2026-06-04 21:27:01 +02:00
<!doctype html>
< html lang = "en" class = "no-js" >
< head >
< meta charset = "utf-8" >
< meta name = "viewport" content = "width=device-width,initial-scale=1" >
2026-08-15 20:56:29 +02:00
< link rel = "prev" href = "../select/" >
2026-06-04 21:27:01 +02:00
< link rel = "next" href = "../../architecture/sequences/invariant/" >
< link rel = "icon" href = "../../assets/images/favicon.png" >
< meta name = "generator" content = "mkdocs-1.6.1, mkdocs-material-9.7.6" >
2026-08-15 20:56:29 +02:00
< title > obitaxonomy crate - obikmer</ title >
2026-06-04 21:27:01 +02:00
< link rel = "stylesheet" href = "../../assets/stylesheets/main.484c7ddc.min.css" >
< link rel = "preconnect" href = "https://fonts.gstatic.com" crossorigin >
< link rel = "stylesheet" href = "https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback" >
< style >: root { --md-text-font : "Roboto" ; --md-code-font : "Roboto Mono" }</ style >
< script > __md_scope = new URL ( "../.." , location ), __md_hash = e =>[... e ]. reduce ((( e , _ )=>( e << 5 ) - e + _ . charCodeAt ( 0 )), 0 ), __md_get = ( e , _ = localStorage , t = __md_scope )=> JSON . parse ( _ . getItem ( t . pathname + "." + e )), __md_set = ( e , _ , t = localStorage , a = __md_scope )=>{ try { t . setItem ( a . pathname + "." + e , JSON . stringify ( _ ))} catch ( e ){}}</ script >
</ head >
< body dir = "ltr" >
< input class = "md-toggle" data-md-toggle = "drawer" type = "checkbox" id = "__drawer" autocomplete = "off" >
< input class = "md-toggle" data-md-toggle = "search" type = "checkbox" id = "__search" autocomplete = "off" >
< label class = "md-overlay" for = "__drawer" ></ label >
< div data-md-component = "skip" >
2026-08-15 20:56:29 +02:00
< a href = "#obitaxonomy-taxonomy-concept-paths" class = "md-skip" >
2026-06-04 21:27:01 +02:00
Skip to content
</ a >
</ div >
< div data-md-component = "announce" >
</ div >
< header class = "md-header md-header--shadow" data-md-component = "header" >
< nav class = "md-header__inner md-grid" aria-label = "Header" >
< a href = "../.." title = "obikmer" class = "md-header__button md-logo" aria-label = "obikmer" data-md-component = "logo" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" >< path d = "M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54" /></ svg >
</ a >
< label class = "md-header__button md-icon" for = "__drawer" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" >< path d = "M3 6h18v2H3zm0 5h18v2H3zm0 5h18v2H3z" /></ svg >
</ label >
< div class = "md-header__title" data-md-component = "header-title" >
< div class = "md-header__ellipsis" >
< div class = "md-header__topic" >
< span class = "md-ellipsis" >
obikmer
</ span >
</ div >
< div class = "md-header__topic" data-md-component = "header-topic" >
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
obitaxonomy crate
2026-06-04 21:27:01 +02:00
</ span >
</ div >
</ div >
</ div >
< script > var palette = __md_get ( "__palette" ); if ( palette && palette . color ){ if ( "(prefers-color-scheme)" === palette . color . media ){ var media = matchMedia ( "(prefers-color-scheme: light)" ), input = document . querySelector ( media . matches ? "[data-md-color-media='(prefers-color-scheme: light)']" : "[data-md-color-media='(prefers-color-scheme: dark)']" ); palette . color . media = input . getAttribute ( "data-md-color-media" ), palette . color . scheme = input . getAttribute ( "data-md-color-scheme" ), palette . color . primary = input . getAttribute ( "data-md-color-primary" ), palette . color . accent = input . getAttribute ( "data-md-color-accent" )} for ( var [ key , value ] of Object . entries ( palette . color )) document . body . setAttribute ( "data-md-color-" + key , value )}</ script >
</ nav >
</ header >
< div class = "md-container" data-md-component = "container" >
< main class = "md-main" data-md-component = "main" >
< div class = "md-main__inner md-grid" >
< div class = "md-sidebar md-sidebar--primary" data-md-component = "sidebar" data-md-type = "navigation" >
< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--primary" aria-label = "Navigation" data-md-level = "0" >
