welcome! Please firstly establish a new branch based on the dev branch ( ) of this repo. In order to integrate our existing database, lets delete this database and remove connection string information for it from the 'Web.config' file as shown below. DbVisualizer is The Ultimate Universal Database Tool for developers, analysts and DBAs. We hope that this work could set a solid base in modelling simulation and systematic utilization of different yeast species for the wide research community. With the gap-filling and model test verified by the experimental data from different sources, the quality and prediction performances of species GEM will be improved continuously. Next, with the gene function annotation of each yeast species, yeast species-specific GEMs of high quality can be built automatically.
With the advanced GEM of S.cerevisiae (Yeast8, ) developed in our lab, the pan-GEM of for all these sequenced yeast species can be built by adding the new reactions with the gene association into Yeast8 through the detailed pan-genome annotation and mounts of physiological data mining. To further explore how different yeast species with interesting traits evolved in the long history, we built a pan-GEM for nearly all currently sequenced yeast species based on the latest research (Cell, 2018 DOI: 10.1016/j.cell.2018.10.023). Some yeast species, like Saccharomyces cerevisiae and Candida albicans, are very important to our human life and health. Yeast-Species-GEM: The pan-GEM and strain specific GEMs for yeast species with whole-genome sequence.Īs the unicellular fungi, the budding yeasts contain over 1000 different yeast species, which are widely distributed on our earth.
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