# 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;
```

## Resolution

This has been resolved in 533c8d85809b, cfcfa78e0149 in:

=> https://git.genenetwork.org/gn-transform-databases/ gn-transform-databases

* closed