Human Tumor Atlas Network - Data Schemas

[inodb]

Background: The Human Tumor Atlas Network (HTAN) is a National Cancer Institute (NCI)-funded Cancer Moonshot initiative to construct 3-dimensional atlases of the dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease. We have developed a data portal (https://humantumoratlas.org/) that allows easy access to the data generated as part of this consortium. For this particular project we would like to improve the visualization of the data standards that were developed as part of this effort.

There are two places where the data standards get visualized

• The standards description pages (code):
• https://sage-bionetworks.github.io/schema_visualization/ (code):

The full spec of the data standards is coming from the JSON model defined here. Both places use the same model for visualization. In both places it's still hard to search for an individual field in the schema. E.g. say you download some data from the HTAN portal and you find that there is a field "Ischemic Time". Now figuring out exactly whether this is a clinical attribute or a biospecimen attribute is not easy and requires many clicks. We would like to add a search field on both these pages to quickly identify where this attribute is. E.g. for the standards description page it could look like this:

Goal:

• Improve navigatability of the HTAN data standards

Approach:

• Add a search field to the standards description page that when searched displays only matching attributes (175h project)
• Add a search field to the schema visualizer that opens the correct table (350h project)

Need skills: JavaScript/TypeScript, CSS, HTML

Possible mentors: @onursumer @inodb @linglp @milen-sage

[msaini28r]

@inodb @onursumer @linglp Dear Mentors, I am really interested in this project, just wondering will you be able to provide me feedback for the proposal as the GSOC deadline is tomorrow or I can directly submit the proposal directly.

[inodb]

@msaini0r sure if you share the proposal tomorrow we might be able to provide additional feedback. But def make sure to submit it regardless

[nitishsaini706]

I would like to work on this project

[gautamsarawagi]

I would like to work on this project, please assign this task to me.

[AritraLeo]

@inodb I'd like to start working on this issue it seems interesting but before I do, I'd like to discuss my approach towards the problem and a few queries I have.

1. RDF format is being used in the response provided. Is the schema converted to the format shown already by the team or that'll be my 1st task.

2. Considering the schema is converted to this given structure to optimize search I'll have to find a way to iterate exactly to the searched element via the relation provided from the response(graph).

Please let me know if my approach is towards the right direction or not! Thank you.