galaxyproject / galaxyproject/idc

Organize IDC data around the concept of *ALIAS* labels for accessions, dbkeys, chromosome/scaffold identifiers

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Description

**Meta concept**

The label used to designate genomic information across data providers can differ, even for the same underlying information. UCSC has addressed this need with the concept of **aliases**. The IDC would benefit from leveraging this information in Galaxy-adjacent projects and applications.

**Example: mm39**

Source file `https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/chromAlias.txt.gz`

Shared history with that file loaded -> https://test.galaxyproject.org/u/jenjackson/h/mouse-alias-table

_Screenshots_

![Screen Shot 2024-11-07 at 11 08 33 AM](https://github.com/user-attachments/assets/657a305b-cb25-4c8e-b42b-4b8b072273ce)

![Screen Shot 2024-11-07 at 11 13 31 AM](https://github.com/user-attachments/assets/6a3cb62f-ec5c-48c1-8c7d-14dfa2b7f2a2)

If this file had more rows added, specifically the UCSC source with the root dbkey, the IDC could consume the data, and Galaxy could use it for file fetching on workflow forms, external applications (link outs and data pushes), and possibly implicit conversion of data at runtime for tool consumption. There are likely other practical uses such as improved error trapping and automated use suggestions e.g. chatGXY training data.

This is hard but seems possible, and maybe required for long term scaling goals across the project.

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