Table 3 A non-exhaustive list of organisational databases pooling data from other sources as an analytical tool
From: Ecosystem-specific microbiota and microbiome databases in the era of big data
Functional database | Purpose | Description | References |
|---|---|---|---|
Functional Ontology Assignments for Metagenomes (FOAM) | Functional analysis | Groups environmental metagenomic sequences based on gene functionality instead of taxonomy | [228] |
EXPath | Functional analysis | Groups microarray expression profiles used to infer metabolic pathways for six model plants | [229] |
Ecopath with Ecosim (EWE) (now grouped under EcoBase) | Functional analysis | Information repository of EwE models (modeling software for ecological phenomena) | [230] |
Gulf of Mexico Ecosystem Services Valuation Database (GecoServ) (now called BlueValue) | Ecosystem service evaluation | Worldwide depository of ecosystem valuation data | [231] |
Open access database on climate change effects on littoral and oceanic ecosystems (OCLE) | Ecosystem service evaluation | Ecological-driven database of present and future hazards for European marine life | [232] |
Biofuel Ecophysiological Traits and Yields Database (BETYdb) | Functional analysis | Open-access repository to facilitate the organisation, discovery, and exchange of information about plant traits, crop yields, and ecosystem functions | [233] |
jae-f-database | Functional analysis | Global database and ‘state of the field’ review of research into ecosystem engineering by land animals | [234] |
Genomes OnLine Database (GOLD) | Metadatabase | Collection of genome projects and associated metadata | [235] |
Omics Discovery Index (OmicsDI) | Metadatabase | Groups datasets across multiple public meta-omics data resources | [236] |
Omics database generator (ODG) | Metadatabase | Groups genomics data, integrates with experimental data to create a comparative, multi-dimensional graphical database | [237] |