Glossary

Terms that appear across the vault. Library-specific terms link to their note.

Python data stack

Array — see ndarray. A fixed-size, homogeneously-typed, n-dimensional block of memory plus a shape and strides.

Axis — a dimension of an array. axis=0 is rows (down), axis=1 is columns (across). See Axes and Reductions.

Broadcasting — automatic expansion of array shapes so elementwise operations work on mismatched shapes without copying. See Broadcasting.

Copy-on-Write (CoW) — pandas 3.0 semantics where every indexing result behaves as an independent copy, with the actual copy deferred until a write. See Copy-on-Write.

dtype — the element type of an array or Series (int64, float32, str, category). See NumPy dtypes, pandas dtypes.

Index — the row labels of a pandas object. Not a position. See Index Objects.

ufunc — a NumPy universal function: elementwise, compiled, broadcasting-aware. See ufuncs.

Vectorization — expressing a loop as a whole-array operation so it runs in compiled code. See Vectorization.

View — an array sharing memory with another. Writing to it changes the original. See Views vs Copies.

Plotting

Artist — any drawable matplotlib object: a line, a text, an Axes, the Figure itself. See Matplotlib Artists.

Axes — one plotting panel (confusingly, not "axis"). A Figure holds many Axes. See Figure and Axes.

Figure-level function — a seaborn function that creates and owns its own Figure (relplot, catplot, displot). See Figure-level vs Axes-level.

Facet — a small-multiples grid, one panel per subset. See Faceting.

Sequences and biology

Accession — a versioned database identifier, e.g. NM_000546.6, NC_000017.11. The version suffix matters; sequences change between versions.

CDS — coding sequence: the ATG-to-stop portion of a transcript.

Contig / scaffold — an assembled sequence fragment; in practice, anything in your reference FASTA that is not a primary chromosome.

FASTA / FASTQ — sequence without / with per-base quality. See Applied - FASTA and FASTQ Workflows.

GFF / GTF — feature annotation formats, 1-based closed. See Applied - GFF and Genomic Intervals.

MSA — multiple sequence alignment. See AlignIO.

Phred score — Q = -10 log10(P_error), stored as ASCII with an offset of 33. Q30 = 1 error in 1000.

Reference assembly — GRCh37 (hg19) or GRCh38 (hg38). Coordinates are not comparable between them without liftover.

SeqRecord — Biopython's sequence-plus-metadata container. See SeqRecord.

VCF — variant call format, 1-based. See Applied - Reading VCF with pandas.

Variants and nomenclature

Allele frequency (AF) — proportion of chromosomes in a population carrying the alternate allele.

AssemblyMapper — the hgvs class that projects variants between g., c., n. and p. for a chosen assembly. See AssemblyMapper.

c. / g. / n. / p. / m. — HGVS reference-sequence types: coding DNA, genomic, non-coding RNA, protein, mitochondrial. See HGVS Nomenclature.

HGVS — Human Genome Variation Society; also the nomenclature standard they publish, and the Python library implementing it. See biocommons hgvs.

Left/right shifting — moving an ambiguously-placed indel to the most 5' or most 3' equivalent position. VCF convention is left; HGVS convention is 3'-most (right, on the transcript). Source of endless confusion. See hgvs Normalizer.

Normalization — rewriting a variant into a canonical form so equivalent variants compare equal. See hgvs Normalizer.

Projection — mapping a variant from one reference sequence to another (genome ↔ transcript ↔ protein). See Projection c to g to p.

SeqRepo — biocommons' local, immutable, versioned sequence store. See SeqRepo.

UTA — Universal Transcript Archive: the PostgreSQL database of transcript–genome alignments that hgvs queries. See UTA and Data Providers.

VRS — Variation Representation Specification (GA4GH). A computed, hash-based identifier scheme for variants. The successor concept to string-matching variants; worth knowing about after you master HGVS.

Data modelling

Long / wide — see Tidy Data.

Observational unit — the thing one row represents. Mixing two in one table is the classic tidiness violation.

Split-apply-combine — the grouped-computation pattern. See Split-Apply-Combine.

See also

START HERE · Map of Content · Ecosystem Map