galaxyproject / galaxyproject/ga2

Organism list

Open
#11 3 comments 0 reactions 1 assignee Claimed by @NoopDog View on GitHub
Dominant language
TypeScript
Stars
0
Forks
0
PR merge metrics
No merged PRs in 30d

Description

# List view
It would be useful to display the following columns:

| Column Name | Minimum fetaure | json key | Always Visibly | Visible by default | Could be empty | Type | Description
|---|---|---|---|---|---|---|---|
| | | Y | Y | checkbox | N | option used to select one or more species |
| Name | Y | name | Y | Y | N | String | Genus and Species name |
| Taxid | Y | taxon_id | Y| Y | N | Number | Taxonomic identifier |
| # assemblies | Y | num_assemblies | Y | Y | Y | Number | Number of assemblies for species. |
| N50 | N | n50 | N | Y | Y | Number | n50 value for best assembly, if any exist|
| Scaffolds | N | scaffolds | N | Y | Y| Number | number of scaffolds for best assembly, if any exist |
| Project | N | project | N | Y | Y | String| project(s) where the species is included |
| Progress | N | progress tag | N | Y | Y | List of String | progress of assembly construction |
| Assembly Data | N | tags_assembly | Y | N | Y | List of String | Tags indicating what assemblies exists |
| Genomic Data | N | tags_genomic | N | N | Y| List of String | Tags indicating what kind of raw genomic data exist |
| Transcriptomic Data | N | tags_transcriptomic | N | N | Y | List of String | Tags indicating what kind of raw transcriptomic data exist |

Some thoughts:

1. For the first column, it could also be an option to instead have it possible to select multiple rows in the table by clicking on a row.
2. After the user has selected one or multiple species we need an intuitive way of providing the option to move to the Genome Page. Possible options could be, when at least one species have been selected:
1. a button appears.
2. a existing button goes from disable to enabled.
3. other suggestions?
3. We should maybe add the option of entering the Species Page, the name could be a link to that page.

I have divided the implementation into three phases:
- [ ] **Initial Setup** – The goal of this phase is to get a basic version up and running. This will serve as the foundation for implementing other pages. I believe we have everything needed to generate the required data.
- [ ] **Enhancements using NCBI API** – Once we have a simple page working, we will expand it by incorporating additional information from the NCBI REST API.
- [ ] **Additional Data Integration** – In this final phase, we will integrate raw data and other generated information to enrich the content further.

The main goal to divide the implementation into multiple steps is to get a page up and running.

### Initial Setup (Minimum feature)

The following columns should be included:

1. Name
2. Taxid
3. assemblies

And make it possible to select one or multiple species.

### Enhancements using NCBI API

The following columns should be included:

1. N50
2. Scaffolds

In these step we need to extend the data extraction script to fetch more information from the NCBI API

### Additional Data Integration

1. Project
2. Assembly Data
3. Genomic Data
4. Transcriptomic Data
5. Assemblies found in the s3 bucket

We extend the data extraction script to fetch information about raw data belonging to the assemblies. We should also look into adding path/displaying data from downstream analysis.

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.