Organism list

[Smeds]

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.

[NoopDog]

How do we tell what the "best" assembly" is? Thx! @Smeds

[Smeds]

we can consider the one with highest N50 as the best one.