TreeJuxtaposer: A Scalable Visualization Method for Ultra-Large Hierarchies (such as the Phylogenetic Tree)

[werererer]

Describe feature

Even though some people in the community might not believe it, there is a very real scientific need to organize hierarchies far larger than what “normal” users have ever dealt with.

Most people assume huge hierarchies are inherently incomprehensible. I disagree.

I believe these people just put the blame on the subject even though the real blame is on the tooling that makes it difficult to get an overview. Nowdays you need extremely specialized knowledge in tooling to manage these hierarchies. Normal people do not have access to "big data". And that is something that PKM i believe has the possibility to solve. Especially Trilium.

If Trilium should one day become a serious tool for research (e.g. biology, genealogy), it needs a benchmark-grade visualization method for extremely large trees. That means being able to visualize things like:

• phylogenetic trees ¹
• gene databases ²³

⁴

After some research I found a paper for this exact use:
Treejuxtaposer:
https://dl.acm.org/doi/10.1145/882262.882291
With youtube:
https://www.youtube.com/watch?v=eIK3ItXyMi0
Presentation:
https://pdfs.semanticscholar.org/70c7/fbfe7a3fef95f0d1282b84f90f7077e5a1a0.pdf
Code
https://sourceforge.net/p/olduvai/code/HEAD/tree/branches/Branch-04-05-18/olduvai/TreeJuxtaposer/

So my request is making Trilium implement everything that treejuxtaposer has.

However if someone finds even more scalable approaches I would love to hear about them, before wasting time with outdated methods. And send a link to a paper for that here.

I plan to start work on it later. Want to focus on search first.

Additional Information

No response

Footnotes

1. https://itol.embl.de/ ↩

2. https://www.ncbi.nlm.nih.gov/gene ↩

3. https://geneontology.org/ ↩

4. https://dl.acm.org/doi/pdf/10.1145/882262.882291 ↩

[eliandoran]

I had a look at the paper and the YouTube video and the ideas are pretty interesting. At the same time, they are pretty domain-specific for research (as you mentioned biology, genealogy).

Due to that I don't see it become core of Trilium, since it must stay true to its nature of being a personal knowledge management application. Even if we disregard this aspect, I'm pretty sure that Trilium is not yet research-grade due to lack of multi-user; because I suppose researches need to share their work with co-workers and swapping gigabyte-sized exports back and forth between colleagues is probably not the way to go.

Either way, theoretically, implementing a new visualisation method could work for collections.

We plan to implement a plugin system, so someone can pick this up (perhaps even you). The plugin system would allow the creation of new note types and collections.

So my request is making Trilium implement everything that treejuxtaposer has.

Probably we would need to be a little more specific.

[werererer]

@eliandoran While it was used first in biology its not Domain specific, in that every deeper hierarchie will lead to the same problems.

But it needs a library first. Keeping this as discussion is fine, and we can Look later if there is use for it. After I've found time to convert it to a standalone library first. so then we can have a proper discussion with a prototype.

[eliandoran]

@werererer , yes, a library would be a good idea since it can be reused in other applications as well.

Perhaps a good starting point would be to look at the TreeJuxtaposer implementation itself, is the source code available anywhere? I see there's a home page for it on SourceForge but I couldn't find the source code, only some Javadoc.

[werererer]

@eliandoran https://olduvai.sourceforge.net/tj/download.shtml the source code is here

[werererer]

Appearently during Covid 19 virologists had similar need. That lead to this software

Paper
https://www.crick.ac.uk/research/publications/taxonium-a-web-based-tool-for-exploring-large-phylogenetic-trees

Github
https://github.com/theosanderson/taxonium

Website
https://taxonium.org/

Covid 19 visualized
https://taxonium.org/sars-cov-2/public?xType=x_dist

I will explore later

[rom1dep]

very tame compared to https://nextstrain.org/ncov/open/global/6m

[werererer]

@rom1dep very cool! It seems to be self hostable. The code is here:

https://github.com/nextstrain/nextstrain.org