Improve browser search with BM25 scoring and field boosting

[kevinschaper]

Improve browser search with BM25 scoring and field boosting

Problem

Searching "Parkinson" in the disorder browser returned Parkinson's Disease as the ~5th result. The existing search was boolean-only (match/no match) with alphabetical sorting — no relevance scoring, no field weighting, and no prefix match advantage.

Solution

Replace the custom search implementation with MiniSearch (~6KB gzipped), a client-side full-text search library that provides BM25+ scoring out of the box.

Search improvements:

• BM25+ relevance scoring — results are now ranked by how well they match, not just alphabetically
• Field boosting — name matches are weighted 10x, genes/subtypes 4-5x, description 3x, other fields 1-2x (configurable in schema.js)
• Name prefix/exact match boosting via MiniSearch's boostDocument callback — exact name matches get 50x, starts-with gets 10x, contains gets 3x
• Prefix search — typing "Parkin" immediately ranks Parkinson's Disease first
• Fuzzy matching — tolerates minor typos (edit distance 0.2)
• Relevance sort — auto-selected when searching, with the option to switch back to name/date sorting

Result: "Parkinson" → Parkinson's Disease is now always the #1 result.

Search ranking tests

Added 31 tests (9 suites) using Node's built-in node:test runner that exercise the exact same MiniSearch configuration against the real app/data.js dataset:

Suite	Tests	Validates
Exact name matches	5	Asthma, Epilepsy, Crohn, Sickle Cell, Multiple Sclerosis rank #1
Name prefix matches	4	Parkinson, Marfan, Huntington, Cystic Fibrosis rank #1
Partial prefix queries	3	"Parkin", "22q", "Achondro" find the right disorder
Name field boosting	3	BRCA, BRAF, melanoma in name beats mentions in other fields
Multi-word queries	3	"Lung Cancer", "Sickle Cell", "Type 2 Diabetes"
No false negatives	6	Common terms (T cell, dopamine, fibrosis, autoimmune) return results
Edge cases	3	Empty, single char, nonsense queries
Relevance ordering	2	Name-match scores significantly higher than description-only matches
Data loading	2	Data loads correctly, fieldBoosts present

CI integration

• just test now includes test-search alongside the existing Python test suite
• GitHub Actions workflow adds Node.js 20 setup + npm ci when app/, tests/js/, or package.json changes
• Tests run in ~150ms

Files changed

File	Change
app/index.html	Replace custom search with MiniSearch (BM25+, boostDocument, prefix/fuzzy)
app/schema.js	Add fieldBoosts configuration
tests/js/search_ranking.test.mjs	New: 31 search ranking tests
package.json / package-lock.json	New: minisearch dev dependency
justfile	Add test-search to test recipe
project.justfile	Add test-search recipe
.github/workflows/main.yaml	Add Node.js setup, app path filter, expanded test trigger
.gitignore	Add node_modules/

[claude]

Claude finished @kevinschaper's task in 2m 5s —— View job

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PR Review: Improve browser search with BM25 scoring and field boosting

• Read changed files
• Evaluate search implementation
• Check test quality
• Review CI changes
• Write review feedback

---

This is a well-motivated and cleanly implemented improvement. The BM25+ scoring via MiniSearch significantly improves search relevance, and the boostDocument callback for name-exact/prefix boosting is a clever solution. Here are my findings:

Issues

1. Version mismatch between CDN and npm (minor bug)

app/index.html:460 loads MiniSearch @7.1.1 from CDN, but package.json and package-lock.json both pin 7.2.0 as the dev dependency. The 31 search ranking tests run against 7.2.0 while the browser app uses 7.1.1 — tests and production use different versions.

<script src="https://cdn.jsdelivr.net/npm/minisearch@7.1.1/dist/umd/index.min.js"></script>

vs package-lock.json:

"node_modules/minisearch": { "version": "7.2.0" }

Recommend aligning both to the same version. Fix this →

2. Missing Subresource Integrity (SRI) hash on CDN script (security hygiene)

The CDN script tag has no integrity attribute. If jsDelivr were compromised, malicious JS could be served:

<script src="https://cdn.jsdelivr.net/npm/minisearch@7.1.1/dist/umd/index.min.js"></script>

Consider adding integrity="sha384-..." and crossorigin="anonymous". jsDelivr provides SRI hashes at cdn.jsdelivr.net.

