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| author | Munyoki Kilyungi | 2023-12-20 01:26:39 +0300 |
|---|---|---|
| committer | Munyoki Kilyungi | 2023-12-20 01:26:39 +0300 |
| commit | 798deb388638f13ed40ecc19eed8c53d44b6ab99 (patch) | |
| tree | a1d4ca2026d20dd88fa478ebae827d1de17de8c6 | |
| parent | d0714caaa88df251584ed9cb47745c1b35069533 (diff) | |
| download | gn-gemtext-798deb388638f13ed40ecc19eed8c53d44b6ab99.tar.gz | |
Update genelist issue.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| -rw-r--r-- | issues/transform-genelist-to-rdf.gmi | 16 |
1 files changed, 13 insertions, 3 deletions
diff --git a/issues/transform-genelist-to-rdf.gmi b/issues/transform-genelist-to-rdf.gmi index 3c20b5e..bc0f1b8 100644 --- a/issues/transform-genelist-to-rdf.gmi +++ b/issues/transform-genelist-to-rdf.gmi @@ -47,11 +47,21 @@ Identifying duplicates: SELECT GeneSymbol, GeneId, SpeciesId, COUNT(CONCAT(GeneSymbol, "_", GeneId, "_", SpeciesId)) AS `count` FROM GeneList GROUP BY BINARY GeneSymbol, GeneId, chromosome, txStart, txEnd HAVING COUNT(CONCAT(GeneSymbol, "_", GeneId, "_", SpeciesId)) > 1; ``` -## Resolution -This has been resolved in 533c8d85809b, cfcfa78e0149 in: +## Unique Gene Identifiers + +In the GeneList table, some genes share GeneIds and GeneSymbols. GeneIds are unique within a species, while GeneSymbols are unique across species. In cases where GeneSymbols and GeneIDs match, different AlignIDs exist. To create unique identifiers for genes in the GeneList table, we use a query like: + +```sql +SELECT CONCAT_WS("_", GeneSymbol, GeneID, AlignID) FROM GeneList; +``` + +For the GeneList_rn33 table, due to ambiguous cases, we rely on the table's id as a unique identifier. Here's an example of duplicate entries for a gene, differing only in txStart/txEnd/cdsStart/cdsEnd/exonStarts/exonEnd values: + +```sql +SELECT * FROM GeneList_rn33 WHERE geneSymbol="Cbara1" AND NM_ID="NM_199412"\G +``` -=> https://git.genenetwork.org/gn-transform-databases/ gn-transform-databases * closed |