User talk:Claes Lindhardt

Your submission at Articles for creation: Bjørn Bjerregaard (April 14)

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Theroadislong (talk) 19:25, 14 April 2019 (UTC)

Hello, Claes Lindhardt! Having an article declined at Articles for Creation can be disappointing. If you are wondering why your article submission was declined, please post a question at the Articles for creation help desk. If you have any other questions about your editing experience, we'd love to help you at the Teahouse, a friendly space on Wikipedia where experienced editors lend a hand to help new editors like yourself! See you there! Theroadislong (talk) 19:25, 14 April 2019 (UTC)

CS1 error on List of distinct cell types in the adult human body

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Talk:Human body

On my talk page, you said: You removed my post on the talk page of the human body, where I suggest we make an overview of the different abstraction levels, I made an updated version of the drafted figure here along with a bunch of defintions. But I am still not sure why the topic on the talk page was removed in the first place, please elaborate?

Hello - rules for article talk page discussions concerning human content are that a specific revision be proposed with a WP:MEDRS source. I felt your proposal made no sense. "Different abstraction levels" doesn't mean anything to me as a physiologist, and the image doesn't help a common user to understand the human body. The image is not based on a MEDRS source. Zefr (talk) 15:31, 23 May 2023 (UTC)

Ahh allright what do you think would be a better word? Different levels of complexity? different levels of understanding? different starting-points? Different levels of mechanisms? different size of parts? Claes Lindhardt (talk) 09:16, 29 June 2023 (UTC)

I am not sure what the MEDRS source refer to here? Thank you for your feedback Claes Lindhardt (talk) 09:17, 29 June 2023 (UTC)

CS1 error on List of proteins in the human body

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It is the article from the national health institute no? Claes Lindhardt (talk) 18:20, 12 July 2023 (UTC)

Nomination of List of proteins in the human body for deletion

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Elmidae (talk · contribs) 06:48, 13 July 2023 (UTC)

I am not sure I understand this message, if you have the time I would appriciate futher explanation? Claes Lindhardt (talk) 17:13, 15 July 2023 (UTC)

CS1 error on List of proteins in the human body

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ANLN

Hi there, I saw you added a link to your page List of proteins in the human body to the top of the page ANLN. I can also see from your contributions that you are adding this en masse to human protein pages. I really don't think that it makes sense as a "see also" at the top of the page- someone arriving at the page for an individual protein will get *less* information about the protein if they go to the giant list page. Mentions of List of proteins in the human body should be at the bottom of the page, if included at all. GraziePrego (talk) 13:15, 22 July 2023 (UTC)

Makes sense, will add it to the bottom thank you Claes Lindhardt (talk) 13:16, 22 July 2023 (UTC)

PLEASE STOP. This is not how "see also" links should be added. They should be placed as an unordered list under a See also section heading. Read MOS:SEEALSO or see other articles before continuing. — kashmīrī ^TALK 13:26, 22 July 2023 (UTC)

If there is not a such one should simply add a new heading? some of the onces that I have added have been added under a new heading in the end of the article. Can you unrevert those please? is there a way to automatically add a link in the corect way for a list of articles that you have? Claes Lindhardt (talk) 13:29, 22 July 2023 (UTC)

The article you are linking to is currently considered for deletion. Do not add links until there's consensus to keep the article, not least because if it's deleted, it will be much more work then to remove all those links you added. — kashmīrī ^TALK 13:31, 22 July 2023 (UTC)

Scrolling back through your contributions Claes, you've added a link to your page to quite literally hundreds of pages, even those with marginal relevance. I don't think it's acceptable to do that when your page is being considered for deletion. GraziePrego (talk) 13:37, 22 July 2023 (UTC)

isen't there an automatic way of removing them in that case? Right now the deletion discussion seems to tend more towards merging the article into another article, also a lot of these article seems to face a lot of simmilar problems to the the one I created, doesen't it seem relevant to link them to solve the problems in both cases and show that there is a history of people trying to address these problems? Claes Lindhardt (talk) 14:02, 22 July 2023 (UTC)

In the start I was also told that it was good to link the article to other articles to de-orphan it? Claes Lindhardt (talk) 14:03, 22 July 2023 (UTC)

How can we link all protein articles together in a way that makes the creaters of them part take in a central discussion on how best make all the proteins on wiki sortable and navigable? Claes Lindhardt (talk) 14:05, 22 July 2023 (UTC)

There’s a difference between de-orphaning and adding your article to the start of every single protein. I think it actually shows why List of proteins in the human body should just be a category, as there’s no problem with adding all human proteins into that category. GraziePrego (talk) 22:56, 22 July 2023 (UTC)

Did you read the deletion discussion part where a category was also discussed? Claes Lindhardt (talk) 08:00, 23 July 2023 (UTC)

We already have Category:Human proteins and Category:Genes by human chromosome. Please note that in almost all cases, the scope of the articles that contained in these two categories are about the gene and the protein encoded by this gene. Hence these categories are essentially duplicates of each other. Please also note that articles that transcribe the {{infobox gene}} are automatically added to the Category:Genes by human chromosome.

