https://github.com/omicsdi/omicsdi-databases

https://github.com/omicsdi/omicsdi-databases

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• Host: GitHub
• URL: https://github.com/omicsdi/omicsdi-databases
• Owner: OmicsDI
• Created: 2018-02-06T15:32:43.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2018-02-06T16:23:37.000Z (over 8 years ago)
• Last Synced: 2025-02-05T15:17:58.054Z (over 1 year ago)
• Size: 8.79 KB
• Stars: 0
• Watchers: 9
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

          
# List of omics databases by type omicst-type 

## Genomics 

- dbGap : https://www.ncbi.nlm.nih.gov/gap

- SRA : https://www.ncbi.nlm.nih.gov/sra

- Epigenomics: http://www.roadmapepigenomics.org/

- Rat Genome Database: http://rgd.mcw.edu/

- ClinVar : https://www.ncbi.nlm.nih.gov/clinvar/

- ENA: http://www.ebi.ac.uk/ena

- Ensembl: http://www.ensembl.org/index.html

- Ensembl Genomes: http://ensemblgenomes.org/

- EGA: https://www.ebi.ac.uk/ega/home

- GeneCards http://www.genecards.org/

## Gene Expression: 

- Gemma: http://www.chibi.ubc.ca/Gemma/home.html

- GEO http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4356

- BioGPS http://biogps.org/#goto=welcome

- Expression Atlas - https://www.ebi.ac.uk/gxa/home

- Brain Map Project http://brain-map.org/ 

- ArrayExpress: https://www.ebi.ac.uk/arrayexpress/

- Mouse Expression Atlas http://www.emouseatlas.org/

- Bgee https://bgee.org/

## GWAS Databases

 

- GWAS Central: http://help.gwascentral.org/info/web-services/search/ 

 

## Interactions 

- Intact: Protein http://www.ebi.ac.uk/intact/

- STRING-db: http://string-db.org/

- MINT: http://mint.bio.uniroma2.it/mint

 

## Models 

- BioModel. (BioModels/System Biology)

 

## Pathways:

- Reactome www.reactome.org 

- Wikipathways http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice/API, API     http://webservice.wikipathways.org/listPathways

- KEEG (http://www.kegg.jp/kegg/rest/keggapi.html)

## Proteomics:

- Yed Med Database: https://yped.med.yale.edu:8443/repository/

- ProteomeForms : http://repository.topdownproteomics.org/proteoforms/?DataSetId=1

- ProteomicsDB : https://www.proteomicsdb.org/

- PaxDB. https://pax-db.org/

- Chorus https://chorusproject.org/pages/index.html 

- PRIDE: https://www.ebi.ac.uk/pride/archive/

- PeptideAtlas: www.peptideatlas.org 

- HPA : http://www.proteinatlas.org

 

## Structures:

- Biological Magnetic Resonance Data Bank http://www.bmrb.wisc.edu/

- PDB : www.rcsb.org/pdb/

 

## Metabolomics & Small molecules 

- ChEBI: https://www.ebi.ac.uk/chebi/

- ChEMBL: https://www.ebi.ac.uk/chembl/

- MetaboLights: http://www.ebi.ac.uk/metabolights/

## Protein Sequences & Profein families 

- UniProt: http://www.uniprot.org/

- InterPro: https://www.ebi.ac.uk/interpro/

- Pfam: http://pfam.xfam.org/

- CATH/Gene3D: http://www.cathdb.info/

- GlycoSuiteDB http://www.unicarbkb.org/

- MobiDB - http://mobidb.bio.unipd.it/

## Enzymes 

- Cazy: http://www.cazy.org/

- Enzyme Portal: www.ebi.ac.uk/enzymeportal

## Other Databases

- SILVA: https://www.arb-silva.de/

- BRENDA: www.brenda-enzymes.org

- CATH-Gene3D: http://www.cathdb.info/

- IUPHAR/BPS: http://www.guidetopharmacology.org/

- Pathogen-Host Interaction Database: http://www.phi-base.org/

- Biomedical Atlas Centre: 

- ORCAE: http://bioinformatics.psb.ugent.be/orcae/

- PLAZA: http://bioinformatics.psb.ugent.be/plaza/

- NGS-Logistics: https://ngsl.esat.kuleuven.be

- BBMRI.fi: http://www.bbmri.fi

- IS Finder: https://www-is.biotoul.fr

- CRISPRdb: http://crispr.u-psud.fr/crispr/

- MetExplore: http://www.metexplore.fr

- GiantVirus: http://www.giantvirus.org

- RNAspace: http://www.rnaspace.org

- GnpIS: http://urgi.versailles.inra.fr/gnpis

- Orphanet: http://www.orpha.net

- RaDICO: http://www.radico.fr/fr/

- ACSN: https://acsn.curie.fr

- IMGT: http://www.imgt.org

- HOVERGEN: http://pbil.univ-lyon1.fr/databases/hovergen.php

- HOGENOM: http://doua.prabi.fr/databases/hogenom/home.php?contents=query

- HOMOLENS: http://pbil.univ-lyon1.fr/databases/homolens.php

- ASPicDB

- DIGIT

- CoarkOakDB

- TreePortal

- GOMapMan: http://www.gomapman.org

- BASE: http://base.thep.lu.se

- FireDB

- MoDEL

- CellBase

- CentrosomeDB

- ABS

- HCAD

- EPD

- Progenetix

- OrthoDB

- ImmunoDB

- miROrtho

- http://bigg.ucsd.edu/advanced_search

- PROSITE