< label class = "md-nav__title" for = "__drawer" >
< a href = "../.." title = "obikmer" class = "md-nav__button md-logo" aria-label = "obikmer" data-md-component = "logo" >
< svg xmlns = "http://www.w3.org/2000/svg" viewBox = "0 0 24 24" >< path d = "M12 8a3 3 0 0 0 3-3 3 3 0 0 0-3-3 3 3 0 0 0-3 3 3 3 0 0 0 3 3m0 3.54C9.64 9.35 6.5 8 3 8v11c3.5 0 6.64 1.35 9 3.54 2.36-2.19 5.5-3.54 9-3.54V8c-3.5 0-6.64 1.35-9 3.54" /></ svg >
</ a >
obikmer
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../.." class = "md-nav__link" >
< span class = "md-ellipsis" >
Home
</ span >
</ a >
</ li >
2026-08-15 20:56:29 +02:00
< li class = "md-nav__item" >
< a href = "../../installation/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Installation
</ span >
</ a >
</ li >
2026-06-04 21:27:01 +02:00
< li class = "md-nav__item md-nav__item--nested" >
2026-08-15 20:56:29 +02:00
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_3" >
2026-06-04 21:27:01 +02:00
2026-08-15 20:56:29 +02:00
< label class = "md-nav__link" for = "__nav_3" id = "__nav_3_label" tabindex = "0" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
Theory
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_3_label" aria-expanded = "false" >
< label class = "md-nav__title" for = "__nav_3" >
2026-06-04 21:27:01 +02:00
< span class = "md-nav__icon md-icon" ></ span >
Theory
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../../kmers/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmers and super-kmers
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../theory/encoding/" class = "md-nav__link" >
< span class = "md-ellipsis" >
DNA encoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../theory/entropy/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Entropy filter
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../theory/minimizer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Minimizer selection
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../theory/indexing/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Partitioning architecture
</ span >
</ a >
</ li >
2026-08-15 20:56:29 +02:00
< li class = "md-nav__item" >
< a href = "../../theory/evolutionary_distances/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Central-position SNP distance (discussion)
</ span >
</ a >
</ li >
2026-06-04 21:27:01 +02:00
</ ul >
</ nav >
</ li >
< li class = "md-nav__item md-nav__item--active md-nav__item--nested" >
2026-08-15 20:56:29 +02:00
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_4" checked >
2026-06-04 21:27:01 +02:00
2026-08-15 20:56:29 +02:00
< label class = "md-nav__link" for = "__nav_4" id = "__nav_4_label" tabindex = "0" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
Implementation
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_4_label" aria-expanded = "true" >
< label class = "md-nav__title" for = "__nav_4" >
2026-06-04 21:27:01 +02:00
< span class = "md-nav__icon md-icon" ></ span >
Implementation
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../superkmer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
SuperKmer
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../kmer/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../chunkreader/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Chunk reader
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../pipeline/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Construction pipeline
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../obipipeline/" class = "md-nav__link" >
< span class = "md-ellipsis" >
obipipeline library
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../storage/" class = "md-nav__link" >
< span class = "md-ellipsis" >
On-disk storage
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../mphf/" class = "md-nav__link" >
< span class = "md-ellipsis" >
MPHF selection
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../unitig_evidence/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Unitig evidence encoding
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../evidence_elimination/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Evidence elimination (discussion)