As discussed here and here, we have tried to make clear in the lead sentence that Gene Wiki articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:

• <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.

The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human. Boghog (talk) 08:47, 23 July 2023 (UTC)

You have also asked on several occassions which infobox is appropriate for which articles. Appropriate uses have been carefully described here:

• WP:MCBMOS#Infoboxes

Boghog (talk) 08:47, 23 July 2023 (UTC)

Would it make sense to have an explanation in the start of the category saying how many proteins we think there i in the human body vs. how many have been listed? to automatically clarify that it is not a compleate list and how much there is left to contribute with? Claes Lindhardt (talk) 09:00, 23 July 2023 (UTC)

No. Category pages are not there to educate people about the subject matter. For this, we have articles. A reader interested in learning about proteins in general will certainly go and read protein. — kashmīrī ^TALK 09:28, 23 July 2023 (UTC)

Wikipedia:Articles for deletion/List of proteins in the human body

Please also ensure you sign your comments with ~~ ~~ (without the space in the middle) when you post on the discussion page- if you don’t then there’s no “reply” button and it’s not shown who posted the comment. GraziePrego (talk) 23:36, 22 July 2023 (UTC)

AFD

Hello, Claes Lindhardt,

I should have posted this comment to you days ago but please do not respond to every comment in an AFD deletion discussion. It causes people to tune out what you are saying, ignore your comments and, ultimately, resent you for dominating the discussion. It does not help to convince others of your viewpoint if you bludgeon the discussion. In fact, the more you go on and on, the more likely it is that editors will take an opposing side because they are tired of seeing your constant comments. It's not to late to stop. You've dominated this discussion so far and said what you needed to say, now leave some space for other editors to participate in a discussion about what should happen to this article.

I should note that although it's unlikely at this stage, if this happens again, I would give you a partial block from the AFD discussion page after the first dozen comments were made. But this discussion is on its last relisting so I'll just request that you cease from commenting further. Thank you. Liz ^{Read! Talk!} 06:57, 23 July 2023 (UTC)

Thank you Liz for stating this so politely.

Claes: I've removed the latest wave of your replies as they were totally off topic. You seem to have confused a deletion discussion with some sort of group brainstorming about your future work, about deleting other articles and categories, etc. This is not a place to do it! AFD is a structured discussion about whether the article as it is should stay on Wikipedia. If you'd like to develop the article, you can always ask to WP:DRAFTIFY it, or you can even move it yourself to your own WP:USERSPACE (and get the original deleted per WP:CSD#G7). There, in Draft space or in userspace, you will be free to work on it without pressure, reach out to editors active in the WikiProject Molecular Biology, and finally develop a quality article, which I encourage you to do. — kashmīrī ^TALK 10:09, 23 July 2023 (UTC)

Please elaborte how how suggesting a new column as a soltution to indicate which proteins are produced by the human body and which comes from elsewhere is off the topic of how to deal with things like Regular insulin in the list?

(talk page stalker) By definition, human gene/protein lists should only contain human proteins. The solution is to remove entries from the list that are not human proteins. No need to add an extra "species" column. Boghog (talk) 12:41, 23 July 2023 (UTC)

How does one ask to WP:DRAFTIFY it? and will it still be visable to regular readers or only readers with an account? Claes Lindhardt (talk) 11:41, 23 July 2023 (UTC)

Is there an option to merge it into Seppi article and then draftify it from there? so that Seppis get some more column that you can sort according to? but the article can still be accesed Claes Lindhardt (talk) 11:56, 23 July 2023 (UTC)

(talk page stalker) We can easily add additional columns to List of human protein-coding genes 1, 2, 3, 4. As long as we get consesus before making changes to the list, there no need to WP:DRAFTIFY it. However a sandbox to test the bot would be a good idea. It will take a bit more work to modify the bot script to populate and maintain these extra fields. I would suggest adding (1) <recommended UniProt name>, (2) function, and (3) tissue distribution, but drop "folding variations". Generally each protein has a single fold. There are metamorphic proteins that adopt different folds (e.g., XCL1), but these are rare. For human generated text, I suppose we chould add a comment field in a seperate page and the bot could automatically merge this text back into the list. There might be better ways of doing this, but this solution should be clean and robust. If you want to pursue this further, I suggest moving this discussion to Talk:Lists of human genes and get buy in from User:Seppi333 who will be critical in implementing changes to the list. Boghog (talk) 13:12, 23 July 2023 (UTC)

Generally speaking, I'm open to adding more information columns/fields to the list. It shouldn't be particularly difficult to add a manually-editable comment field for every gene entry in these lists since I could accomplish that fairly easily using WP:SELECTIVETRANSCLUSION from the sections of another page (preferably with a very short pagename - like Template:HGNC list - as each additional character in the pagename will add 5000 bytes of text to each list). All I'd need to do to make it appear in the list would be to create a comment column and selectively transclude the sections of Template:HGNC list, which would contain about ~20000 sections in total, one for each gene symbol. The sections on that page could then be manually edited by anyone, and anything written in the sections on that page would appear in the protein-coding gene lists' "Comment" column in the entry for the gene symbol that they edit the section entry for on this Template:HGNC list page.

