Collapse taxonomy into a single grouped Taxon facet

.github/ISSUE_TEMPLATE/suggest-method.yml

@@ -25,19 +25,15 @@ body:
     validations:
       required: true
   - type: dropdown
-    id: kingdom
+    id: taxon
     attributes:
-      label: Kingdom*
-      multiple: true
-      options: [Animalia, Plantae, Fungi, Chromista, Bacteria, Archaea]
-    validations:
-      required: true
-  - type: dropdown
-    id: phylum
-    attributes:
-      label: Phylum / Division*
+      label: Taxon — phylum / division*
+      description: >-
+        Pick the phylum/division(s). Grouped by kingdom for reference (Animalia,
+        Plantae, Fungi). Choose "Other" if yours isn't listed and describe it below.
       multiple: true
       options:
+        # Animalia
         - Chordata
         - Arthropoda
         - Mollusca
@@ -47,8 +43,10 @@ body:
         - Nematoda
         - Platyhelminthes
         - Porifera
+        # Plantae
         - Tracheophyta
         - Bryophyta
+        # Fungi
         - Ascomycota
         - Basidiomycota
         - "Other (describe in detail box)"

CONTRIBUTING.md

@@ -20,8 +20,7 @@ Add one Markdown file per entry, then open a PR. CI validates it automatically.
 ```yaml
 ---
 title: "Genome skimming from a 40-year-old pinned beetle"
-kingdom: [Animalia]           # one or more, from _data/tags.yml
-phylum: [Arthropoda]          # "Phylum / Division", from _data/tags.yml
+taxon: [Arthropoda]           # phylum/division, from _data/tags.yml (kingdom is implied)
 preservation: [dry-pinned]
 extraction: [silica-column]
 library: [tagmentation]
@@ -37,10 +36,14 @@ Full detail in Markdown. Renders when the card is expanded: protocol notes,
 yields, caveats, links to SOPs in the bibliography, etc.
 ```
 
-Required: `title`, `kingdom`, `phylum`, `preservation`, `extraction`,
-`library`, `sequencing`, `summary`, `contributor`, `date`.
+Required: `title`, `taxon`, `preservation`, `extraction`, `library`,
+`sequencing`, `summary`, `contributor`, `date`.
 Optional: `outcome`, `doi`, body.
 
+`taxon` values are phyla/divisions, grouped under their kingdom in
+`_data/tags.yml`; the kingdom is inferred from that grouping (we represent
+animals, plants and fungi).
+
 ### Bibliography entry — `_bibliography/<short-slug>.md`
 
 ```yaml

README.md

@@ -6,9 +6,9 @@ types, backed by a curated bibliography of supporting papers and SOPs.
 
 🌐 **Site:** https://museomics.github.io/methods/
 
-- **Methods** (`/`) — filter working methods by kingdom, phylum/division,
-  preservation, extraction, library prep, and sequencing. Cards expand to full
-  protocol notes.
+- **Methods** (`/`) — filter working methods by taxon (phylum/division grouped
+  under kingdom), preservation, extraction, library prep, and sequencing. Cards
+  expand to full protocol notes.
 - **Bibliography** (`/bibliography/`) — papers and SOPs, filterable by type and
   method tag.
 - **Contribute** (`/contribute/`) — suggest an entry via issue form, or by PR.

SPEC.md

@@ -1,8 +1,10 @@
 # museomics/methods — Build Spec & Implementation Plan (revised)
 
 > Revision note: this supersedes the original draft. Changes from the review:
-> two-level taxonomy (Kingdom + Phylum/Division) replacing a single taxon
-> facet; GitHub Actions build instead of stock GitHub Pages; a single
+> a single Taxon facet whose values are phyla/divisions grouped under kingdom
+> (Animalia / Plantae / Fungi), presented as one dropdown with per-kingdom
+> select-all — replacing the original flat taxon tag; GitHub Actions build
+> instead of stock GitHub Pages; a single
 > canonical controlled vocabulary enforced by CI; free-text search; sort
 > control; empty state; accessible chips (not colour-alone); optional DOI;
 > optional outcome signal; separate content licence (CC BY 4.0).
