UniProt
UniProtKB provides protein sequence and functional knowledge. Its ID Mapping service supports many cross-database identifiers including UniProtKB, Ensembl, GeneID, RefSeq and HGNC identifiers.
Official programmatic mapping docs ↗Identifier provenance · v0.16
Mappings should say where they came from.
VennScope treats identifier conversion as an explicit, reviewable step. It does not silently relabel identifiers or pretend that related gene, transcript and protein identifiers are interchangeable.
Live mapping in v0.16
UniProt ID Mapping is the live mapping engine enabled in the v0.16 beta for supported source/target routes. When you choose Map IDs and explicitly confirm the online action, the selected identifiers are sent directly from your browser to the UniProt REST ID Mapping service. UniProt does not permit every external-database pair as one direct request, so VennScope uses the documented UniProtKB hub when necessary (for example, source identifier → UniProtKB → target identifier). The mapping route is shown and recorded. The original VennScope dataset is preserved and a new mapped dataset is created only after you review the results.
Recorded provenance
Mapped datasets retain the declared input type, target identifier type, organism metadata, source service, mapping route, mapping access date, original identifiers, mapped identifiers and one-to-many/unmapped status. Publication packages can include identifier-mapping.csv.
Identifier authorities represented
Ensembl
Ensembl assigns stable identifiers to genes, transcripts and translations/proteins and maintains cross-references to external databases.
Official REST documentation ↗HGNC
HGNC maintains approved human gene nomenclature and stable HGNC identifiers. HGNC IDs apply to human genes and should not be treated as cross-species identifiers.
HGNC ↗NCBI
NCBI Gene provides gene identifiers and metadata; RefSeq provides curated/reference sequence accessions; NCBI Taxonomy provides organism identifiers.
NCBI Datasets API ↗Why VennScope does not convert automatically
Mappings can be one-to-many, many-to-one, obsolete, species-dependent or absent. A gene-level comparison can also collapse multiple transcript or protein records. VennScope therefore requires an explicit mapping action, reports ambiguous/one-to-many results and preserves the original list.
Privacy during mapping
Standard set analysis remains local in the browser. Online mapping is different: the identifiers you choose to map are transmitted to the external mapping service. In v0.16 the browser contacts the UniProt service directly; VennScope does not send the other datasets, figure, project file or unrelated identifiers with that request.
Versioning
Database mappings can change as reference resources are updated. For reproducibility, retain the VennScope mapping CSV and access date with your analysis.