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feat: remove observation reification layer (closes #371)
Removes the 22 observation classes (METPO:1001000-1001023), 21 object properties (has *observation family), and 6 orphaned data properties (has observed/min/max/comment/negative, observation data property) that made up the reification pattern. Rationale: zero downstream usage in kg-microbe — no transform ever instantiated observation individuals. The flat data properties (METPO:2000701-2000734, released 2026-03-24) replace this pattern. Changes: - src/templates/metpo_sheet.tsv: 281 → 260 classes (pulled from Sheet) - src/templates/metpo-properties.tsv: 135 → 108 properties (pulled from Sheet) - src/templates/deprecated.tsv: 48 new rows, all with IAO:0000226 - reports/id-allocation-audit.md: regenerated (416 → 368 active IDs) Discussed: 2026-03-25 CultureBot/KG-Microbe/METPO sync (Mark + Marcin) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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‎reports/id-allocation-audit.md‎

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@@ -6,10 +6,10 @@
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| Metric | Count |
88
|--------|-------|
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| Active IDs (current templates) | 416 |
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| Active classes | 281 |
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| Active properties | 135 |
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| Burned IDs (ever used, not currently active) | 1168 |
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| Active IDs (current templates) | 368 |
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| Active classes | 260 |
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| Active properties | 108 |
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| Burned IDs (ever used, not currently active) | 1216 |
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| Total unique IDs ever allocated | 1584 |
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| Highest active class ID | METPO:1005040 |
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| Highest active property ID | METPO:2000734 |
@@ -23,7 +23,18 @@ These properties appeared in tagged releases or BioPortal submissions but are no
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| ID | Label | Provenance |
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|---|---|---|
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| METPO:2000000 | has susceptibility profile (last in sub6) | sub6 |
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| METPO:2000052 | has temperature observation (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000053 | has optimum temperature observation (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000054 | has growth temperature observation (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000055 | has range temperature observation (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000056 | has temperature delta observation (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000057 | has culture temperature observation (last in 2025-10-03) | sub9, sub10, tag:2025-09-23, tag:2025-10-03 |
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| METPO:2000058 | has observed spot value (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000059 | has minimum observed value (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000060 | has maximum observed value (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000061 | has value comments (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000062 | is negative data (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000063 | observation data property (last in 2026-03-24) | sub9, sub10, tag:2025-09-23, tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000201 | lyses (last in 2025-11-21) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21 |
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| METPO:2000203 | fixes (last in 2025-11-21) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21 |
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| METPO:2000204 | catabolizes (last in 2025-11-21) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21 |
@@ -47,16 +58,32 @@ These properties appeared in tagged releases or BioPortal submissions but are no
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| METPO:2000236 | does not solubilize (last in 2025-11-21) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21 |
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| METPO:2000237 | does not volatilize (last in 2025-11-21) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21 |
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| METPO:2000238 | does not crystallize (last in 2025-11-21) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21 |
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| METPO:2000239 | has pH observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000501 | has optimum pH observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000502 | has growth pH observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000503 | has range pH observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000504 | has pH delta observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000505 | has culture pH observation (last in 2025-10-03) | tag:2025-10-03 |
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| METPO:2000506 | has NaCl observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000507 | has optimum NaCl observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000508 | has growth NaCl observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000509 | has range NaCl observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000510 | has NaCl delta observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000511 | has observation (last in 2026-03-24) | tag:2025-10-03, tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000512 | has oxygen observation (last in 2026-03-24) | tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000513 | has optimum oxygen observation (last in 2026-03-24) | tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000514 | has growth oxygen observation (last in 2026-03-24) | tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000515 | has range oxygen observation (last in 2026-03-24) | tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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| METPO:2000516 | has oxygen delta observation (last in 2026-03-24) | tag:2025-10-15, tag:2025-10-31, tag:2025-11-17, tag:2025-11-21, tag:2025-11-24, tag:2025-12-12, tag:2026-03-24 |
