Talk:List of human cell types

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Some notes on precision and scope

Hi! @Claes Lindhardt and @Sergioo Hernandeez.

Thanks for all the work in the page!

I think that pulling markers from HuBMAP is an interesting idea, but I really do not think we should be pulling their data automatically at this point!

Classifying cell types is quite hard, and not all types used by HuBMAP are in fact consolidated. Katy and the team are wonderful, but there is still much basic progress to do in general. We have ways of verifying the types into the Cell Ontology (I wrote a paper about it with some HuBMAP people in the past: https://arxiv.org/abs/2204.09673.

A better place for the markers, where we can work on updating and crossing with different resources is Wikidata. Some cell types have hundreds of reported markers in the literature, so we need some kind of rule before pulling them to ~~Wikidata~~ Wikipedia. I also wrote a paper related to that: https://www.biorxiv.org/content/10.1101/2024.04.12.589259v1

There is also a mix in the table of "name", "type" and "subtype" that is not really referenced.

So, don't take it personally, but I am going to do some clean up in the article. I think the work you have been doing is wonderful. The modifications will be because we should be careful with terminology and coverage on Wikipedia. TiagoLubiana (talk) 21:53, 14 June 2024 (UTC)[reply]

Hey it seems a lof ot the content on this article interlinks well with the contents of:

A very rough draft for what kind of a structure a database like overview of the interlinking between a bunch of list relevant to human organs might have

List of organs of the human body
List of distinct cell types in the adult human body
List of medical tests
List of human microbiota(Human microbiome)
Composition of the human body
Lists of human genes
as well as all the list of the specefic organ systems:like e. g: List of skeletal muscles of the human body, List of bones of the human skeleton, Tendon, List of nerves of the human body, List of arteries of the human body, List of veins of the human body
I properly forgot something?

Woulden't it make sense to try and make a kind of overview of the interlinking? so we can reflect on how meaningful the interlinking is? also to make it eaiser to maintain, and so that each of the list feels like an appetizing menu card from which one can easily navigate to the relevant information one need and quickly grounp things to try and test connections one thing might be there? so that is all starts to feel more like a map of the human body rather then a bunch of random articles? some of these already have templates, but not all of them? and the templates does not seem to interplay yet?

Claes Lindhardt (talk) 11:17, 21 June 2024 (UTC)[reply]

Dear TiagoLubiana,

thank you for making the talk page easier to overview for newcomers :)

I noticed that you removed the numbers on the left side of the table, dosen't it make sense to have a number there so a reader not into the subject yet, can easily get an overview of how many cells we are talking about? and that you removed the function for it to be scrollable, doesen't this make the site less userfriendly for mobile users?

I hope to be able to give the papers a read before the end of the year,

Do you have any suggestions for databases that we can add to 'List of databases'? so that we can look at as many different databases with cell data in them as possible before deciding what the rules for pulling data to these wiki-list to hopefully make the large amount of articles on this topic on wiki more easy to navigate? Claes Lindhardt (talk) 11:24, 21 June 2024 (UTC)[reply]

and yes the whole "name", "type" and "subtype" is kind of messy, step by step :) I have no doubt about the good intention of your modifications, and I am sure we will find a good way to get to our common goal together. Step by step :) Claes Lindhardt (talk) 11:29, 21 June 2024 (UTC)[reply]

there is a lot of cases of like: List of human microbiota and Human microbiome, where I ask myself if it would make sense to combine them into 1 article such as is done in Tendon or if it is better to keep them seperate? if we keep them seperate, how do we ensure that curiosity flows one naturally from the one site to the other? Claes Lindhardt (talk) 11:37, 21 June 2024 (UTC)[reply]

Sure! Sorry for the delay in the reply.

I think I removed the numbers by accident, it is indeed very good. Also the function for scrolling, removed by accident. My bad,I am sorry.

By the way, I made this little tool for one particular list of cell types, it could be relevant to this discussion: https://cellcatalog.toolforge.org/

These are all very good questions. The list of databases is growing day by day. HuBMAP ASCT+B tables are one of the highest quality resources (good pick). CELLxGENE is also particularly good: https://cellxgene.cziscience.com/cellguide

In any case, by all means, feel free to modify/change the page!

I don't really have an answer on what is the best way to cover the subject and make curiosity flow, and that is the beauty of Wikipedia :) TiagoLubiana (talk) 20:22, 5 July 2024 (UTC)[reply]

Any chance that someone could re-insert the enumaration and scroll function? 128.0.73.13 (talk) 08:02, 9 July 2024 (UTC)[reply]

Hey, @TiagoLubiana would you be able to re-insert the two(enumaration and scroll function)? I worked a bit more with the DB analogy, it almost caputres List of medical tests in a meaningful way, whick i kind of where I started as i assumed that is what we use to collect data about organs and the point from which most of our current up to data knowlagede about them stem? - this also got me on the track of open source patient journals like: https://openehr.org/products_tools/platform/ : Eletronic Health Records(also somtimes refered to as Electronic/digital Patient Records/journals - EHR's) seem to be a kind of end state for much of this information? - but here it is often presented in a way which becomes overwealming to any patients who is fortunate enough to acess them. A lot of contires officially give acces to these, but in pratice. Ideally we would be able to create something here which also makes it easier for patient to navigate thier journals? we need something which is first a very rough overview and from which you can then easily navigate into the deeper details no? is there a better way then relational DBs to outline the architecture for such?

A draft for the interlinking between different wikiepedia articles for the theme of Organs shown as a relational database

Claes Lindhardt (talk) 10:32, 31 July 2024 (UTC)[reply]

Hey! I am not super sure on how to that. To be honest, I did not even know I had removed it, so its my bad. I'll check! If you know how to do it, please, go ahead! TiagoLubiana (talk) 13:46, 31 July 2024 (UTC)[reply]

Should be done now! Sorry for the trouble. TiagoLubiana (talk) 13:49, 31 July 2024 (UTC)[reply]