prefix table: 774 redundant rows, and 3 prefixes carrying another resource's base

The `prefix` table ships 1,275 rows that reduce to 489 distinct prefixes. Two separable problems: redundant rows, and prefixes with more than one expansion.

Identical in every build checked, so this is the shipped map rather than ontology content.

```sql
SELECT COUNT(*) AS rows, COUNT(DISTINCT prefix) AS distinct_prefixes,
COUNT(DISTINCT prefix||' '||base) AS distinct_pairs FROM prefix;
```

| rows | distinct_prefixes | distinct_pairs |
|---|---|---|
| 1275 | 489 | 501 |

## 1. Redundant rows: 774 of 1,275

Same prefix, same base, repeated.

```sql
SELECT SUM(extra) AS exact_duplicate_rows FROM
(SELECT COUNT(*)-1 AS extra FROM prefix GROUP BY prefix, base HAVING COUNT(*)>1);
```

`774`. 247 prefixes appear exactly 4 times, one appears 8 times.

## 2. Twelve prefixes have two different expansions

```sql
SELECT prefix, COUNT(DISTINCT base) AS n_bases FROM prefix
GROUP BY prefix HAVING n_bases > 1 ORDER BY prefix;
```

Nine are alternate expansions of the same resource, which may be intended:

| prefix | expansions |
|---|---|
| CHEMINF | `obo/CHEMINF_`, `semanticscience.org/resource/CHEMINF_` |
| FMA | `obo/FMA_`, `purl.org/sig/ont/fma/fma` |
| MESH | `id.nlm.nih.gov/mesh/`, `identifiers.org/mesh/` |
| RESID | `obo/RESID_`, `proteininformationresource.org/cgi-bin/resid?id=` |
| SWO | `obo/SWO_`, `ebi.ac.uk/swo/SWO_` |
| dbpedia | `dbpedia.org/`, `dbpedia.org/resource/` |
| qudt | `qudt.org/schema/qudt#`, `qudt.org/schema/qudt/` |
| reactome.biopax | `reactome.org/biopax/77/48887#`, `.../81/48887#` |
| schema | `http://schema.org/`, `https://schema.org/` |

None collapse under case normalisation (still 12 with `lower(base)`).

## 3. Three prefixes carry a different resource's base

| prefix | own base | also mapped to |
|---|---|---|
| complexportal | `obo/complexportal_` | `obo/wikipathways_` |
| drugbank | `obo/drugbank_` | `obo/drugcentral_` |
| pathbank | `obo/pathbank_` | `obo/kegg.genome_` |

`wikipathways`, `drugcentral` and `kegg.genome` have **no prefix rows of their own**:

```sql
SELECT DISTINCT prefix, base FROM prefix
WHERE prefix IN ('wikipathways','drugcentral','kegg.genome');
```

Returns nothing. Each of those three resources exists in the table only as a base attached to a different prefix.

This resembles the symptom reported in https://github.com/INCATools/semantic-sql/issues/71 (a prefix picking up a neighbouring entry's expansion), which was closed by shipping a newer semsql through ODK rather than by changing the table. I am not claiming the same root cause, only that the shape is still present in current builds.

Relevant because the map is not configurable: https://github.com/INCATools/semantic-sql/issues/51 is still open.

## Impact

Any lookup of the form `SELECT base FROM prefix WHERE prefix = ?` can return either expansion, decided by row order. For the three above it can return a different resource entirely.

## Checked against

`ncbitaxon.db` (downloaded 2026-05-19) and `envo.db` (downloaded 2026-09-01) from the SemanticSQL CDN. Both give byte-identical prefix sets and the same 1,275 rows, so this is not specific to one ontology or one build date.

Start by reproducing the supplied queries against ncbitaxon.db and envo.db, focusing on the prefix table and the listed duplicate and cross-resource mappings. Compare the generated prefix data with the expected resource ownership and expansion behavior, then verify that duplicate rows and unintended mappings are absent in both databases.

Written by the indexing model from the issue text.