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## Burned ID Counts by Era
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| Era | Description | Burned IDs |
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|-----|-------------|-----------|
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| Era 1 | 6-digit (000xxx), submissions 2-3 | 274 |
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| Era 2 | 7-digit (0000xxx), submissions 3-5 | 301 |
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| Era 3 classes | 1xxxxxx, retired literature-mining terms | 566 |
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| Era 3 properties | 2xxxxxx, removed without deprecation | 26 |
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| Era 3 classes | 1xxxxxx, retired literature-mining terms | 587 |
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| Era 3 properties | 2xxxxxx, removed without deprecation | 53 |
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| Test | 9999999 | 1 |
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## Safe Ranges for New Terms
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| Source | IDs found |
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|--------|----------|
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| `src/templates/metpo_sheet.tsv` | 281 |
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| `src/templates/metpo-properties.tsv` | 135 |
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| `src/templates/metpo_sheet.tsv` | 260 |
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| `src/templates/metpo-properties.tsv` | 108 |
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| BioPortal submission 2 | 274 |
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| BioPortal submission 3 | 300 |
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| BioPortal submission 4 | 296 |

‎src/templates/deprecated.tsv‎

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METPO:2000238 obsolete does not crystallize owl:ObjectProperty true IAO:0000226
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METPO:2000505 obsolete has culture pH observation owl:ObjectProperty true IAO:0000226
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METPO:9999999 obsolete obsolete owl:Class true IAO:0000226
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METPO:1001000 obsolete observation owl:Class true IAO:0000226
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METPO:1001001 obsolete optimum temperature observation owl:Class true IAO:0000226
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METPO:1001002 obsolete growth temperature observation owl:Class true IAO:0000226
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METPO:1001003 obsolete temperature range observation owl:Class true IAO:0000226
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METPO:1001004 obsolete temperature delta observation owl:Class true IAO:0000226
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METPO:1001007 obsolete growth NaCl observation owl:Class true IAO:0000226
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METPO:1001008 obsolete NaCl delta observation owl:Class true IAO:0000226
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METPO:1001009 obsolete NaCl range observation owl:Class true IAO:0000226
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METPO:1001010 obsolete optimum NaCl observation owl:Class true IAO:0000226
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METPO:1001012 obsolete growth pH observation owl:Class true IAO:0000226
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METPO:1001013 obsolete optimum pH observation owl:Class true IAO:0000226
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METPO:1001014 obsolete pH delta observation owl:Class true IAO:0000226
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METPO:1001015 obsolete pH range observation owl:Class true IAO:0000226
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METPO:1001016 obsolete optimum oxygen observation owl:Class true IAO:0000226
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METPO:1001017 obsolete growth oxygen observation owl:Class true IAO:0000226
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METPO:1001018 obsolete oxygen range observation owl:Class true IAO:0000226
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METPO:1001019 obsolete oxygen delta observation owl:Class true IAO:0000226
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METPO:1001020 obsolete oxygen observation owl:Class true IAO:0000226
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METPO:1001021 obsolete temperature observation owl:Class true IAO:0000226
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METPO:1001022 obsolete NaCl observation owl:Class true IAO:0000226
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METPO:1001023 obsolete pH observation owl:Class true IAO:0000226
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METPO:2000052 obsolete has temperature observation owl:ObjectProperty true IAO:0000226
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METPO:2000053 obsolete has optimum temperature observation owl:ObjectProperty true IAO:0000226
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METPO:2000054 obsolete has growth temperature observation owl:ObjectProperty true IAO:0000226
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METPO:2000055 obsolete has range temperature observation owl:ObjectProperty true IAO:0000226
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METPO:2000056 obsolete has temperature delta observation owl:ObjectProperty true IAO:0000226
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METPO:2000058 obsolete has observed spot value owl:DataProperty true IAO:0000226
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METPO:2000059 obsolete has minimum observed value owl:DataProperty true IAO:0000226
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METPO:2000060 obsolete has maximum observed value owl:DataProperty true IAO:0000226
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METPO:2000061 obsolete has value comments owl:DataProperty true IAO:0000226
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METPO:2000062 obsolete is negative data owl:DataProperty true IAO:0000226
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METPO:2000063 obsolete observation data property owl:DataProperty true IAO:0000226