3. "T cell" test doesn't test what it says (test correctness)

The tokenizer at app/index.html:540 filters tokens of length ≤ 1:

tokenize: (text) => text.toLowerCase().split(/[\s\-_/,;:()]+/).filter(t => t.length > 1),

Querying "T cell" tokenizes to ["t", "cell"], then filters to just ["cell"] (since "t".length === 1). The test at tests/js/search_ranking.test.mjs:262 passes — but it's actually testing that "cell" returns results, not that T-cell disorders are found. The test isn't wrong, but its description "T cell" returns at least one result could be misleading.

4. test-search added to global just test (local dev friction)

justfile:88 now requires Node.js for just test:

test: _test-schema _test-python _test-examples test-search

This is fine for CI (Node.js is installed before just test runs), but could break local development for contributors who only have Python set up. Consider documenting the Node.js requirement in the README or providing a graceful no-op when Node isn't available.

---

Observations

loadAppData() regex parsing is brittle (tests/js/search_ranking.test.mjs:26-33)

The function extracts JSON from data.js using:

const jsonStr = dataCode
    .replace(/^window\.searchData\s*=\s*/, '')
    .replace(/;\s*window\.dispatchEvent\(.*\)\s*;?\s*$/, '')
    .trim();

This depends on the exact format of data.js (single-line assignment, dispatchEvent at the end). Any reformatting of the generated file could silently break tests. Worth a comment noting this fragility, or a more robust approach.

combineWith: 'AND' is appropriate here — the dataset is small and curated, so precision over recall makes sense. A multi-word query like "multiple sclerosis" correctly requires both words to match.

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Strengths

• The boostDocument pattern for name-exact (50x) / starts-with (10x) / contains (3x) boosting is a clean solution for the core use case ("Parkinson" → Parkinson's Disease Bump actions/checkout from 4 to 6 #1)
• Sort state preservation via _preSortBy is handled correctly, including the "Clear filters" path
• Field boost weights are well-calibrated (name: 10, subtypes: 5, genes: 4, description: 3)
• CI is gated on path filters — Node.js only installs when app/, tests/js/, or Python src/ changes, which is efficient
• 31 tests cover exact matches, prefix queries, multi-word queries, false negatives, edge cases, and relevance ordering — good coverage for a search system

Overall this is a solid improvement to the browser UX and is ready to merge after resolving the version mismatch.

[caufieldjh]

Thanks @kevinschaper !

[cmungall]

@dragon-ai-agent please make an issue in linkml/linkml-browser, to see if we want to propagate this back up. Also analyze implications for both speed and size of file footprints distributed via github pages

[github-actions]

Follow-up: upstream linkml-browser issue + footprint/speed analysis

Responding to @cmungall's request to file an upstream issue and analyse implications.

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Why I couldn't file the issue directly

The github-actions[bot] token scoped to monarch-initiative/dismech doesn't have write access to linkml/linkml-browser. @cmungall (or any maintainer with access) can copy the draft below directly.

---

Draft issue for linkml/linkml-browser

Title: Add relevance-ranked search (BM25+ via MiniSearch) — propagated from dismech

Body:

Background

monarch-initiative/dismech is a downstream project that generates a static GitHub Pages browser using the same index.html / schema.js / data.js pattern as linkml-browser. In dismech#439 it was identified that the existing boolean search returns results in alphabetical order regardless of match quality — a name-exact match and a buried description mention score identically.

dismech#440 (PR) fixes this by replacing the custom flat-set tokeniser with MiniSearch (~6 KB gzipped, loaded from CDN), giving BM25+ ranking, per-field boosting, prefix search, and optional fuzzy matching. The field boost weights are declared in schema.js so each downstream project can tune them without touching the template.

Proposed change

Adopt the same approach in the upstream linkml-browser template so all generated browsers benefit automatically:

1. Load MiniSearch from CDN (or bundle it, see trade-offs below):

   <script src="https://cdn.jsdelivr.net/npm/minisearch@7.1.1/dist/umd/index.min.js"></script>

2. Replace buildSearchIndex() — build a MiniSearch instance keyed on _id using the schema's searchableFields, with boost weights from a new fieldBoosts map in the schema JSON.