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../obilayeredmap/" class = "md-nav__link" >
< span class = "md-ellipsis" >
obilayeredmap crate
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../persistent_compact_int_vec/" class = "md-nav__link" >
< span class = "md-ellipsis" >
PersistentCompactIntVec
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../persistent_bit_vec/" class = "md-nav__link" >
< span class = "md-ellipsis" >
PersistentBitVec
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../merge/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Merge command
</ span >
</ a >
</ li >
2026-08-15 20:56:29 +02:00
< li class = "md-nav__item" >
< a href = "../merge_parallelism/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Merge parallelism & memory
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../filtering/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer filtering
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../select/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Select command
</ span >
</ a >
</ li >
2026-06-04 21:27:01 +02:00
< li class = "md-nav__item md-nav__item--active" >
< input class = "md-nav__toggle md-toggle" type = "checkbox" id = "__toc" >
< label class = "md-nav__link md-nav__link--active" for = "__toc" >
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
obitaxonomy crate
2026-06-04 21:27:01 +02:00
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
< a href = "./" class = "md-nav__link md-nav__link--active" >
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
obitaxonomy crate
2026-06-04 21:27:01 +02:00
</ span >
</ a >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" ></ span >
Table of contents
</ label >
< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#concept-path-syntax" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Concept path syntax
2026-06-04 21:27:01 +02:00
</ span >
</ a >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" aria-label = "Concept path syntax" >
2026-06-04 21:27:01 +02:00
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#reserved-character" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Reserved character
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#parse-errors" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Parse errors
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#public-api" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Public API
2026-06-04 21:27:01 +02:00
</ span >
</ a >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" aria-label = "Public API" >
2026-06-04 21:27:01 +02:00
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#taxsegment" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
TaxSegment
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#taxpath" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
TaxPath
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#integration-with-genomeinfo" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Integration with GenomeInfo
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#predicate-operators-in-filter-select" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Predicate operators (in filter / select)
</ span >
</ a >
< nav class = "md-nav" aria-label = "Predicate operators (in filter / select)" >
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
< a href = "#path-pattern-syntax" class = "md-nav__link" >
< span class = "md-ellipsis" >
Path pattern syntax
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
2026-08-15 20:56:29 +02:00
< li class = "md-nav__item" >
< a href = "#rank-aware-queries" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Rank-aware queries
2026-06-04 21:27:01 +02:00
</ span >
</ a >
2026-08-15 20:56:29 +02:00
</ li >
</ ul >
</ nav >
2026-06-04 21:27:01 +02:00
</ li >
</ ul >
</ nav >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item md-nav__item--nested" >
2026-08-15 20:56:29 +02:00
< input class = "md-nav__toggle md-toggle " type = "checkbox" id = "__nav_5" >
2026-06-04 21:27:01 +02:00
2026-08-15 20:56:29 +02:00
< label class = "md-nav__link" for = "__nav_5" id = "__nav_5_label" tabindex = "0" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