@@ -53,16 +55,18 @@ Nav bar on every page: **Methods | Bibliography | Contribute**
 
 ## 1. Methods page (`/`)
 
-Let visitors find and filter working methods by **kingdom**, **phylum/division**,
-preservation, extraction, library prep, and sequencing/downstream method.
-Multi-tagging per entry is supported on every facet.
+Let visitors find and filter working methods by **taxon** (phylum/division,
+grouped under kingdom — Animalia / Plantae / Fungi), preservation, extraction,
+library prep, and sequencing/downstream method. Multi-tagging per entry is
+supported on every facet.
 
 ### Layout (top to bottom)
 1. Header — title + one-line purpose.
-2. Tag legend — collapsible explainer of the six facets and their chip
+2. Tag legend — collapsible explainer of the five facets and their chip
    colours/badges.
 3. Controls — free-text search box + sort control (newest / oldest / A–Z), then
-   a filter bar of six collapsible multi-select facets, populated from
+   a filter bar of five collapsible multi-select facets (Taxon is one grouped
+   dropdown), populated from
    `_data/tags.yml`. OR within a facet, AND across facets.
 4. Results count (live) + "Clear all filters".
 5. Card grid.
@@ -80,8 +84,7 @@ Multi-tagging per entry is supported on every facet.
 ```yaml
 ---
 title: "Genome skimming from a 40-year-old pinned beetle"
-kingdom: [Animalia]
-phylum: [Arthropoda]
+taxon: [Arthropoda]           # phylum/division; kingdom implied by grouping
 preservation: [dry-pinned]
 extraction: [silica-column]
 library: [tagmentation]
@@ -94,7 +97,7 @@ doi: "10.xxxx/xxxxx"          # OPTIONAL — omit for unpublished methods
 ---
 Full detail body as Markdown (renders on expand).
 ```
-Required: title, kingdom, phylum, preservation, extraction, library,
+Required: title, taxon, preservation, extraction, library,
 sequencing, summary, contributor, date. DOI is optional so unpublished /
 in-house methods are not excluded.
 
@@ -108,7 +111,7 @@ in-house methods are not excluded.
   (`window.SITE`) so JS never guesses the baseurl and filter options come from
   the config, not just from values present in the data.
 - Active filters, search text and non-default sort are reflected in the URL
-  query string (`?kingdom=Animalia&preservation=dry-pinned&q=beetle`) and
+  query string (`?taxon=Arthropoda&preservation=dry-pinned&q=beetle`) and
   restored on load.
 
 ---

_data/facets.yml

@@ -3,18 +3,13 @@
 # `abbr` is shown as a small badge on each chip so facets are distinguishable
 # without relying on colour alone (accessibility).
 # `methods` / `bibliography` flag which page a facet applies to.
-- key: kingdom
-  label: Kingdom
-  abbr: K
+- key: taxon
+  label: Taxon
+  abbr: Tx
   color: green
   methods: true
   bibliography: false
-- key: phylum
-  label: Phylum / Division
-  abbr: P
-  color: teal
-  methods: true
-  bibliography: false
+  grouped: true   # values come from a kingdom -> [phyla] map in tags.yml
 - key: preservation
   label: Preservation
   abbr: Pr

_data/tags.yml

@@ -14,31 +14,29 @@
 # except taxonomy, which uses conventional capitalised names.
 # -----------------------------------------------------------------------------
 
-# Taxonomy is split into two levels so visitors can filter broadly (Kingdom) or
-# more specifically (Phylum / Division). Curated by the maintainer; extend as
-# real contributions arrive rather than pre-populating exhaustively.