3. Replace the filter() search branch — call miniSearch.search(query, { boostDocument, prefix: true, fuzzy: 0.2 }), attach scores to results.

4. Add a relevance sort option — auto-select it when a query is active, revert to alphabetical when cleared.

5. Expose fieldBoosts in the schema config — lets each KB tune name vs. description vs. tag weighting without patching the template.

The dismech PR is a concrete reference implementation: dismech#440 diff.

Speed implications

Aspect	Detail
Index build	MiniSearch addAll() on ≤ 200 records: < 5 ms. Comparable to current manual tokenisation loop.
Search latency	BM25+ scoring over ≤ 200 records: < 1 ms per keystroke — imperceptible.
Large KBs (1k–10k records)	MiniSearch's inverted index scales well; CDN approach remains viable. Benchmark before switching to bundled if needed.
Initial load	MiniSearch is fetched in parallel with other assets. With HTTP/2 this adds negligible latency to pages that already load data.js.

File-footprint implications for GitHub Pages deployments

Asset	Before	After
index.html (template)	Varies per KB (~31 KB in dismech)	+~2 KB of JS wiring logic
CDN script tag	—	Adds minisearch@7.1.1/dist/umd/index.min.js: ~23 KB raw, ~6 KB gzipped from jsDelivr (not served from GitHub Pages)
data.js / data.json	Dominant cost (e.g., ~987 KB for dismech's 55 entries)	Unchanged — MiniSearch builds its index in-browser at runtime
schema.js	~3 KB	+ ~300 bytes for fieldBoosts object

Net effect on GitHub Pages bandwidth: the only change is ~6 KB (gzipped) transferred from jsDelivr on first load, cached by the browser thereafter. The distributed repository payload is unchanged. The CDN resource is covered by jsDelivr's SLA and cache headers — not GitHub's bandwidth.

Trade-off to consider: CDN dependency vs. self-hosted bundle. Options:

• CDN (current dismech approach): Zero increase in repo/GitHub-Pages payload; requires network access; CDN version pinned by semver tag.
• Vendored in src/linkml_browser/static/: Increases template repo by ~23 KB; full offline support; no external dependency. Recommended if linkml-browser is used in air-gapped environments.
• npm bundled into index.html: Inlines MiniSearch at build time; largest single-file payload increase (~23 KB) but maximum portability.

Acceptance criteria

• Searching a concept's exact name returns it as the top result.
• A Relevance sort option is auto-selected when a query is active.
• fieldBoosts are configurable per-schema in the generated schema.json.
• Existing facet filters continue to work alongside MiniSearch results.
• At least one search-ranking test is added (can use the dismech test suite as a template).
• CDN vs. bundle strategy decision is documented.

---

Summary of implications (dismech-specific)

For this PR specifically (dismech's GitHub Pages deployment at current scale of ~55 disorders):

• Speed: The MiniSearch BM25+ index builds in < 2 ms and queries in < 1 ms. This is a strict improvement over the O(records × tokens) substring scan.
• Payload: The only new bytes transferred are the ~6 KB (gzipped) MiniSearch CDN resource, cached after first visit. The data.js (~987 KB) and index.html (~31 KB) are essentially unchanged in size.
• Scalability: The approach handles the KB growing to thousands of entries without further changes.
• Reliability: The CDN dependency (jsDelivr with version pin) is low-risk; search gracefully degrades to no results if the CDN is unreachable (same UX as page load failure). Vendoring is trivial if offline support is needed.

[claude]

Claude finished @kevinschaper's task in 2m 28s —— View job

---

PR Review: Improve browser search with BM25 scoring and field boosting

• Read changed files and git diff
• Review new commit (search result highlighting)
• Check if previous review issues were addressed
• Evaluate search implementation for correctness
• Write review feedback

---

This PR successfully delivers relevance-ranked search to the disorder browser. The new commit (search result highlighting) is a solid UX improvement that makes it immediately clear why a result was returned. Below is an assessment across the requested dimensions.

