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# Add GeneList to Metadata
## Tags
* assigned: bonfacem
* priority: high
* type: RDF
* keywords: virtuoso
## Description:
=> https://www.gene-list.com/about About GeneList
The GeneList table in GN fetches metadata about given Genes under Resource Links.
Example:
=> https://genenetwork.org/show_trait?trait_id=1460303_at&dataset=HC_M2_0606_P Trait Data and Analysis for 1460303_at
When transforming data, it's unclear how resources (GeneMANIA, STRING, PANTHER, etc.) become links---they are manually constructed in GN's source code. This transformation is crucial when converting data to RDF.
## GeneList Metadata
Consider GN's approach for fetching GeneList entries for a specific trait.
=> https://github.com/genenetwork/genenetwork2/blob/371cbaeb1b05a062d7f75083aa4ff7209e4e06b3/wqflask/wqflask/show_trait/show_trait.py#L398 Fetching GeneList for a given trait
The GeneList table lacks unique GeneSymbols and GeneIds, as illustrated in the following examples:
```
SELECT * FROM GeneList WHERE SpeciesId = 1 AND GeneSymbol = "Sp3" AND GeneId = 20687 AND Chromosome = "2"\G
```
Duplicate entry examples:
```
SELECT * FROM GeneList WHERE GeneSymbol = "AB102723" AND
GeneId=3070 AND SpeciesId = 4 \G
SELECT * FROM GeneList WHERE SpeciesId = 1 AND GeneSymbol = "Sp3" AND GeneId = 20687 AND Chromosome = "2"\G
```
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;
```
## 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
```
* closed
|