Architecture
</ span >
< span class = "md-nav__icon md-icon" ></ span >
</ label >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" data-md-level = "1" aria-labelledby = "__nav_5_label" aria-expanded = "false" >
< label class = "md-nav__title" for = "__nav_5" >
2026-06-04 21:27:01 +02:00
< span class = "md-nav__icon md-icon" ></ span >
Architecture
</ label >
< ul class = "md-nav__list" data-md-scrollfix >
< li class = "md-nav__item" >
< a href = "../../architecture/sequences/invariant/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Sequences
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../architecture/index_architecture/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Kmer index
</ span >
</ a >
</ li >
2026-08-15 20:56:29 +02:00
< li class = "md-nav__item" >
< a href = "../../architecture/siblings/" class = "md-nav__link" >
< span class = "md-ellipsis" >
Sibling annex (discussion)
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../architecture/numa_worker_pools/" class = "md-nav__link" >
< span class = "md-ellipsis" >
NUMA-aware worker pools
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
< a href = "../../architecture/numa_partition_runner/" class = "md-nav__link" >
< span class = "md-ellipsis" >
NUMA-aware partition runner
</ span >
</ a >
</ li >
2026-06-04 21:27:01 +02:00
</ ul >
</ nav >
</ li >
</ ul >
</ nav >
</ div >
</ div >
</ div >
< div class = "md-sidebar md-sidebar--secondary" data-md-component = "sidebar" data-md-type = "toc" >
< div class = "md-sidebar__scrollwrap" >
< div class = "md-sidebar__inner" >
< nav class = "md-nav md-nav--secondary" aria-label = "Table of contents" >
< label class = "md-nav__title" for = "__toc" >
< span class = "md-nav__icon md-icon" ></ span >
Table of contents
</ label >
< ul class = "md-nav__list" data-md-component = "toc" data-md-scrollfix >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#concept-path-syntax" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Concept path syntax
2026-06-04 21:27:01 +02:00
</ span >
</ a >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" aria-label = "Concept path syntax" >
2026-06-04 21:27:01 +02:00
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#reserved-character" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Reserved character
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#parse-errors" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Parse errors
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#public-api" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Public API
2026-06-04 21:27:01 +02:00
</ span >
</ a >
2026-08-15 20:56:29 +02:00
< nav class = "md-nav" aria-label = "Public API" >
2026-06-04 21:27:01 +02:00
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#taxsegment" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
TaxSegment
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#taxpath" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
TaxPath
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
</ ul >
</ nav >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#integration-with-genomeinfo" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Integration with GenomeInfo
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
< li class = "md-nav__item" >
2026-08-15 20:56:29 +02:00
< a href = "#predicate-operators-in-filter-select" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Predicate operators (in filter / select)
</ span >
</ a >
< nav class = "md-nav" aria-label = "Predicate operators (in filter / select)" >
< ul class = "md-nav__list" >
< li class = "md-nav__item" >
< a href = "#path-pattern-syntax" class = "md-nav__link" >
< span class = "md-ellipsis" >
Path pattern syntax
2026-06-04 21:27:01 +02:00
</ span >
</ a >
</ li >
2026-08-15 20:56:29 +02:00
< li class = "md-nav__item" >
< a href = "#rank-aware-queries" class = "md-nav__link" >
2026-06-04 21:27:01 +02:00
< span class = "md-ellipsis" >
2026-08-15 20:56:29 +02:00
Rank-aware queries
2026-06-04 21:27:01 +02:00
</ span >
</ a >
2026-08-15 20:56:29 +02:00
</ li >
</ ul >
</ nav >
2026-06-04 21:27:01 +02:00
</ li >
</ ul >
</ nav >