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METPO:2000239 obsolete has pH observation owl:ObjectProperty true IAO:0000226
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METPO:2000501 obsolete has optimum pH observation owl:ObjectProperty true IAO:0000226
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METPO:2000502 obsolete has growth pH observation owl:ObjectProperty true IAO:0000226
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METPO:2000503 obsolete has range pH observation owl:ObjectProperty true IAO:0000226
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METPO:2000504 obsolete has pH delta observation owl:ObjectProperty true IAO:0000226
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METPO:2000506 obsolete has NaCl observation owl:ObjectProperty true IAO:0000226
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METPO:2000507 obsolete has optimum NaCl observation owl:ObjectProperty true IAO:0000226
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METPO:2000508 obsolete has growth NaCl observation owl:ObjectProperty true IAO:0000226
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METPO:2000509 obsolete has range NaCl observation owl:ObjectProperty true IAO:0000226
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METPO:2000510 obsolete has NaCl delta observation owl:ObjectProperty true IAO:0000226
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METPO:2000511 obsolete has observation owl:ObjectProperty true IAO:0000226
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METPO:2000512 obsolete has oxygen observation owl:ObjectProperty true IAO:0000226
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METPO:2000513 obsolete has optimum oxygen observation owl:ObjectProperty true IAO:0000226
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METPO:2000514 obsolete has growth oxygen observation owl:ObjectProperty true IAO:0000226
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METPO:2000515 obsolete has range oxygen observation owl:ObjectProperty true IAO:0000226
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METPO:2000516 obsolete has oxygen delta observation owl:ObjectProperty true IAO:0000226

‎src/templates/metpo-properties.tsv‎

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@@ -53,17 +53,6 @@ METPO:2000048 uses for anaerobic catabolization owl:ObjectProperty organism i
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METPO:2000049 uses for anaerobic growth owl:ObjectProperty organism interacts with chemical oboInOwl:hasRelatedSynonym 'anaerobic growth' https://bacdive.dsmz.de/ +
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METPO:2000050 uses for anaerobic growth in the dark owl:ObjectProperty organism interacts with chemical oboInOwl:hasRelatedSynonym 'anaerobic growth in the dark' https://bacdive.dsmz.de/ +
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METPO:2000051 uses for anaerobic growth with light owl:ObjectProperty organism interacts with chemical oboInOwl:hasRelatedSynonym 'anaerobic growth with light' https://bacdive.dsmz.de/ +
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METPO:2000052 has temperature observation owl:ObjectProperty microbe temperature observation has observation Relates a microbe to a temperature observation.
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METPO:2000053 has optimum temperature observation owl:ObjectProperty microbe optimum temperature observation has temperature observation Relates a microbe to an optimum temperature observation.
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METPO:2000054 has growth temperature observation owl:ObjectProperty microbe growth temperature observation has temperature observation Relates a microbe to a growth temperature observation.
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METPO:2000055 has range temperature observation owl:ObjectProperty microbe temperature range observation has temperature observation Relates a microbe to a growth temperature range observation.
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METPO:2000056 has temperature delta observation owl:ObjectProperty microbe temperature delta observation has temperature observation Relates a microbe to a temperature tolerance breadth (delta) observation.
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METPO:2000058 has observed spot value owl:DataProperty observation xsd:decimal observation data property A reported temperature value (°C) for this observation.
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METPO:2000059 has minimum observed value owl:DataProperty observation xsd:decimal observation data property The minimum temperature (°C) associated with this observation.
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METPO:2000060 has maximum observed value owl:DataProperty observation xsd:decimal observation data property The maximum temperature (°C) associated with this observation.
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METPO:2000061 has value comments owl:DataProperty observation xsd:string observation data property Free-text comments associated with this observation.
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METPO:2000062 is negative data owl:DataProperty observation xsd:boolean observation data property True if this observation indicates no growth at the reported temperature (negative result).
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METPO:2000063 observation data property owl:DataProperty
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METPO:2000071 has value owl:DataProperty xsd:decimal Relates any instance to a numerical value
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METPO:2000101 has quality owl:ObjectProperty microbe quality
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METPO:2000102 has phenotype owl:ObjectProperty microbe phenotype has quality https://biolink.github.io/biolink-model/has_phenotype
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METPO:2000230 does not accumulate owl:ObjectProperty organism interacts with chemical
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METPO:2000231 does not sequester owl:ObjectProperty microbe chemical entity does not accumulate
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METPO:2000232 does not compartmentalize owl:ObjectProperty microbe chemical entity does not accumulate
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METPO:2000239 has pH observation owl:ObjectProperty microbe pH observation has observation Relates a microbe to a pH observation.
