Glossary
Plain-language definitions for domain-specific terms used throughout this platform.
DSI
Digital Sequence Information — genetic sequence data and related metadata (genomes, proteins, eDNA reads, etc.), as distinct from the physical biological material it was derived from.
ABS
Access and Benefit-Sharing — the framework (under the Convention on Biological Diversity/Nagoya Protocol) governing fair use of and benefit-sharing from genetic resources, including DSI.
PIC
Prior Informed Consent — permission obtained from the country/community of origin before accessing a genetic resource, as required by ABS frameworks.
MAT
Mutually Agreed Terms — the negotiated conditions (e.g. benefit-sharing arrangements) under which a genetic resource is accessed and used.
IRCC
Internationally Recognized Certificate of Compliance — evidence, under the Nagoya Protocol, that a genetic resource was accessed with proper consent and terms.
Access tier
Who may access a record's raw bytes: public (anyone), regional_researcher (approved request, may involve identity verification), or restricted (approved request, never auto-approved).
License tag
The reuse license attached to a record, independent of its access tier: CC0 (public domain), CC BY (attribution required), or restricted (consult the record).
Citable id
A stable, durable local identifier of the form AFDSI-{TYPE}-{id} minted for every record that reaches the Hub's catalog — not a registered DOI. See "Citation Policy" in Terms of Use.
Hop chain
The sequence of nodes a record has passed through as it was aggregated upward through the federation (e.g. Spoke → National Hub → Sub-regional Hub → Continental Hub).
Origin
How a record entered the platform: native (captured at a node and synced up), mirrored (harvested from an external repository like NCBI/ENA/GBIF), or contributed (submitted directly to the Hub by a node operator, pending review).
Node
A deployed instance of the platform's node service, at one of three tiers: Spoke (an institution's own data holder), National Hub (aggregates Spokes in a country), or Sub-regional Hub (aggregates National Hubs in an AU region).
Continental Hub
The single top-level aggregation point for the whole federation — the Global Access Point for the catalog, admin/curation, mirroring, and access/consent tracking.
Shannon diversity
A measure of species/taxon diversity at a site that accounts for both richness (how many taxa) and evenness (how balanced their relative abundances are) — higher means more diverse.
Simpson diversity
Another alpha-diversity index, measuring the probability that two randomly picked individuals from a site belong to different taxa — higher means more diverse.
Bray-Curtis
A beta-diversity measure of how dissimilar the taxon composition is between two sites (0 = identical, 1 = completely different).
pLDDT
Predicted Local Distance Difference Test — a per-residue confidence score (0–100) for a predicted protein structure; higher means the model is more confident in that region's position.
BUSCO
Benchmarking Universal Single-Copy Orthologs — a genome-assembly-quality metric reporting what percentage of expected single-copy genes were found complete in an assembly.
N50 (scaffold N50)
A genome-assembly contiguity statistic: the length such that half of the assembly's total size is contained in scaffolds at least that long. Higher generally means a more contiguous assembly.
GoaT
Genomes on a Tree (goat.genomehubs.org) — an external service this platform queries to enrich eukaryotic genome records with assembly-quality metadata (level, size, N50, BUSCO, chromosome count).
INSDC
International Nucleotide Sequence Database Collaboration — the joint arrangement between NCBI, ENA, and DDBJ, which mirror each other's submissions daily under a shared open-data policy.
eDNA / metabarcoding
Environmental DNA — genetic material collected from an environmental sample (soil, water, air) rather than a specific organism, classified by comparing short marker sequences against a reference library.
Metagenomics
Shotgun sequencing of all genetic material in an environmental sample, profiled for both taxonomic composition and functional (metabolic pathway) content.
Ortholog
Genes in different species that evolved from a common ancestral gene — this platform clusters proteins across the federated catalog by sequence similarity to surface likely orthologs.