pku-embl/metagenomics-skills/biosurfdb

BioSurfDB

Portal: https://www.biosurfdb.org/ · Tutorial: https://www.biosurfdb.org/tutorial.php

Citation

Oliveira, J. S. et al. BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies. Database 2015, bav033 (2015). https://doi.org/10.1093/database/bav033

See also docs/references.md.

Analytical thinking

BioSurfDB integrates biosurfactant catalogues, biodegradation-relevant genes / pathways, and metagenome-oriented BLAST utilities. Useful for surfactant class exploration and HC biodegradation context. Large private metagenome uploads may need admin/contact per portal policy — for fully local pipelines prefer hadeg FASTA + DIAMOND.

MEGAN users sometimes map DIAMOND hits onto BioSurfDB classifications — cite both MEGAN and BioSurfDB if used.

Portal contract

BioSurfDB is an interactive web resource; the reviewed public site does not expose a stable versioned CLI/API, so do not invent one. Before upload, confirm data policy and avoid sensitive/unreleased sequence. Record access date, database/site version if displayed, query IDs/checksum, search program, database scope, all thresholds and downloaded raw hit/pathway tables. Take a local copy of the result schema and portal citations.

For auditable local sequence analysis, route to $hadeg with its pinned FASTA/Proteinortho workflow or another licensed downloadable reference. If MEGAN mapping is used, preserve its mapping database release and parameters separately; portal screenshots alone are not machine-readable evidence.

Required deliverable

Export a query manifest, no-hit-inclusive raw result table, threshold/settings record, database/site version or access date, and a candidate table separating sequence similarity, pathway membership, and supporting literature. If the portal cannot export machine-readable rows or disclose its active database, label the analysis exploratory/non-reproducible and route production screening to a pinned local reference.

Decision tree

Biosurfactant / biodegradation portal need?
├─ Curated portal / pathway browse → biosurfdb
├─ Local experimental gene DB → hadeg
├─ Glycan DOM → dbcan
└─ BGC structure → antismash

Validation and interpretation

Reconcile every portal result to submitted query IDs, retain no-hit queries, verify coordinates/scores/annotations where exported, and cross-check priority hits against HADEG, profile HMMs, gene neighborhood or curated literature. If version/database details cannot be recovered, label the run non-reproducible and do not merge it into a frozen production table.

BioSurfDB similarity/pathway labels support candidate biodegradation or biosurfactant potential; they do not establish pathway completeness, expression, compound production or degradation rate.

Related skills

dom-biosurfactant · hadeg · dbcan · antismash · dram · microbial-mining · tool-selection