# 测试 **Repository Path**: jiang-lichun/test ## Basic Information - **Project Name**: 测试 - **Description**: 测试是否可以用超级链接 - **Primary Language**: Unknown - **License**: Not specified - **Default Branch**: master - **Homepage**: None - **GVP Project**: No ## Statistics - **Stars**: 0 - **Forks**: 0 - **Created**: 2021-05-19 - **Last Updated**: 2021-05-19 ## Categories & Tags **Categories**: Uncategorized **Tags**: None ## README # Introduction of major biomedical databases and usage ## Index - [Introduction of major biomedical databases and usage](#Introduction-of-major-biomedical-databases-and-usage) - [Index](#index) - [With exploding of biomedical data databases are in need](#with-exploding-of-biomedical-data-databases-are-in-need) - [Classification of database](#classification-of-database) - [Basic functions of databases](#basic-functions-of-databases) - [Some tricks and suggestions](#some-tricks-and-suggestions) - [references](#references) ## Biomedical data databases are in need - volume - 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 - [classification of database](#classification-of-database) - [Primary database majorlly deal with data deposit](#primary-database-majorlly-deal-with-data-deposit) - [Secondary and curated database from big projects](#secondary-and-curated-database-from-big-projects) - [Secondary and curated database from analysis and integration](#secondary-and-curated-database-from-analysis-and-integration) - [Other classifications for databases](#other-classifications-for-databases) ### primary-database-majorlly-deal-with-data-deposit - [NCBI](https://www.ncbi.nlm.nih.gov/) - [EBI](https://www.ebi.ac.uk/) - [DDBJ](https://www.ddbj.nig.ac.jp/index-e.html) - [CNCB-NGDC](https://bigd.big.ac.cn/) - [CNGB](https://db.cngb.org/) - [NODE](https://www.biosino.org/node/) - [PDB](https://www.rcsb.org/) - [PDBE](https://www.ebi.ac.uk/pdbe/) - [PDBJ](https://pdbj.org/) - [pride](https://www.ebi.ac.uk/pride/) - [GASID](https://www.gisaid.org/) ### Secondary and curated database from big projects - [Secondary and curated database from big projects](#secondary-and-curated-database-from-big-projects) - [Population Genetics](#population-Genetics) - [Baseline expression](#baseline-expression) - [Cancer genome](#cancer-genome) - [Epigenome](#epigenome) - [High dimension of Genome structure](#high-dimension-of-Genome-structure) - [Single cell sequencing](#single-cell-sequencing) #### Population Genetics - [1000genome](https://www.internationalgenome.org/) - [Human Genetics on T2D](https://t2d.hugeamp.org/) - [pggpopulation](https://www.pggpopulation.org/) - [mbiobank](http://mbiobank.com/search/) #### Baseline expression - [GTEX](https://www.ebi.ac.uk/gxa/baseline/experiments) - [EBI baseline expression](https://www.ebi.ac.uk/gxa/baseline/experiments) - [proteinatlas](http://www.proteinatlas.org/) #### Cancer genome - [TCGA](https://gdac.broadinstitute.org/) - [depmap](https://depmap.org/portal/) - [Target](https://ocg.cancer.gov/programs/target/data-matrix) - [ICGC](https://dcc.icgc.org/) - [CCLE](https://portals.broadinstitute.org/ccle/) #### Epigenome - [ENCODE](https://www.encodeproject.org/) - [Epigenome Roadmap](http://www.roadmapepigenomics.org/data/) #### High dimension of Genome structure - [4Dnucleome](https://commonfund.nih.gov/4Dnucleome) #### Single cell sequencing - [HCA](https://data.humancellatlas.org/) - [MCA](http://bis.zju.edu.cn/MCA/gallery.html) - [HCA-organoid](https://hca-organoid.eu/) - [Single cell portal broadinstitute](https://singlecell.broadinstitute.org/single_cell) ### Secondary and curated database from analysis and integration - [Secondary and curated database from big projects](#Secondary and curated database from big projects) - [General](#general) - [Genetics](#genetics) - [Cancer genomics](#cancer-genomics) - [Single cell sequencing](#single-cell-sequencing) - [Disease and Target](#disease-and-target) - [Drug and Target](#drug-and-target) - [Immune](#immune) - [Ontology and nomenclature](#ontology-and-nomenclature) - [Relationship between moleculars](#relationship-between-moleculars) - [Patents](#patents) - [Other useful database](#other-useful-database) ### Secondary and curated database from analysis and integration #### General - [uniprot](https://www.uniprot.org/) - [UCSC genome browser](https://genome.ucsc.edu/) - [BioGPS](http://biogps.org/#goto=genereport&id=7157) - [Genecards](https://www.genecards.org/) ## 这个其实非常全面了，甚至包括了做实验的试剂、细胞系等的可能来源 #### Genetics - [gnomad](https://gnomad.broadinstitute.org/) - [Exac](http://exac.hms.harvard.edu/#rest-variant) - [dbSNP](https://www.ncbi.nlm.nih.gov/snp/) - [omim](https://www.ncbi.nlm.nih.gov/omim) - [clinvar](https://www.ncbi.nlm.nih.gov/clinvar/intro/) - [HGMD](http://www.hgmd.cf.ac.uk/ac/index.php) commercial - [Decipher](https://www.deciphergenomics.org/) - [GWAS](https://www.ebi.ac.uk/gwas/) - [phewas](https://phewascatalog.org/) - [orphanet](https://www.orpha.net/consor/cgi-bin/index.php) - [retnet](https://sph.uth.edu/retnet/) - [human mitochondrial DNA variatio](https://www.mitomap.org/MITOMAP) #### Cancer genomics - [Cosmic](https://cancer.sanger.ac.uk/cosmic) - [cancer Biportal](https://www.cbioportal.org/) - [Gepia](http://gepia2.cancer-pku.cn/#index) - [drbioright](https://drbioright.org/landing/) --人工智能理解问题并给出结果 - [CIVICdb](https://civicdb.org/) 可以直接用 - [oncokb](https://www.oncokb.org/about) 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](https://ckb.jax.org/) 公开能看到的内容很少 #### Single cell sequencing - [panglaodb](https://panglaodb.se/) - [asap](https://asap.epfl.ch/) - [CancerSEA](http://biocc.hrbmu.edu.cn/CancerSEA/) #### Disease and Target - [opentargets](https://www.opentargets.org/) - [disgenet](https://www.disgenet.org/home/) - [monarch](https://monarchinitiative.org/) Connecting phenotypes to genotypes across species #### Drug and Target - [drugbank](https://go.drugbank.com/about) - [BioGrid](https://thebiogrid.org/) - [chEMBL](https://www.ebi.ac.uk/chembl/) - [bindingdb](https://www.bindingdb.org/ ) - [drugcentral](https://drugcentral.org/) - [dgidb](https://dgidb.org/) DRUG GENE interaction - [pharmgkb](https://www.pharmgkb.org/) - [drug interaction DIDB](https://www.druginteractionsolutions.org/solutions/drug-interaction-database/) - [drug sideeffects](http://sideeffects.embl.de/) - [connectivity map](https://www.broadinstitute.org/connectivity-map-cmap) #### Immune - [IMGT](http://www.imgt.org/) - [TCRdb](http://bioinfo.life.hust.edu.cn/TCRdb/#/) #### Ontology and nomenclature - [Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) - [ICD10](https://www.icd10data.com/ICD10CM/Codes/) - [Disease-Ontology](https://disease-ontology.org/) - [HPO](https://hpo.jax.org/app/) - [Geneontology](http://geneontology.org/) - [KEGG](https://www.genome.jp/kegg/) - [reactome](https://reactome.org/) - [MSIGDB](https://www.gsea-msigdb.org/gsea/msigdb/index.jsp) - [Metabolic Pathway Database](https://metacyc.org/) - 其他商业化的QIGEN的Biobase ingenuity, clarivate Metacore #### Relationship between moleculars - [string PPI](https://string-db.org/) - [BIND](https://www.bindingdb.org/bind/index.jsp) - [genemania](http://genemania.org/) - [protein interaction network](https://omics.bjcancer.org/pina/) - [ligand and receptor](https://www.cellphonedb.org/) - [miRNAtargetscan](http://www.targetscan.org/) - [mirDB](http://mirdb.org/) - [dna motif](https://meme-suite.org/meme/db/motifs) #### Patents - [EPO](https://www.epo.org/) - [USPTO](https://www.uspto.gov/patents/search ) - [WIPO](https://www.wipo.int/patents/en ) - incopat 公司数据 学校有购买使用权 #### Other useful database - [CellMarker](http://biocc.hrbmu.edu.cn/CellMarker/) - [clinicaltrials](https://clinicaltrials.gov/) - [protocol io](https://www.protocols.io/) - [addgene](https://www.addgene.org/) on plasmids - [biotools](https://bio.tools/) 另外有omictools,关于生物信息学分析工具 - [ourworldindata](https://ourworldindata.org/) ### Other classifications for databases By species - [MGI](http://www.informatics.jax.org/) - [flybase](https://flybase.org/) - [tbdb](http://www.tbdb.org/) By type of molecular - [crisprlnc](http://www.crisprlnc.org/) - [licRNA](https://lncipedia.org/) - [brenda-enzyme](https://www.brenda-enzymes.org/) On diease or study area - [brain atlas](https://portal.brain-map.org/) #胡GL老师补充 - [BrainSpan](http://www.brainspan.org/) #胡GL老师补充 - [Human Brain Transcriptome](https://hbatlas.org/） #胡GL老师补充 - [PsychENCODE](http://evolution.psychencode.org/) #胡GL老师补充 - [development.psychencode](http://development.psychencode.org/) #胡GL老师补充 - [risk factors for AD](http://alzrisk.org/) - [scRNA-seq for AD](https://bmbls.bmi.osumc.edu/scread/) single cell RNA-seq for AD By technology - [proteomexchange](http://www.proteomexchange.org/) on proteomics ## Basic functions of databases - Search [NCBI](https://www.ncbi.nlm.nih.gov/) - Analysis [NCBI Blast](https://blast.ncbi.nlm.nih.gov/Blast.cgi) - Visulization [PDB visualize](https://www.rcsb.org/#Category-visualize) ## Some tricks and suggestions - Collect and record databases you find useful from talk, publication, searching - Understand datasoure and limitation, permit issue [uniprot](https://www.uniprot.org/help/uniprotkb_sections) - 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 - [biomedical database Israel Science and Technology Directory](https://www.science.co.il/biomedical/databases) - [bioinformatics-tools database fda](https://www.fda.gov/science-research/bioinformatics-tools)