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METPO:2000301 enzyme activity analyzed owl:ObjectProperty microbe enzyme oboInOwl:hasRelatedSynonym 'Physiology and metabolism.enzymes.[].activity' https://bacdive.dsmz.de/
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METPO:2000302 shows activity of owl:ObjectProperty microbe enzyme enzyme activity analyzed oboInOwl:hasRelatedSynonym 'Physiology and metabolism.enzymes.[].activity' https://bacdive.dsmz.de/ +
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METPO:2000303 does not show activity of owl:ObjectProperty microbe enzyme enzyme activity analyzed oboInOwl:hasRelatedSynonym 'Physiology and metabolism.enzymes.[].activity' https://bacdive.dsmz.de/ -
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METPO:2000501 has optimum pH observation owl:ObjectProperty microbe optimum pH observation has pH observation Relates a microbe to an optimum pH observation.
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METPO:2000502 has growth pH observation owl:ObjectProperty microbe growth pH observation has pH observation Relates a microbe to a growth pH observation.
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METPO:2000503 has range pH observation owl:ObjectProperty microbe pH range observation has pH observation Relates a microbe to a growth pH range observation.
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METPO:2000504 has pH delta observation owl:ObjectProperty microbe pH delta observation has pH observation Relates a microbe to a pH tolerance breadth (delta) observation.
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METPO:2000506 has NaCl observation owl:ObjectProperty microbe NaCl observation has observation Relates a microbe to a NaCl observation.
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METPO:2000507 has optimum NaCl observation owl:ObjectProperty microbe optimum NaCl observation has NaCl observation Relates a microbe to an optimum NaCl observation.
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METPO:2000508 has growth NaCl observation owl:ObjectProperty microbe growth NaCl observation has NaCl observation Relates a microbe to a growth NaCl observation.
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METPO:2000509 has range NaCl observation owl:ObjectProperty microbe NaCl range observation has NaCl observation Relates a microbe to a growth NaCl range observation.
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METPO:2000510 has NaCl delta observation owl:ObjectProperty microbe NaCl delta observation has NaCl observation Relates a microbe to a NaCl tolerance breadth (delta) observation.
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METPO:2000511 has observation owl:ObjectProperty microbe observation
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METPO:2000512 has oxygen observation owl:ObjectProperty microbe oxygen observation has observation Relates a microbe to an oxygen observation.
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METPO:2000513 has optimum oxygen observation owl:ObjectProperty microbe optimum oxygen observation has oxygen observation Relates a microbe to an optimum oxygen observation.
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METPO:2000514 has growth oxygen observation owl:ObjectProperty microbe growth oxygen observation has oxygen observation Relates a microbe to a growth oxygen observation.
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METPO:2000515 has range oxygen observation owl:ObjectProperty microbe oxygen range observation has oxygen observation Relates a microbe to a growth oxygen range observation.
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METPO:2000516 has oxygen delta observation owl:ObjectProperty microbe oxygen delta observation has oxygen observation Relates a microbe to a oxygen tolerance breadth (delta) observation.
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METPO:2000517 grows in owl:ObjectProperty microbe growth medium A relation between a microbe and a growth medium indicating that the microbe has been demonstrated to grow in that medium under some set of conditions. This relation represents a generalization from experimental observations reported in the literature or databases; it does not imply that the microbe will grow in the medium under all conditions.
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METPO:2000518 does not grow in owl:ObjectProperty microbe growth medium A relation between a microbe and a growth medium indicating that the microbe has been demonstrated to fail to grow in that medium under some set of conditions. This relation represents a generalization from experimental observations reported in the literature or databases; it does not imply that the microbe cannot grow in the medium under any conditions.
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METPO:2000601 denitrifies owl:ObjectProperty organism interacts with chemical oboInOwl:hasRelatedSynonym 'denitrification' https://metatraits.embl.de/ +

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