</ div >
</ div >
</ div >
< div class = "md-content" data-md-component = "content" >
< article class = "md-content__inner md-typeset" >
2026-08-15 20:56:29 +02:00
< h1 id = "obitaxonomy-taxonomy-concept-paths" >< code > obitaxonomy</ code > — taxonomy concept paths</ h1 >
< p >< code > obitaxonomy</ code > is a dependency-free crate that defines a typed representation
of hierarchical concept paths (taxonomic or otherwise) stored in genome metadata.</ p >
< hr />
< h2 id = "concept-path-syntax" > Concept path syntax</ h2 >
< p > A concept path is stored as a metadata value with the prefix < code > taxonomy:/</ code > :</ p >
< div class = "highlight" >< pre >< span ></ span >< code > taxonomy:/enterobacteriaceae@family/Escherichia@genus/Escherichia coli@species
2026-06-04 21:27:01 +02:00
</ code ></ pre ></ div >
2026-08-15 20:56:29 +02:00
< p > Structure:</ p >
2026-06-04 21:27:01 +02:00
< ul >
2026-08-15 20:56:29 +02:00
< li > The < code > taxonomy:/</ code > prefix is the type discriminator. Any metadata value starting
with it is parsed as a < code > TaxPath</ code > ; all others remain plain strings.</ li >
< li > The remainder is one or more < code > /</ code > -separated segments.</ li >
< li > Each segment is < code > name</ code > or < code > name@rank</ code > , where < code > rank</ code > is a label for the
taxonomic level (e.g. < code > family</ code > , < code > genus</ code > , < code > species</ code > ).</ li >
< li > Rank annotations are < strong > optional per segment</ strong > and can be mixed freely.</ li >
< li > Spaces are allowed in both names and ranks.</ li >
2026-06-04 21:27:01 +02:00
</ ul >
2026-08-15 20:56:29 +02:00
< h3 id = "reserved-character" > Reserved character</ h3 >
< p >< code > @</ code > is reserved throughout the taxonomy system and may < strong > not</ strong > appear in:</ p >
2026-06-04 21:27:01 +02:00
< table >
< thead >
< tr >
2026-08-15 20:56:29 +02:00
< th > Context</ th >
< th > Constraint</ th >
2026-06-04 21:27:01 +02:00
</ tr >
</ thead >
< tbody >
< tr >
2026-08-15 20:56:29 +02:00
< td > Segment name</ td >
< td > forbidden</ td >
2026-06-04 21:27:01 +02:00
</ tr >
< tr >
2026-08-15 20:56:29 +02:00
< td > Rank/class label</ td >
< td > forbidden</ td >
</ tr >
< tr >
< td > Metadata key names</ td >
< td > forbidden (used as < code > key@rank</ code > in predicate syntax)</ td >
2026-06-04 21:27:01 +02:00
</ tr >
</ tbody >
</ table >
2026-08-15 20:56:29 +02:00
< p >< code > @</ code > is freely allowed in plain-text metadata values (non-taxonomy).</ p >
< h3 id = "parse-errors" > Parse errors</ h3 >
< table >
< thead >
< tr >
< th > Condition</ th >
< th > Error</ th >
</ tr >
</ thead >
< tbody >
< tr >
< td > Value does not start with < code > taxonomy:/</ code ></ td >
< td >< code > MissingPrefix</ code ></ td >
</ tr >
< tr >
< td > No segments after the prefix</ td >
< td >< code > EmptyPath</ code ></ td >
</ tr >
< tr >
< td > Segment with empty name (consecutive < code > /</ code > )</ td >
< td >< code > EmptySegmentName</ code ></ td >
</ tr >
< tr >
< td > Segment with trailing < code > @</ code > and no rank (< code > name@</ code > )</ td >
< td >< code > EmptyRankName</ code ></ td >
</ tr >
< tr >
< td > Segment with more than one < code > @</ code ></ td >
< td >< code > AmbiguousRank</ code ></ td >
</ tr >
</ tbody >
</ table >
< hr />
< h2 id = "public-api" > Public API</ h2 >
< h3 id = "taxsegment" >< code > TaxSegment</ code ></ h3 >
< p > A single node: a name and an optional rank.</ p >
< div class = "highlight" >< pre >< span ></ span >< code >< span class = "n" > seg</ span >< span class = "p" > .</ span >< span class = "n" > name</ span >< span class = "p" > ()</ span >< span class = "w" > </ span >< span class = "c1" > // & str</ span >
< span class = "n" > seg</ span >< span class = "p" > .</ span >< span class = "n" > rank</ span >< span class = "p" > ()</ span >< span class = "w" > </ span >< span class = "c1" > // Option<& str> </ span >
< span class = "n" > seg</ span >< span class = "p" > .</ span >< span class = "n" > to_string</ span >< span class = "p" > ()</ span >< span class = "w" > </ span >< span class = "c1" > // " name" or " name@rank" </ span >
