{"id":22777281,"url":"https://github.com/omicsdi/omicsdi-databases","last_synced_at":"2026-01-08T07:36:12.972Z","repository":{"id":143170339,"uuid":"120479462","full_name":"OmicsDI/omicsdi-databases","owner":"OmicsDI","description":null,"archived":false,"fork":false,"pushed_at":"2018-02-06T16:23:37.000Z","size":9,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":9,"default_branch":"master","last_synced_at":"2025-02-05T15:17:58.054Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OmicsDI.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-02-06T15:32:43.000Z","updated_at":"2018-02-06T15:32:53.000Z","dependencies_parsed_at":null,"dependency_job_id":"58af50ea-a897-479b-8724-c94c796cfd94","html_url":"https://github.com/OmicsDI/omicsdi-databases","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2Fomicsdi-databases","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2Fomicsdi-databases/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2Fomicsdi-databases/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OmicsDI%2Fomicsdi-databases/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OmicsDI","download_url":"https://codeload.github.com/OmicsDI/omicsdi-databases/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246323313,"owners_count":20758946,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-12-11T19:13:39.690Z","updated_at":"2026-01-08T07:36:12.946Z","avatar_url":"https://github.com/OmicsDI.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# List of omics databases by type omicst-type \n\n## Genomics \n\n- dbGap : https://www.ncbi.nlm.nih.gov/gap\n- SRA : https://www.ncbi.nlm.nih.gov/sra\n- Epigenomics: http://www.roadmapepigenomics.org/\n- Rat Genome Database: http://rgd.mcw.edu/\n- ClinVar : https://www.ncbi.nlm.nih.gov/clinvar/\n- ENA: http://www.ebi.ac.uk/ena\n- Ensembl: http://www.ensembl.org/index.html\n- Ensembl Genomes: http://ensemblgenomes.org/\n- EGA: https://www.ebi.ac.uk/ega/home\n- GeneCards http://www.genecards.org/\n\n## Gene Expression: \n\n- Gemma: http://www.chibi.ubc.ca/Gemma/home.html\n- GEO http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4356\n- BioGPS http://biogps.org/#goto=welcome\n- Expression Atlas - https://www.ebi.ac.uk/gxa/home\n- Brain Map Project http://brain-map.org/ \n- ArrayExpress: https://www.ebi.ac.uk/arrayexpress/\n- Mouse Expression Atlas http://www.emouseatlas.org/\n- Bgee https://bgee.org/\n\n## GWAS Databases\n \n- GWAS Central: http://help.gwascentral.org/info/web-services/search/ \n \n## Interactions \n\n- Intact: Protein http://www.ebi.ac.uk/intact/\n- STRING-db: http://string-db.org/\n- MINT: http://mint.bio.uniroma2.it/mint\n \n## Models \n- BioModel. (BioModels/System Biology)\n \n## Pathways:\n\n- Reactome www.reactome.org \n- Wikipathways http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice/API, API     http://webservice.wikipathways.org/listPathways\n- KEEG (http://www.kegg.jp/kegg/rest/keggapi.html)\n\n## Proteomics:\n\n- Yed Med Database: https://yped.med.yale.edu:8443/repository/\n- ProteomeForms : http://repository.topdownproteomics.org/proteoforms/?DataSetId=1\n- ProteomicsDB : https://www.proteomicsdb.org/\n- PaxDB. https://pax-db.org/\n- Chorus https://chorusproject.org/pages/index.html \n- PRIDE: https://www.ebi.ac.uk/pride/archive/\n- PeptideAtlas: www.peptideatlas.org \n- HPA : http://www.proteinatlas.org\n \n## Structures:\n\n- Biological Magnetic Resonance Data Bank http://www.bmrb.wisc.edu/\n- PDB : www.rcsb.org/pdb/\n \n## Metabolomics \u0026 Small molecules \n\n- ChEBI: https://www.ebi.ac.uk/chebi/\n- ChEMBL: https://www.ebi.ac.uk/chembl/\n- MetaboLights: http://www.ebi.ac.uk/metabolights/\n\n## Protein Sequences \u0026 Profein families \n\n- UniProt: http://www.uniprot.org/\n- InterPro: https://www.ebi.ac.uk/interpro/\n- Pfam: http://pfam.xfam.org/\n- CATH/Gene3D: http://www.cathdb.info/\n- GlycoSuiteDB http://www.unicarbkb.org/\n- MobiDB - http://mobidb.bio.unipd.it/\n\n## Enzymes \n\n- Cazy: http://www.cazy.org/\n- Enzyme Portal: www.ebi.ac.uk/enzymeportal\n\n\n## Other Databases\n\n- SILVA: https://www.arb-silva.de/\n- BRENDA: www.brenda-enzymes.org\n- CATH-Gene3D: http://www.cathdb.info/\n- IUPHAR/BPS: http://www.guidetopharmacology.org/\n- Pathogen-Host Interaction Database: http://www.phi-base.org/\n- Biomedical Atlas Centre: \n- ORCAE: http://bioinformatics.psb.ugent.be/orcae/\n- PLAZA: http://bioinformatics.psb.ugent.be/plaza/\n- NGS-Logistics: https://ngsl.esat.kuleuven.be\n- BBMRI.fi: http://www.bbmri.fi\n- IS Finder: https://www-is.biotoul.fr\n- CRISPRdb: http://crispr.u-psud.fr/crispr/\n- MetExplore: http://www.metexplore.fr\n- GiantVirus: http://www.giantvirus.org\n- RNAspace: http://www.rnaspace.org\n- GnpIS: http://urgi.versailles.inra.fr/gnpis\n- Orphanet: http://www.orpha.net\n- RaDICO: http://www.radico.fr/fr/\n- ACSN: https://acsn.curie.fr\n- IMGT: http://www.imgt.org\n- HOVERGEN: http://pbil.univ-lyon1.fr/databases/hovergen.php\n- HOGENOM: http://doua.prabi.fr/databases/hogenom/home.php?contents=query\n- HOMOLENS: http://pbil.univ-lyon1.fr/databases/homolens.php\n- ASPicDB\n- DIGIT\n\n- CoarkOakDB\n- TreePortal\n- GOMapMan: http://www.gomapman.org\n- BASE: http://base.thep.lu.se\n- FireDB\n- MoDEL\n- CellBase\n- CentrosomeDB\n- ABS\n- HCAD\n- EPD\n- Progenetix\n- OrthoDB\n- ImmunoDB\n- miROrtho\n- http://bigg.ucsd.edu/advanced_search\n- PROSITE\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomicsdi%2Fomicsdi-databases","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fomicsdi%2Fomicsdi-databases","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fomicsdi%2Fomicsdi-databases/lists"}