-kingdom:
-  - Animalia
-  - Plantae
-  - Fungi
-  - Chromista
-  - Bacteria
-  - Archaea
-
-phylum:            # "Phylum / Division" — divisions are the botanical equivalent
-  - Chordata
-  - Arthropoda
-  - Mollusca
-  - Annelida
-  - Echinodermata
-  - Cnidaria
-  - Nematoda
-  - Platyhelminthes
-  - Porifera
-  - Tracheophyta   # vascular plants
-  - Bryophyta      # mosses
-  - Ascomycota
-  - Basidiomycota
+# Taxonomy: a single facet whose values are phyla / divisions, grouped under
+# their kingdom. Entries are tagged at phylum/division level (e.g. taxon:
+# [Arthropoda]); the kingdom is implied by the grouping below. In the filter UI
+# these render as one dropdown with kingdom sub-headings, and each kingdom
+# heading is a "select all" toggle. We only represent animals, plants and fungi.
+# Curated by the maintainer; extend as real contributions arrive.
+taxon:
+  Animalia:
+    - Chordata
+    - Arthropoda
+    - Mollusca
+    - Annelida
+    - Echinodermata
+    - Cnidaria
+    - Nematoda
+    - Platyhelminthes
+    - Porifera
+  Plantae:
+    - Tracheophyta   # vascular plants
+    - Bryophyta      # mosses
+  Fungi:
+    - Ascomycota
+    - Basidiomycota
 
 preservation:
   - dry

_methods/genome-skimming-pinned-beetle.md

@@ -1,7 +1,6 @@
 ---
 title: "Genome skimming from a 40-year-old pinned beetle"
-kingdom: [Animalia]
-phylum: [Arthropoda]
+taxon: [Arthropoda]
 preservation: [dry]
 extraction: [silica-column]
 library: [diy-approach]

_methods/herbarium-plant-target-capture.md

@@ -1,7 +1,6 @@
 ---
 title: "Target capture from herbarium sheets using CTAB extraction"
-kingdom: [Plantae]
-phylum: [Tracheophyta]
+taxon: [Tracheophyta]
 preservation: [dry]
 extraction: [ctab]
 library: [single-stranded]

_methods/study-skin-bird-mitogenome.md

@@ -1,7 +1,6 @@
 ---
 title: "Mitogenome from a historical bird study skin toe pad"
-kingdom: [Animalia]
-phylum: [Chordata]
+taxon: [Chordata]
 preservation: [dry]
 extraction: [magnetic-bead]
 library: [single-stranded]

assets/css/style.css

@@ -98,6 +98,10 @@ main.container { padding-top: 1.6rem; padding-bottom: 3rem; }
 .facet-opts { padding: .5rem .7rem; max-height: 240px; overflow-y: auto; }
 .opt { display: flex; align-items: center; gap: .45rem; padding: .15rem 0; cursor: pointer; }
 .opt input { margin: 0; }
+.facet-subgroup { margin-bottom: .4rem; }
+.facet-subgroup + .facet-subgroup { border-top: 1px solid var(--border); padding-top: .4rem; }
+.opt--group { font-size: .95rem; }
+.opt--child { padding-left: 1.3rem; }
 
 .controls-foot { display: flex; align-items: center; gap: 1rem; margin-top: .9rem; }
 .results-count { margin: 0; font-weight: 600; }

assets/js/app.js

@@ -229,13 +229,56 @@
     }
 
     CONFIG.facets.forEach(function (f) {
+      if (f.grouped) {
+        bar.appendChild(groupedFacet(f));
+        return;
+      }
       var vocab = SITE.vocab[f.key] || [];
       bar.appendChild(facetGroup(f, vocab, filters[f.key], function (val, on) {
         toggleIn(filters[f.key], val, on); update();
       }));
     });
   }
 
+  // A grouped facet (e.g. Taxon): one dropdown whose options are nested under
+  // group headings (kingdoms). Each heading is a select-all toggle for its
+  // children (phyla/divisions). Only the children (leaf values) are stored in
+  // the filter state.
