Get the colour-coded class landscape of an ontology as SVG
has assertion: assertion
has provenance: provenance
has publication info: pubinfo
type: Nanopublication
created: 2026-08-26T13:28:51Z
creator: Tobias Kuhn
license: https://creativecommons.org/publicdomain/zero/1.0/
embeds: Get the colour-coded class landscape of an ontology as SVG

Get the colour-coded class landscape of an ontology as SVG
description: Renders the classes of the given ontology or vocabulary as an inline SVG figure: an Euler ('Venn-style') diagram in which every class is one small dot, positioned by which of four sets it belongs to and coloured by a chosen facet. The four sets are: whether the class sits in a chemical group (it declares an rdfs:subClassOf other than the vocabulary's top class peh:BioChemEntity), whether it is a metabolite of another entity (peh:isMetaboliteOf), whether it is an isomer of another entity (peh:isIsomerOf), and whether it has a role (obo:RO_0000087). Metabolite and isomer are disjoint in this data and every isomer is also in a chemical group, so the isomer set is drawn nested inside the chemical-group set; the sets are drawn as overlapping rounded rectangles rather than circles, so that each resulting region holds an exactly aligned grid of dots, and a class in none of the four sets sits in the surrounding 'universe' frame. Each region is annotated with its own count and each set with its total. The optional colourby parameter selects what the dot colour means: with colourby=role the dots are coloured by the class's role, and with the parameter left out (the default) they are coloured by its chemical group. Either way the eight largest values get their own colour, ranked at query time, with separate shades for a smaller value and for classes that have none, and the legend is generated from the same ranking and gives each value's full size in the vocabulary. This is the simpler sibling of 'Get the class landscape of an ontology as SVG', which instead subdivides the chemical-group and role sets into labelled sub-boxes: the same information, but split over two colourings that are easier to read one at a time. Role identifiers are normalised to a CHEBI:NNNNN key, so that the same role expressed as an obolibrary or an identifiers.org URI counts once, and their display names are supplied by a lookup table inside the query, falling back to the bare CHEBI identifier for a role…
license: LICENSE-2.0
type: grlc-query
sparql: prefix owl: <http://www.w3.org/2002/07/owl#> prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> prefix dct: <http://purl.org/dc/terms/> prefix np: <http://www.nanopub.org/nschema#> prefix npa: <http://purl.org/nanopub/admin/> prefix npx: <http://purl.org/nanopub/x/> prefix gen: <https://w3id.org/kpxl/gen/terms/> prefix peh: <https://w3id.org/peh/terms/> prefix obo: <http://purl.obolibrary.org/obo/> prefix foaf: <http://xmlns.com/foaf/0.1/> prefix xsd: <http://www.w3.org/2001/XMLSchema#> select ?svg where { { select (group_concat(?cellBlock; separator="") as ?body) (sum(?ccount) as ?total) (sum(if(contains(?sets, "G"), ?ccount, 0)) as ?nGroup) (sum(if(contains(?sets, "M"), ?ccount, 0)) as ?nMet) (sum(if(contains(?sets, "I"), ?ccount, 0)) as ?nIso) (sum(if(contains(?sets, "R"), ?ccount, 0)) as ?nRole) where { { select ?sets ?x0 ?y0 ?cols (count(?class) as ?ccount) (group_concat(?dot; separator="") as ?dots) where { { select ?class ?label ?sets ?groupKey ?roleKey ?parentLabel (count(?o2) - 1 as ?rank) where { { select ?class ?label (?sets_ as ?sets) (?groupKey_ as ?groupKey) (?roleKey_ as ?roleKey) (?parentLabel_ as ?parentLabel) (min(?sortkey_) as ?sortkey) where { values ?_ontology_multi_iri {} service <https://w3id.org/np/l/nanopub-query-1.1/repo/spaces> { select (group_concat(?mpk; separator=" ") as ?memberPubkeys) where { graph npa:graph { npa:thisRepo npa:hasCurrentSpaceState ?stateG . } values ?_ontology_multi_iri {} graph ?stateG { ?_ontology_multi_iri npa:isMaintainedBy? ?space . ?ri a gen:RoleInstantiation ; npa:forSpace ?space ; npa:forAgent ?agent ; npa:hasRoleType ?rt . filter(?rt in (gen:AdminRole, gen:MaintainerRole, gen:MemberRole)) ?acct a npa:AccountState ; npa:agent ?agent ; npa:pubkey ?mpk . } } } graph npa:graph { ?np npx:hasNanopubType owl:Class ; npa:hasValidSignatureForPublicKeyHash ?pubkey ; dct:created ?date ; npx:introduces ?class ; np:hasAssertion ?a . filter not exists { ?npx npx:invalidates ?np ; npa:hasValidSignatureForPublicKeyHash ?pu…

sig
has algorithm: RSA
signed by: Tobias Kuhn