< span class = "n" > TaxSegment</ span >< span class = "p" > ::</ span >< span class = "n" > parse</ span >< span class = "p" > (</ span >< span class = "n" > s</ span >< span class = "p" > )</ span >< span class = "w" > </ span >< span class = "c1" > // Result< TaxSegment, TaxError> </ span >
</ code ></ pre ></ div >
< h3 id = "taxpath" >< code > TaxPath</ code ></ h3 >
< div class = "highlight" >< pre >< span ></ span >< code >< span class = "n" > TaxPath</ span >< span class = "p" > ::</ span >< span class = "n" > parse</ span >< span class = "p" > (</ span >< span class = "n" > s</ span >< span class = "p" > )</ span >< span class = "w" > </ span >< span class = "c1" > // Result< TaxPath, TaxError> </ span >
< span class = "n" > path</ span >< span class = "p" > .</ span >< span class = "n" > segments</ span >< span class = "p" > ()</ span >< span class = "w" > </ span >< span class = "c1" > // & [TaxSegment]</ span >
< span class = "n" > path</ span >< span class = "p" > .</ span >< span class = "n" > depth</ span >< span class = "p" > ()</ span >< span class = "w" > </ span >< span class = "c1" > // usize — number of segments</ span >
< span class = "n" > path</ span >< span class = "p" > .</ span >< span class = "n" > is_ancestor_of</ span >< span class = "p" > (</ span >< span class = "o" > & </ span >< span class = "n" > other</ span >< span class = "p" > )</ span >< span class = "w" > </ span >< span class = "c1" > // bool — prefix match by name, ranks ignored</ span >
< span class = "n" > path</ span >< span class = "p" > .</ span >< span class = "n" > name_at_rank</ span >< span class = "p" > (</ span >< span class = "s" > " genus" </ span >< span class = "p" > )</ span >< span class = "w" > </ span >< span class = "c1" > // Option<& str> </ span >
< span class = "n" > path</ span >< span class = "p" > .</ span >< span class = "n" > to_string</ span >< span class = "p" > ()</ span >< span class = "w" > </ span >< span class = "c1" > // reconstructs " taxonomy:/…" </ span >
</ code ></ pre ></ div >
< p >< code > is_ancestor_of</ code > compares segment < strong > names</ strong > only — rank annotations are
informational and do not affect the ancestry relation.</ p >
< div class = "highlight" >< pre >< span ></ span >< code >< span class = "kd" > let</ span >< span class = "w" > </ span >< span class = "n" > a</ span >< span class = "p" > :</ span >< span class = "w" > </ span >< span class = "nc" > TaxPath</ span >< span class = "w" > </ span >< span class = "o" > =</ span >< span class = "w" > </ span >< span class = "s" > " taxonomy:/Enterobacteriaceae@family/Escherichia@genus" </ span >< span class = "p" > .</ span >< span class = "n" > parse</ span >< span class = "p" > ()</ span >< span class = "o" > ?</ span >< span class = "p" > ;</ span >
< span class = "kd" > let</ span >< span class = "w" > </ span >< span class = "n" > b</ span >< span class = "p" > :</ span >< span class = "w" > </ span >< span class = "nc" > TaxPath</ span >< span class = "w" > </ span >< span class = "o" > =</ span >< span class = "w" > </ span >< span class = "s" > " taxonomy:/Enterobacteriaceae@family/Escherichia@genus/Escherichia coli@species" </ span >< span class = "p" > .</ span >< span class = "n" > parse</ span >< span class = "p" > ()</ span >< span class = "o" > ?</ span >< span class = "p" > ;</ span >
< span class = "fm" > assert!</ span >< span class = "p" > (</ span >< span class = "n" > a</ span >< span class = "p" > .</ span >< span class = "n" > is_ancestor_of</ span >< span class = "p" > (</ span >< span class = "o" > & </ span >< span class = "n" > b</ span >< span class = "p" > ));</ span >< span class = "w" > </ span >< span class = "c1" > // true</ span >
< span class = "fm" > assert!</ span >< span class = "p" > (</ span >< span class = "n" > b</ span >< span class = "p" > .</ span >< span class = "n" > is_ancestor_of</ span >< span class = "p" > (</ span >< span class = "o" > & </ span >< span class = "n" > a</ span >< span class = "p" > ));</ span >< span class = "w" > </ span >< span class = "c1" > // false</ span >
