Microbial Ecology Value Sets
Microbial ecology research spans taxonomy, physiology, environmental genomics, and ecosystem interactions. This view collects value sets from across multiple schema domains -- biology, earth science, and investigation -- that are commonly needed when describing microbial communities and their environments.
Coverage Summary
| Domain | Schema Sources | Enums | Ontologies |
|---|---|---|---|
| Taxonomy and Organisms | bio/taxonomy | 4 | NCBITaxon, ENVO |
| Physiology and Metabolism | bio/relationship_to_oxygen, bio/bio_entities | 3 | ENVO, GO |
| Ecological Interactions | ecological_interactions, bio/bio_entities, industry/mining | 3 | RO, ENVO |
| Sequencing and Genomics | bio/sequencing_platforms, bio/genome_features | 5 | OBI, GENEPIO |
| Aquatic and Subsurface Environments | earth_science/water_resources, earth_science/hydrogeology, earth_science/subsurface | 5 | ENVO, CHEBI |
| Study Design | investigation | 2 | OBI |
Taxonomy and Organisms
Microbial community studies require precise taxonomic classification from domain level through strain. These enums support both fixed lists of common taxa and dynamic lookups against the NCBI Taxonomy.
Enums
- CommonOrganismTaxaEnum -- frequently studied bacteria, archaea, and proteobacteria
- OrganismTaxonEnum -- dynamic taxonomy lookup
- TaxonomicRank -- domain through strain
- BiologicalKingdom -- high-level kingdoms of life
Physiology and Metabolism
Oxygen tolerance and metabolic capabilities are fundamental to characterizing microbial isolates and interpreting metagenome-assembled genomes.
Enums
- RelToOxygenEnum -- aerobe, anaerobe, facultative, microaerophilic
- BiologicalProcess -- biological processes (dynamic, GO-backed)
- BiologicalRole -- functional roles of chemical entities
Ecological Interactions
Microbes exist in complex webs of competition, mutualism, and parasitism. These enums describe biotic interactions and the environmental materials and impacts relevant to microbial ecology fieldwork.
Enums
- BioticInteractionType -- predation, parasitism, mutualism, symbiosis, commensalism
- EnvironmentalMaterial -- soil, sediment, water, biofilm, and other environmental materials
- EnvironmentalImpact -- environmental impacts from industrial and natural processes
Sequencing and Genomics
Amplicon sequencing (16S/18S/ITS), metagenomics, and metatranscriptomics are core methods in microbial ecology. These enums standardize platform, chemistry, library preparation, and genomic feature descriptions.
Enums
- SequencingPlatform -- Illumina, PacBio, Oxford Nanopore, Ion Torrent
- SequencingChemistry -- platform-specific chemistries
- LibraryPreparation -- amplicon, shotgun, Hi-C, and other library types
- GeneFeature -- gene-level features (dynamic)
- GenomeFeatureType -- CDS, rRNA, tRNA, CRISPR, and other genome features
Aquatic and Subsurface Environments
Many microbial ecology studies focus on aquatic systems, groundwater, or subsurface formations. These enums from the earth science domain describe water resources, aquifer types, and subsurface geological contexts.
Enums
- WaterResourceType -- surface water, groundwater, produced water
- WaterQualityParameterType -- pH, dissolved oxygen, turbidity, nitrate
- AquiferType -- unconfined, confined, artesian, karst
- GroundwaterProcessType -- recharge, discharge, saltwater intrusion
- SubsurfaceFormationType -- permafrost, karst, shale, fault zones
Study Design
Microbial ecology experiments range from controlled mesocosms to large-scale field surveys. These investigation enums capture study-level metadata.
Enums
- StudyDesignEnum -- observational, experimental, longitudinal, cross-sectional
- StudyTypeEnum -- field study, laboratory study, computational study