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Better classification of the repositories and minimum information standards #25

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xiaoranzhou opened this issue Jul 3, 2024 · 0 comments

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@xiaoranzhou
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I need suggestions and ideas to better connect the

  1. Type of data:
    Genetic data
    Other NGS (genomics)
    Cloned DNA
    Transcriptomics
    RNAseq
    Metabolomics
    Proteomics
    Plant phenotypic data
    Targeted assays (e.g. glucose and fructose content)
    Image datasets
    Models
    Code
    Excel
  2. The repositories:
    NCBI-GenBank
    NCBI-SRA (Sequence Read Archive)
    NCBI-GEO (Gene Expression Omnibus)
    EBI-ENA (European Nucleotide Archive)
    EBI-ArrayExpress
    EBI-Metabolights
    EBI-PRIDE (PRoteomics IDEntifications Database)
    EBI-BioImage Archive
    IDR (Image Data Resource)
    e!DAL-PGP (Plant Genomics & Phenomics Research Data Repository)
    Metabolomics Workbench
    PDB (Protein Data Bank)
    Chebi (Chemical Entities of Biological Interest)
    Other Endpoint Repositories:
  3. The minimal information standards:
    MIAPPE (Minimum Information About a Plant Phenotyping Experiment)
    MIxS (Minimum Information about any (X) Sequence)
    MigsEu (Minimum Information about a Genome Sequence: Eucaryote)
    MigsOrg (Minimum Information about a Genome Sequence: Organelle)
    MIMS (Minimum Information about Metagenome or Environmental)
    MIMARKSSpecimen (Minimal Information about a Marker Specimen: Specimen)
    MIMARKSSurvey (Minimal Information about a Marker Specimen: Survey)
    MISAG (Minimum Information about a Single Amplified Genome)
    MIMAG (Minimum Information about Metagenome-Assembled Genome)
    MIAMET (Minimum Information About a METabolomics experiment)
    MINSEQE (Minimum Information about a high-throughput SEQuencing Experiment)
    REMBI (Recommended Metadata for Biological Images)
    MIAPE (Minimum Information About a Proteomics Experiment)
    MIMix (Molecular Interactions)
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