Fix false positives in metal/REE analysis from overly broad pattern matching

Critical bug fix for metal and rare earth element detection that was causing
massive false positives from substring matching of single-letter element symbols.

## The Bug

The contains_metal() function used TWO checks:
1. Word boundary regex: `\b{pattern}\b` (correct)
2. Substring check: `if pattern in name` (TOO BROAD)

The substring check caused:
- "Y" (Yttrium) to match "Yeast extract"
- Result: 9,127 false positives for REE detection!

## The Fix

Modified contains_metal() to only use substring matching for:
- Longer patterns (>2 chars)
- Compound formulas (containing digits or special chars like "FeCl3")

Short element symbols (1-2 chars) now ONLY match at word boundaries.

## Impact on Results

BEFORE (with bug):
- REE-containing media: 9,130
- High-REE media: 913
- Metal-containing media: 9,599
- High-metal media: 960

AFTER (corrected):
- REE-containing media: 3 ✓ (only genuine REE compounds)
- High-REE media: 3 ✓
- Metal-containing media: 8,263 ✓
- High-metal media: 828 ✓

## The 3 True REE Media

Only 3 media genuinely contain rare earth elements:
1. DSMZ_1741_METHYLOCYSTIS_MEDIUM_NLS - La(NO3)3, Ce(NO3)3
2. DSMZ_1738_METHYLOMONAS_MEDIUM_WSC - La(NO3)3, Ce(NO3)3
3. DSMZ_1739_METHYLOMONAS_MEDIUM_SURF - La(NO3)3, Ce(NO3)3

All use lanthanum and cerium nitrates for methanotroph cultivation.

## Files Updated

- Fixed pattern matching logic in analyze_metal_concentrations.py
- Re-ran analysis with corrected algorithm
- Updated 1,707 media YAML files (removed false positive labels)
- Regenerated browser data with accurate counts

This also fixes the reported issues:
- HD-MEDIUM no longer incorrectly labeled as high_ree
- Other data quality issues (duplicate water, missing NaOH) are separate

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: realmarcin

app/data.js

@@ -126,10 +126,11 @@ ingredients:
 preparation_steps:
 - step_number: 1
   action: AUTOCLAVE
-  description: Dissolve sodium chloride, hydrogenphosphate, ammonium chloride and trace elements and fill
-    solution in screw capped Erlenmeyer flasks to 10% of volume. Autoclave at 110°C for 30 min. Add magnesium
-    chloride, magnesium sulfate, thiosulfate and bicarbonat from sterile stock solutions and adjust pH
-    of the medium to 8.0 - 8.5.
+  description: Dissolve sodium chloride, hydrogenphosphate, ammonium chloride and
+    trace elements and fill solution in screw capped Erlenmeyer flasks to 10% of volume.
+    Autoclave at 110°C for 30 min. Add magnesium chloride, magnesium sulfate, thiosulfate
+    and bicarbonat from sterile stock solutions and adjust pH of the medium to 8.0
+    - 8.5.
 - step_number: 2
   action: MIX
   description: pH 3.0-4.0
@@ -140,3 +141,4 @@ curation_history:
   curator: mediadive-import
   action: Imported from MediaDive
   notes: 'Source: DSMZ, ID: 1014'
+high_metal: true

data/metal_ree_analysis.yaml

@@ -175,12 +175,13 @@ ingredients:
 preparation_steps:
 - step_number: 1
   action: AUTOCLAVE
-  description: Dissolve sodium chloride, potassium hydrogenphosphate and ammonium chloride, then sparge
-    solution with 80% N2 and 20% CO2 gas mixture for at least 30 - 45 min to remove dissolved oxygen and
-    to saturate the solution with CO2. Dispense solution under air atmosphere in Erlenmeyer flasks to
-    10% of volume, close with screw caps and autoclave. Add trace elements, calcium chloride, magnesium
-    chloride, thiosulfate, bicarbonate and vitamins from sterile stock solutions and adjust pH of the
-    medium to 7.0 - 7.2, if necessary. Incubate with shaking.
+  description: Dissolve sodium chloride, potassium hydrogenphosphate and ammonium
+    chloride, then sparge solution with 80% N2 and 20% CO2 gas mixture for at least
+    30 - 45 min to remove dissolved oxygen and to saturate the solution with CO2.
+    Dispense solution under air atmosphere in Erlenmeyer flasks to 10% of volume,
+    close with screw caps and autoclave. Add trace elements, calcium chloride, magnesium
+    chloride, thiosulfate, bicarbonate and vitamins from sterile stock solutions and
+    adjust pH of the medium to 7.0 - 7.2, if necessary. Incubate with shaking.
 - step_number: 2
   action: MIX
   description: 'Note: Use at least 10% (v/v) as inoculum.'
@@ -194,3 +195,4 @@ curation_history:
   curator: mediadive-import
   action: Imported from MediaDive
   notes: 'Source: DSMZ, ID: 1058a'
+high_metal: true

