Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Search is much better on the UI than in the open-source package #1708

Open
falexwolf opened this issue Jun 20, 2024 · 5 comments · May be fixed by #2125, #2141 or #2135
Open

Search is much better on the UI than in the open-source package #1708

falexwolf opened this issue Jun 20, 2024 · 5 comments · May be fixed by #2125, #2141 or #2135

Comments

@falexwolf
Copy link
Member

image
@falexwolf
Copy link
Member Author

Search on the UI is good: https://lamin.ai/laminlabs/cellxgene/bionty/celltype

The question is whether we want to somehow wire the "good search endpoint" into lamindb in case somebody runs on a deployed instance. 🤔

@falexwolf falexwolf changed the title Search turned bad for long strings Search is much better on the UI than in the open-source package Aug 22, 2024
@Koncopd
Copy link
Member

Koncopd commented Aug 22, 2024

And why is it so?

@Zethson
Copy link
Member

Zethson commented Aug 30, 2024

Also see laminlabs/bionty#98 (comment)

@Koncopd
Copy link
Member

Koncopd commented Sep 18, 2024

When i created a collection with name="check mapped", i got this results
image
I assume they come from search.
Names are

'Massively multiplex chemical transcriptomics at single-cell resolution'
'Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer'
'A spatially resolved atlas of the human lung characterizes a gland-associated immune niche'

And these look completely irrelevant to me.

@falexwolf
Copy link
Member Author

falexwolf commented Oct 18, 2024 •
edited
Loading

The rapid fuzz search on the public ontology seems to be reasonable here except for the two last automated labels:

{
      'Dendritic cells': 'dendritic cell',
      'CD19+ B': 'B cell, CD19-positive',
      'CD4+/CD45RO+ Memory': 'effector memory CD4-positive, alpha-beta T cell, terminally differentiated',
      'CD8+ Cytotoxic T': 'cytotoxic T cell',
      'CD4+/CD25 T Reg': 'CD8-positive, CD25-positive, alpha-beta regulatory T cell',
      'CD14+ Monocytes': 'CD14-positive, CD16-negative classical monocyte',
      'CD56+ NK': 'CD16-positive, CD56-dim natural killer cell, human',
      'CD8+/CD45RA+ Naive Cytotoxic': 'CD38-positive naive B cell',
      'CD34+': 'CD38-high pre-BCR positive cell'
}

Source https://docs.lamin.ai/scrna2

It's also a good test case.

This was linked to pull requests Nov 7, 2024
⚗️ Benchmark lamindb and bionty search #2125
Open
⚗️ Benchmark search #2141
Open
🚸 Improve search #2135
Open
@falexwolf falexwolf linked a pull request Nov 7, 2024 that will close this issue
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
3 participants
@Koncopd @falexwolf @Zethson