< span class = "fm" > assert!</ span >< span class = "p" > (</ span >< span class = "n" > a</ span >< span class = "p" > .</ span >< span class = "n" > is_ancestor_of</ span >< span class = "p" > (</ span >< span class = "o" > & </ span >< span class = "n" > a</ span >< span class = "p" > ));</ span >< span class = "w" > </ span >< span class = "c1" > // true (equal ⇒ ancestor)</ span >
< span class = "fm" > assert_eq!</ span >< span class = "p" > (</ span >< span class = "n" > b</ span >< span class = "p" > .</ span >< span class = "n" > name_at_rank</ span >< span class = "p" > (</ span >< span class = "s" > " species" </ span >< span class = "p" > ),</ span >< span class = "w" > </ span >< span class = "nb" > Some</ span >< span class = "p" > (</ span >< span class = "s" > " Escherichia coli" </ span >< span class = "p" > ));</ span >
< span class = "fm" > assert_eq!</ span >< span class = "p" > (</ span >< span class = "n" > b</ span >< span class = "p" > .</ span >< span class = "n" > name_at_rank</ span >< span class = "p" > (</ span >< span class = "s" > " genus" </ span >< span class = "p" > ),</ span >< span class = "w" > </ span >< span class = "nb" > Some</ span >< span class = "p" > (</ span >< span class = "s" > " Escherichia" </ span >< span class = "p" > ));</ span >
< span class = "fm" > assert_eq!</ span >< span class = "p" > (</ span >< span class = "n" > b</ span >< span class = "p" > .</ span >< span class = "n" > name_at_rank</ span >< span class = "p" > (</ span >< span class = "s" > " order" </ span >< span class = "p" > ),</ span >< span class = "w" > </ span >< span class = "nb" > None</ span >< span class = "p" > );</ span >
</ code ></ pre ></ div >
< hr />
< h2 id = "integration-with-genomeinfo" > Integration with < code > GenomeInfo</ code ></ h2 >
< p > At index load time, every metadata value is inspected once:</ p >
2026-06-04 21:27:01 +02:00
< ul >
2026-08-15 20:56:29 +02:00
< li > Starts with < code > taxonomy:/</ code > → parsed into < code > TaxPath</ code > , stored in < code > genome.taxonomy</ code > .</ li >
< li > Otherwise → kept as-is in < code > genome.meta</ code > .</ li >
2026-06-04 21:27:01 +02:00
</ ul >
2026-08-15 20:56:29 +02:00
< div class = "highlight" >< pre >< span ></ span >< code >< span class = "k" > struct</ span >< span class = "w" > </ span >< span class = "nc" > GenomeInfo</ span >< span class = "w" > </ span >< span class = "p" > {</ span >
< span class = "w" > </ span >< span class = "n" > label</ span >< span class = "p" > :</ span >< span class = "w" > </ span >< span class = "nb" > String</ span >< span class = "p" > ,</ span >
< span class = "w" > </ span >< span class = "n" > meta</ span >< span class = "p" > :</ span >< span class = "w" > </ span >< span class = "nc" > HashMap</ span >< span class = "o" > < </ span >< span class = "nb" > String</ span >< span class = "p" > ,</ span >< span class = "w" > </ span >< span class = "nb" > String</ span >< span class = "o" > > </ span >< span class = "p" > ,</ span >< span class = "w" > </ span >< span class = "c1" > // plain text metadata</ span >
< span class = "w" > </ span >< span class = "n" > taxonomy</ span >< span class = "p" > :</ span >< span class = "w" > </ span >< span class = "nc" > HashMap</ span >< span class = "o" > < </ span >< span class = "nb" > String</ span >< span class = "p" > ,</ span >< span class = "w" > </ span >< span class = "n" > TaxPath</ span >< span class = "o" > > </ span >< span class = "p" > ,</ span >< span class = "w" > </ span >< span class = "c1" > // parsed taxonomy metadata</ span >
< span class = "p" > }</ span >
</ code ></ pre ></ div >
< p > The raw string is not duplicated. < code > TaxPath::to_string()</ code > reconstructs the
original value losslessly for serialisation.</ p >
< hr />
< h2 id = "predicate-operators-in-filter-select" > Predicate operators (in < code > filter</ code > / < code > select</ code > )</ h2 >
< p > Path predicates use the < code > ~</ code > / < code > !~</ code > operators. The < strong > stored value</ strong > always starts
with < code > /</ code > (rooted path); the < strong > query pattern</ strong > does not need to.</ p >
