BERDL Collections
Tenant-organized database inventory discovered from BERDL and enriched with curated observatory context.
Snapshot: 2026-04-29T21:35:53.838483+00:00 ยท berdl-spark-connect://metrics.berdl.kbase.us:443
Arkinlab
3 databasesArkinlab Dbcan
arkinlab_dbcan
Discovered BERDL database. Add curated description as this collection is used.
Arkinlab Microbeatlas
arkinlab_microbeatlas
Discovered BERDL database. Add curated description as this collection is used.
Arkinlab Mobilome
arkinlab_mobilome
Discovered BERDL database. Add curated description as this collection is used.
Bervodata
3 databasesBervodata Chess
bervodata_chess
Discovered BERDL database. Add curated description as this collection is used.
Bervodata Fao Soils
bervodata_fao_soils
Discovered BERDL database. Add curated description as this collection is used.
Bervodata Hwsd2
bervodata_hwsd2
Discovered BERDL database. Add curated description as this collection is used.
ENIGMA
2 databasesENIGMA CORAL
enigma_coral
Subsurface microbial ecology and geochemistry data from the ENIGMA SFA project at the Oak Ridge Reservation (ORR), Tennessee. Covers environmental sampling (groundwater from boreholes), 16S ...
Enigma Genome Depot Enigma
enigma_genome_depot_enigma
Discovered BERDL database. Add curated description as this collection is used.
KBase
10 databasesKbase All The Bacteria
kbase_all_the_bacteria
Discovered BERDL database. Add curated description as this collection is used.
KBase Genomes
kbase_genomes
Structural genomics data including contigs, features, and protein sequences from the KBase genome repository.
Pangenome Collection
kbase_ke_pangenome
Pangenome data for 293,059 genomes across 27,690 microbial species derived from GTDB r214. Includes core/accessory gene classification, functional annotations, and ANI relationships.
ModelSEED Biochemistry
kbase_msd_biochemistry
Biochemistry reference data for metabolic modeling. Reactions, compounds, and pathway mappings from ModelSEED.
Ontologies
kbase_ontology_source
Ontology reference data including GO, KEGG, EC numbers, and other controlled vocabularies.
Phenotype Collection
kbase_phenotype
Experimental phenotype data including growth conditions, measurements, and phenotypic outcomes.
UniProt Annotations
kbase_uniprot
UniProt protein annotations for bacterial and archaeal proteins.
Kbase Uniref100
kbase_uniref100
Protein sequence clusters at 50%, 90%, and 100% identity thresholds from UniRef.
Kbase Uniref50
kbase_uniref50
Protein sequence clusters at 50%, 90%, and 100% identity thresholds from UniRef.
Kbase Uniref90
kbase_uniref90
Protein sequence clusters at 50%, 90%, and 100% identity thresholds from UniRef.
KE Science
9 databasesKescience Alphafold
kescience_alphafold
Discovered BERDL database. Add curated description as this collection is used.
Kescience Bacdive
kescience_bacdive
Discovered BERDL database. Add curated description as this collection is used.
Fitness Browser
kescience_fitnessbrowser
Gene fitness data from transposon mutant experiments across 40+ bacterial organisms. Identify essential genes and condition-specific fitness effects.
Kescience Interpro
kescience_interpro
Discovered BERDL database. Add curated description as this collection is used.
Kescience Mgnify
kescience_mgnify
Discovered BERDL database. Add curated description as this collection is used.
Kescience Paperblast
kescience_paperblast
Discovered BERDL database. Add curated description as this collection is used.
Kescience Pdb
kescience_pdb
Discovered BERDL database. Add curated description as this collection is used.
Kescience Pubmed
kescience_pubmed
Discovered BERDL database. Add curated description as this collection is used.
Kescience Webofmicrobes
kescience_webofmicrobes
Discovered BERDL database. Add curated description as this collection is used.
Msyscolo
1 databaseNetl
1 databaseNMDC
4 databasesNMDC Multi-omics
nmdc_arkin
Multi-omics analysis data from the National Microbiome Data Collaborative. Includes functional annotations, embeddings, metabolomics, proteomics, lipidomics, and microbial trait data for int...
Nmdc Metadata
nmdc_metadata
Discovered BERDL database. Add curated description as this collection is used.
NMDC BioSamples
nmdc_ncbi_biosamples
Harmonized NCBI BioSample metadata from the National Microbiome Data Collaborative. Standardized attributes, environmental triads, and dimensional statistics for biosample integration.
Nmdc Results
nmdc_results
Discovered BERDL database. Add curated description as this collection is used.
Pangenome
1 databasePhageFoundry
7 databasesPhagefoundry Acinetobacter Genome Browser
phagefoundry_acinetobacter_genome_browser
Phage genome browsers for specific bacterial hosts including Klebsiella, P. aeruginosa, Acinetobacter, and P. viridiflava.
Phagefoundry Ecoliphages Genomedepot
phagefoundry_ecoliphages_genomedepot
Discovered BERDL database. Add curated description as this collection is used.
Phagefoundry Ecoliphagesgenomedepot
phagefoundry_ecoliphagesgenomedepot
Discovered BERDL database. Add curated description as this collection is used.
Phagefoundry Klebsiella Genome Browser Genomedepot
phagefoundry_klebsiella_genome_browser_genomedepot
Phage genome browsers for specific bacterial hosts including Klebsiella, P. aeruginosa, Acinetobacter, and P. viridiflava.
Phagefoundry Paeruginosa Genome Browser
phagefoundry_paeruginosa_genome_browser
Phage genome browsers for specific bacterial hosts including Klebsiella, P. aeruginosa, Acinetobacter, and P. viridiflava.
Phagefoundry Pviridiflava Genome Browser
phagefoundry_pviridiflava_genome_browser
Phage genome browsers for specific bacterial hosts including Klebsiella, P. aeruginosa, Acinetobacter, and P. viridiflava.
Phagefoundry Strain Modelling
phagefoundry_strain_modelling
Discovered BERDL database. Add curated description as this collection is used.
PlanetMicrobe
2 databasesPlanetmicrobe Planetmicrobe
planetmicrobe_planetmicrobe
Marine microbial ecology data including oceanographic sampling campaigns, environmental samples, sequencing experiments, and taxonomic/functional profiles from metagenomic and amplicon studi...
Planetmicrobe Planetmicrobe Raw
planetmicrobe_planetmicrobe_raw
Marine microbial ecology data including oceanographic sampling campaigns, environmental samples, sequencing experiments, and taxonomic/functional profiles from metagenomic and amplicon studi...
Plantmicrobeinterfaces
1 databasePROTECT
3 databasesPROTECT Pathogen Browser
protect_genomedepot
Pathogen genome browser using the GenomeDepot format. Contains genome, gene, annotation, strain, sample, and taxon data for pathogen surveillance and research.
Protect Integration
protect_integration
Discovered BERDL database. Add curated description as this collection is used.
Protect Mind
protect_mind
Discovered BERDL database. Add curated description as this collection is used.
Usgs
1 databaseCross-Collection Analysis
The collection pages show physical BERDL databases. The BERIL Atlas adds interpretation: data-type lenses, reusable joins, derived products, caveats, and missing complementary data.