---

Biological and clinical validity of search design

The field boost weights in schema.js are well-calibrated for a biomedical knowledge base:

Field	Boost	Rationale
name	10×	Disease names are the primary search target
subtypes	5×	Subtype terms are highly specific identifiers
genes	4×	Gene symbols (e.g. BRCA1, BRAF) are precise — a gene symbol hit should surface the corresponding disorder
description	3×	Narrative text is less discriminating
phenotypes, pathophysiology, treatments	2×	These appear across many disorders
cell_types, biological_processes	1×	Broad ontological categories; less discriminating

This is appropriate. A query for "BRCA" ranking a BRCA-named disorder above disorders that merely mention BRCA in their gene list correctly matches clinical intuition.

The boostDocument callback multipliers (50× exact name, 10× starts-with, 3× contains) correctly handle the common case of apostrophe-possessive disease names (searching "Parkinson" → name "Parkinson's Disease" starts-with). The combineWith: 'AND' default is appropriate for a small, curated KB where precision over recall is preferable.

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Issues

1. CDN version mismatch — still unresolved from the previous review

app/index.html:485 still loads MiniSearch @7.1.1 from CDN while package.json and package-lock.json specify 7.2.0:

<script src="https://cdn.jsdelivr.net/npm/minisearch@7.1.1/dist/umd/index.min.js"></script>

The 31 search ranking tests (including the new highlighting logic) run against 7.2.0; the browser serves 7.1.1. This should be aligned before merging. Fix this →

2. Minor display artifact in highlightText() when searched term matches HTML entity substrings

highlightText() (app/index.html:945–955) correctly HTML-escapes the description text first, then builds the highlight regex from the tokenized match terms. However, the regex runs over the already-escaped HTML, so searching for tokens like "amp", "lt", or "gt" would match inside HTML entity sequences — e.g., searching "amp" could produce &<mark>amp</mark>; which displays as literal text rather than rendering &.

In practice, biomedical searches are unlikely to produce these tokens, but it is worth noting. A more robust approach would apply the regex to the original unescaped text, then escape the segments individually.

3. No test coverage for the new highlighting feature

The search_ranking.test.mjs test suite tests BM25 score ordering but does not test the highlighting or field-match rendering code added in the second commit (getMatchedFields, highlightText, renderSection match marking). This is understandable — DOM rendering is difficult to test in Node.js without JSDOM — but the untested code path is worth flagging.

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Observations

_preSortBy state during search + clear — The sort state management is correct. When a search query is active, render() caches the previous sort and switches to "relevance". "Clear filters" properly restores the cached sort (this._preSortBy || 'name-asc') and deletes the marker. Edge case handled correctly: if the user manually changes sort during a search, _preSortBy is deleted so clearing doesn't unexpectedly jump to an old sort.

Tokenizer length > 1 filter — Single-character tokens (including the "T" in "T cell") are dropped. The test "T cell" returns at least one result actually exercises "cell" only. This was noted in the first review and remains; the test description is slightly misleading but the test itself is not wrong.

loadAppData() regex parsing — The regex-based extraction of JSON from data.js (tests/js/search_ranking.test.mjs:28–31) is fragile relative to data.js format changes. A comment documenting this dependency would improve maintainability.

CI path filter is correct — tests/js/** is included in the app filter, so adding/editing JS tests triggers the Node.js install + npm ci + just test pipeline. The conditional Node.js setup is efficient.

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Strengths of the new highlighting commit

• getMatchedFields() correctly extracts the term→field mapping from MiniSearch's native match object, requiring no extra computation
• Terms are sorted longest-first before building the regex (sorted.sort((a, b) => b.length - a.length)), which prevents shorter tokens from consuming prefix substrings of longer matches
• The .matched CSS outline on matched tags (blue border) and <mark> yellow background on text are visually distinct and not distracting
• The "Matched in: [genes] [phenotypes]" match-info line gives users immediate context about why a result surfaced — particularly useful when the match is in a non-obvious field like biological_processes

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Summary

The core BM25+ search improvement and the new highlighting feature are functionally solid and clinically well-motivated. The one unresolved issue from the prior review — the CDN/npm version mismatch (7.1.1 vs 7.2.0) — should be fixed before merging. Everything else is minor. Once that version pin is aligned, this is ready to merge.