< h3 id = "path-pattern-syntax" > Path pattern syntax</ h3 >
2026-06-04 21:27:01 +02:00
< table >
< thead >
< tr >
2026-08-15 20:56:29 +02:00
< th > Pattern</ th >
< th > Semantics</ th >
2026-06-04 21:27:01 +02:00
</ tr >
</ thead >
< tbody >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > A/B</ code ></ td >
< td > contiguous sub-path A then B, anywhere in the value</ td >
2026-06-04 21:27:01 +02:00
</ tr >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > /A/B</ code ></ td >
< td > value starts with A then B (start-anchored)</ td >
2026-06-04 21:27:01 +02:00
</ tr >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > A/B$</ code ></ td >
< td > value ends with A then B (end-anchored)</ td >
2026-06-04 21:27:01 +02:00
</ tr >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > /A/B$</ code ></ td >
< td > value is exactly A then B (fully anchored)</ td >
</ tr >
< tr >
< td >< code > A@x/B</ code ></ td >
< td > A with class < code > x</ code > followed by B with any class</ td >
</ tr >
< tr >
< td >< code > A@x/B@y</ code ></ td >
< td > A with class < code > x</ code > followed by B with class < code > y</ code ></ td >
2026-06-04 21:27:01 +02:00
</ tr >
</ tbody >
</ table >
2026-08-15 20:56:29 +02:00
< p > A segment pattern without < code > @</ code > matches the segment name regardless of its stored class.</ p >
< h3 id = "rank-aware-queries" > Rank-aware queries</ h3 >
< div class = "highlight" >< pre >< span ></ span >< code > key@rank=value
</ code ></ pre ></ div >
2026-06-04 21:27:01 +02:00
< table >
< thead >
< tr >
2026-08-15 20:56:29 +02:00
< th > Predicate form</ th >
< th > Semantics</ th >
2026-06-04 21:27:01 +02:00
</ tr >
</ thead >
< tbody >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > key@rank=value</ code ></ td >
< td > genome's < code > key</ code > has < code > value</ code > at rank < code > rank</ code ></ td >
2026-06-04 21:27:01 +02:00
</ tr >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > key@rank!=value</ code ></ td >
< td > does not</ td >
2026-06-04 21:27:01 +02:00
</ tr >
< tr >
2026-08-15 20:56:29 +02:00
< td >< code > key@rank=v1\|v2</ code ></ td >
< td > value at < code > rank</ code > is < code > v1</ code > or < code > v2</ code ></ td >
2026-06-04 21:27:01 +02:00
</ tr >
</ tbody >
</ table >
2026-08-15 20:56:29 +02:00
< p >< code > ~</ code > combined with < code > @rank</ code > on the key (e.g. < code > key@genus~pattern</ code > ) is not defined
and is rejected at parse time.</ p >
2026-06-04 21:27:01 +02:00
</ article >
</ div >
< script > var target = document . getElementById ( location . hash . slice ( 1 )); target && target . name && ( target . checked = target . name . startsWith ( "__tabbed_" ))</ script >
</ div >
</ main >
< footer class = "md-footer" >
< div class = "md-footer-meta md-typeset" >
< div class = "md-footer-meta__inner md-grid" >
< div class = "md-copyright" >
Made with
< a href = "https://squidfunk.github.io/mkdocs-material/" target = "_blank" rel = "noopener" >
Material for MkDocs
</ a >
</ div >
</ div >
</ div >
</ footer >
</ div >
< div class = "md-dialog" data-md-component = "dialog" >
< div class = "md-dialog__inner md-typeset" ></ div >
</ div >
< script id = "__config" type = "application/json" >{ "annotate" : null , "base" : "../.." , "features" : [], "search" : "../../assets/javascripts/workers/search.2c215733.min.js" , "tags" : null , "translations" : { "clipboard.copied" : "Copied to clipboard" , "clipboard.copy" : "Copy to clipboard" , "search.result.more.one" : "1 more on this page" , "search.result.more.other" : "# more on this page" , "search.result.none" : "No matching documents" , "search.result.one" : "1 matching document" , "search.result.other" : "# matching documents" , "search.result.placeholder" : "Type to start searching" , "search.result.term.missing" : "Missing" , "select.version" : "Select version" }, "version" : null }</ script >
< script src = "../../assets/javascripts/bundle.79ae519e.min.js" ></ script >
< script src = "https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js" ></ script >
</ body >
</ html >
