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蒋立春 / Introduction of public biomedical databases

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README.en.md

Introduction of major biomedical databases and usage

Index

Biomedical data databases are in need

  • volume
    • Growth_of_DNA_sequencing
  • variety
    • Image
    • Genome
    • Transcriptome
    • Epigenome
    • Proteome
    • Structure
    • Metabolome
    • Interactome
    • Microbiome
    • Phenome
    • Exposure
  • value
    • provide standard starting point
    • improve efficiency by sharing
    • reduce reduandant study
    • education

classification of database

primary-database-majorlly-deal-with-data-deposit

Secondary and curated database from big projects

Population Genetics

Baseline expression

Cancer genome

Epigenome

High dimension of Genome structure

Single cell sequencing

Secondary and curated database from analysis and integration

Secondary and curated database from analysis and integration

General

Genetics

Cancer genomics

  • Cosmic
  • cancer Biportal
  • Gepia
  • drbioright --人工智能理解问题并给出结果
  • CIVICdb 可以直接用
  • oncokb 需注册有不同license precision oncology knowledge base that annotates the biological consequences and clinical implications (therapeutic, diagnostic, and prognostic) of genetic variants in cancer.
  • jax 公开能看到的内容很少
  • synthetic lethality

Single cell sequencing

Disease and Target

Drug and Target

Immune

Ontology and nomenclature

Relationship between moleculars

Patents

  • EPO
  • USPTO
  • WIPO
  • incopat 公司数据 学校有购买使用权

Other useful database

Other classifications for databases

By species

By type of molecular

On diease or study area

By technology

Basic functions of databases

Some tricks and suggestions

  • Collect and record databases you find useful from talk, publication, searching
  • Understand datasoure and limitation, permit issue uniprot
  • Read manual or tutorial, run examples
  • Understand matrics and plots
  • Do some sanity check with checking known truth or by cross-checking
  • Read original paper and check citation or visit statistics
  • Record database version information in your results

References

简介

An collection of useful public biomedical databases with brief introduction 生物医学公共数据库 展开 收起
MIT
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