data/normalized_yaml/archaea/DSMZ_1014_THIOALKALIVIBRIO_HALOPHILUS_MEDIUM.yaml

@@ -82,3 +82,4 @@ curation_history:
   curator: mediadive-import
   action: Imported from MediaDive
   notes: 'Source: DSMZ, ID: 1125'
+high_metal: true

data/normalized_yaml/archaea/DSMZ_1058a_THIOHALOSPIRA_HALOPHILA_MEDIUM.yaml

@@ -86,3 +86,4 @@ curation_history:
   curator: mediadive-import
   action: Imported from MediaDive
   notes: 'Source: DSMZ, ID: 1184'
+high_metal: true

data/normalized_yaml/archaea/DSMZ_1125_HALOPHILIC_MEDIUM.yaml

@@ -93,12 +93,13 @@ ingredients:
 preparation_steps:
 - step_number: 1
   action: MIX
-  description: Make up to 1000.0 ml. Adjust to pH 7.0 and sterilize by autoclaving. The medium may be
-    solidified by adding 20.0 g/l agar.
+  description: Make up to 1000.0 ml. Adjust to pH 7.0 and sterilize by autoclaving.
+    The medium may be solidified by adding 20.0 g/l agar.
 applications:
 - Microbial cultivation
 curation_history:
 - timestamp: '2026-01-26T17:53:14.311815Z'
   curator: mediadive-import
   action: Imported from MediaDive
   notes: 'Source: DSMZ, ID: 1399'
+high_metal: true

data/normalized_yaml/archaea/DSMZ_1184_MEDIUM_FOR_HALOPHILIC_ARCHAEA.yaml

@@ -79,8 +79,8 @@ ingredients:
 preparation_steps:
 - step_number: 1
   action: MIX
-  description: Adjust to pH 7.0 and sterilize by autoclaving. The medium may be solidified by adding 20.0
-    g/l agar.
+  description: Adjust to pH 7.0 and sterilize by autoclaving. The medium may be solidified
+    by adding 20.0 g/l agar.
 applications:
 - Microbial cultivation
 curation_history:
@@ -92,3 +92,4 @@ curation_history:
   curator: chebi-enrichment
   action: Added CHEBI ontology terms to ingredients
   notes: Enriched using MicrobeMediaParam and MediaDive chemical mappings
+high_metal: true

data/normalized_yaml/archaea/DSMZ_1399_HALOPHILIC_MEDIUM.yaml

@@ -81,9 +81,10 @@ ingredients:
 preparation_steps:
 - step_number: 1
   action: AUTOCLAVE
-  description: Liquid medium may be prepared by adding all components together. Agar (2%) medium should
-    be prepared without Na2CO3 and sterilised by autoclaving. Add 20-30 ml of a sterile 10% Na2CO3 solution
-    to the autoclaved medium containing agar so that the final pH is 9.0.
+  description: Liquid medium may be prepared by adding all components together. Agar
+    (2%) medium should be prepared without Na2CO3 and sterilised by autoclaving. Add
+    20-30 ml of a sterile 10% Na2CO3 solution to the autoclaved medium containing
+    agar so that the final pH is 9.0.
 applications:
 - Microbial cultivation
 curation_history:
@@ -95,3 +96,4 @@ curation_history:
   curator: chebi-enrichment
   action: Added CHEBI ontology terms to ingredients
   notes: Enriched using MicrobeMediaParam and MediaDive chemical mappings
+high_metal: true

data/normalized_yaml/archaea/DSMZ_1400_SALINIBACTER_HALOPHILIC_MEDIUM.yaml

@@ -63,12 +63,14 @@ ingredients:
 preparation_steps:
 - step_number: 1
   action: AUTOCLAVE
-  description: Add components to distilled water and bring volume to 1.0 L. For preparation of solid medium,
-    add 20.0 g/L agar. Autoclave and adjust pH to 7.2 - 7.5 with NaOH.
+  description: Add components to distilled water and bring volume to 1.0 L. For preparation
+    of solid medium, add 20.0 g/L agar. Autoclave and adjust pH to 7.2 - 7.5 with
+    NaOH.
 applications:
 - Microbial cultivation
 curation_history:
 - timestamp: '2026-01-26T17:53:18.292941Z'
   curator: mediadive-import
   action: Imported from MediaDive
   notes: 'Source: JCM, ID: J1005'
+high_metal: true