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Eric Coissac 8c7017a99d ⬆️ version bump to v4.5

- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5"
- Update version.txt from 4.29 → .30
(automated by Makefile)

2026-04-13 13:34:53 +02:00

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`obitax` Package: Taxonomic Data Model and Navigation

The obitax package provides a semantic model for representing, querying, and manipulating taxonomic hierarchies in biodiversity data processing. Its core abstraction is the Taxon type, which encapsulates both structural (node ID, parent/child relationships) and semantic (scientific name, rank, metadata) information.

Core Features

Taxon Representation: Each Taxon links to a taxonomy and its underlying node, supporting multiple name classes (e.g., "scientific name", "common name"), customizable ranks, and extensible metadata via key-value pairs.
String Interoperability: Implements String() for human-readable output (taxonomy:taxid [name]) and provides typed accessors like ScientificName(), Rank(), or IsRoot().

Name Handling & Matching

Flexible name retrieval via Name(class), case-insensitive equality (IsNameEqual), and regex-based matching (IsNameMatching). Names are interned for memory efficiency.

Path Traversal: IPath() yields an iterator from current taxon up to root; Path() materializes this as a slice. Enables efficient lineage queries.
Rank-Based Lookup: Methods like TaxonAtRank(rank), or convenience wrappers (Species(), Genus(), Family()), allow targeted retrieval of higher-level ancestors.
Child Management: Supports dynamic tree extension via AddChild(), parsing taxon strings and enforcing taxonomy consistency.

Metadata Support

Rich metadata operations: SetMetadata, GetMetadata, key/value iteration, and typed conversion (MetadataAsString). Enables attaching arbitrary annotations (e.g., confidence scores, source references).

Robustness & Safety

Nil-safe accessors prevent panics; logging and error handling ensure correctness (e.g., fatal on missing root in IPath()).
Interning of names/ranks/classes (Innerize) reduces duplication and speeds comparisons.

Designed for scalability in large-scale metabarcoding pipelines, obitax bridges raw taxonomic data with high-level analytical operations.

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obitax Package: Taxonomic Data Model and Navigation