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

Nessuno ha ancora preso questa issue.

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.

Iniziate riproducendo le query fornite su ncbitaxon.db e envo.db, concentrandovi sulla prefix table e sui mapping duplicati e tra risorse elencati. Confrontate i dati prefix generati con la proprietà attesa delle risorse e il comportamento di espansione, quindi verificate che in entrambi i database non siano presenti righe duplicate e mapping non intenzionali.

Scritto dal modello di indicizzazione a partire dal testo della issue.