+  function groupedFacet(facet) {
+    var map = SITE.vocab[facet.key] || {};
+    var selectedRef = filters[facet.key];
+
+    var groups = Object.keys(map).map(function (groupName) {
+      var children = map[groupName];
+      var selectedKids = children.filter(function (c) { return selectedRef.indexOf(c) !== -1; });
+
+      var head = el("input", { type: "checkbox" });
+      head.checked = selectedKids.length === children.length && children.length > 0;
+      head.indeterminate = selectedKids.length > 0 && selectedKids.length < children.length;
+      head.addEventListener("change", function () {
+        children.forEach(function (c) { toggleIn(selectedRef, c, head.checked); });
+        update();
+      });
+      var heading = el("label", { class: "opt opt--group" }, [head, el("strong", { text: groupName })]);
+
+      var kids = children.map(function (c) {
+        var box = el("input", { type: "checkbox", value: c });
+        if (selectedRef.indexOf(c) !== -1) box.checked = true;
+        box.addEventListener("change", function () { toggleIn(selectedRef, c, box.checked); update(); });
+        return el("label", { class: "opt opt--child" }, [box, el("span", { text: c })]);
+      });
+
+      return el("div", { class: "facet-subgroup" }, [heading].concat(kids));
+    });
+
+    var details = el("details", { class: "facet facet--" + facet.color });
+    if (selectedRef.length) details.open = true;
+    var count = selectedRef.length ? " (" + selectedRef.length + ")" : "";
+    details.appendChild(el("summary", { text: facet.label + count }));
+    details.appendChild(el("div", { class: "facet-opts" }, groups));
+    return details;
+  }
+
   function facetGroup(facet, values, selectedRef, onToggle, labelFn) {
     var options = values.map(function (v) {
       var checked = selectedRef.indexOf(v) !== -1;

methods.json

@@ -13,8 +13,7 @@ sitemap: false
     "contributor": {{ m.contributor | jsonify }},
     "date": {{ m.date | date: "%Y-%m-%d" | jsonify }},
     "outcome": {{ m.outcome | jsonify }},
-    "kingdom": {{ m.kingdom | jsonify }},
-    "phylum": {{ m.phylum | jsonify }},
+    "taxon": {{ m.taxon | jsonify }},
     "preservation": {{ m.preservation | jsonify }},
     "extraction": {{ m.extraction | jsonify }},
     "library": {{ m.library | jsonify }},

scripts/validate_entries.rb

@@ -14,14 +14,18 @@
 
 errors = []
 
-# Front-matter fields on method entries that must be drawn from a vocab list.
-METHOD_FACETS = %w[kingdom phylum preservation extraction library sequencing].freeze
-METHOD_REQUIRED = (METHOD_FACETS + %w[title summary contributor date]).freeze
+# `taxon` is a kingdom -> [phyla] map; entries are tagged at phylum level, so
+# the allowed values are the flattened list of phyla/divisions.
+TAXON_VALUES = TAGS["taxon"].values.flatten.freeze
+
+# Flat-list facets on method entries that must be drawn from a vocab list.
+METHOD_FLAT_FACETS = %w[preservation extraction library sequencing].freeze
+METHOD_REQUIRED = (%w[taxon] + METHOD_FLAT_FACETS + %w[title summary contributor date]).freeze
 
 BIB_REQUIRED = %w[type title authors_or_institution year_or_date link].freeze
 # Any tag on a bibliography entry must exist in one of these facet lists.
 BIB_TAG_VOCAB = (TAGS["extraction"] + TAGS["library"] + TAGS["sequencing"] +
-                 TAGS["preservation"] + TAGS["kingdom"] + TAGS["phylum"]).uniq.freeze
+                 TAGS["preservation"] + TAXON_VALUES).uniq.freeze
 
 def front_matter(path)
   raw = File.read(path, encoding: "UTF-8")
@@ -53,7 +57,11 @@ def as_array(v)
     errors << "#{rel}: missing required field `#{field}`" if val.nil? || (val.respond_to?(:empty?) && val.empty?)
   end
 
-  METHOD_FACETS.each do |facet|
+  as_array(fm["taxon"]).each do |v|
+    errors << "#{rel}: `taxon` value \"#{v}\" not in _data/tags.yml" unless TAXON_VALUES.include?(v)
+  end
+
+  METHOD_FLAT_FACETS.each do |facet|
     allowed = TAGS[facet] || []
     as_array(fm[facet]).each do |v|
       errors << "#{rel}: `#{facet}` value \"#{v}\" not in _data/tags.yml" unless allowed.include?(v)