So, it's entirely doable to add a manually-editable field in my human protein-coding gene list pages. Whether or not it should be done is something that should absolutely be discussed with a wider group of editors, though.

That said, if you were asking about additional columns with data that can be auto-generated from databases, then - as I mentioned earlier - I’m open to adding whatever data people would find useful to the bot-generated lists. There are, however, some constraints to doing so. First would be page size; while the lists don’t have a fixed maximum that I need to stay under, if anyone objects to the page sizes of the articles after modification, I have to be responsive to this objection (I.e., remove data or further break up lists) unless other editors voice the opposite view. At the time my bot was approved to generate the lists, the page sizes on Special:LongPages on average were around half what they are now, so page size might be less of an issue now. The second would be data availability/quality; so long as there’s data on all human protein-coding genes in a comprehensive & reputable database for a given variable (column of data/information), it would be feasible to add to the list provided the impact on page sizes isn’t excessive.

The last constraint I face is technical: if the above two constraints are satisfied, then I just need to be able to access the database via an API that allows me to programmatically download the dataset I’d require to add the additional columns of information in the list. Generally speaking, this shouldn’t be an issue for any of the reputable databases that might be considered a potential data source for the protein-coding gene lists; otherwise, the database administrators have a usability problem and ought to overhaul their programmatic accessibility, and I’d email them to address that. Seppi333 (Insert 2¢) 23:13, 23 July 2023 (UTC)

Columns: Sounds good, I am open to dropping the idear of the folding column for now, I would really like the 'can humans produce it in thier own bodies' column. This adds a lot of ustility to the table for people who wants to approach it from a pharma perspective, as well as an understanding of how long our bodies have been needing something. So maybe somthing like

| Index | UniProt ID(s) | function | Tissue | Actual Proteins| Producablity in the human body |Gene Symbol | HGNC ID | ??Comments?? |

I am sorry but I am not sure that I understand if the comments are a column of thier own or a general concept which apply to all columns? it is thought of as a column of thier own right?

Data size: could the structure List of minor planets be of any inspiration as for how we might break up the list futher if each page contains more information?

More datasources: Right now I am focusing on updating the list of databases so that we have as many places to potentially pull data from as possible, for the automated columns. Would it be helpful if I added a colum called API, to this list with a link to the APIs that each provider lists themselves? or how can I make this list more usable in terms of easily accessing APIs? Claes Lindhardt (talk) 20:32, 24 July 2023 (UTC)

I ask myself if a tissue column makes sense or if there is a way to link it directly to List of distinct cell types in the adult human body the concrete cells? Claes Lindhardt (talk) 11:45, 25 July 2023 (UTC)

I don't think it's really that useful to include information on database APIs in a list of databases. There are many programming languages, and each database would probably have multiple APIs in different languages for accessibility.

Regarding the columns in the gene lists, as I mentioned before, I am open to expanding the lists. Even though I am the bot programmer/owner, I can't unilaterally decide to add tons of information to these lists. If the consensus at the AfD is to merge, then there's a consensus to add column information from your lists to mine. If it's to delete, then the alternative way to go about generating a consensus to expand the lists would be for me to reopen the original request for bot approval to discuss the addition of data with a wider group of editors. For the moment, it would probably be best to see how the AfD turns out before planning revisions to the lists because it's a fairly moot issue if the result is keep or delete. Seppi333 (Insert 2¢) 17:16, 25 July 2023 (UTC)

Allright, appricate it :) Claes Lindhardt (talk) 13:03, 27 July 2023 (UTC)

The Draft namespace is visible to everyone and so, everyone can edit drafts. However, as drafts are not linked with each other and it's difficult to find a particular draft without knowing its name, few editors actually join editing other than the creator. There are some rules about using the draftspace – see WP:DRAFTS.

On the other hand, articles in your own userspace, even if also visible to everyone, should not be edited by anyone else other than editors you have explicitly invited to do so.

An article should not be moved while deletion discussion is ongoing. However, if the author or principal contributor ask for it to be draftified or userfied, then it's customary that this is respected. — kashmīrī ^TALK 13:17, 23 July 2023 (UTC)

Allright thank you, it seems that there is still a good bit of usefull discussion going on there. Claes Lindhardt (talk) 20:34, 24 July 2023 (UTC)

UniProt has a field called protein existence that indicates whether the expressed protein has been experimentally detected in human tissue. If the protein has not been detected, please keep in mind that does not necessarily mean it is not expressed. It may be that no one has looked in the right place (e.g., tissue), the right time (e.g., fetal vs. adult), or the right conditions (e.g., healthy vs. stressed vs. diseased). There also may be an experimental reason (the available antibodies used to detect the protein don't work). In addition, the protein might be rapidly degraded after it is expressed making it difficult to detect. I suppose that this field could be included, but I think we need to be selective in the fields that are added to keep the list readable. Consensus will determine what fields are included. There are many sources of data about proteins, but I think HGNC and UniProt is likely to contain all of the data about a gene/protein one would likely need for a human gene/protein list. Finally an API (application programming interface), is not data, but software. In the case of protein WikiData, the API to access that data applies equally to all proteins, therefore it is not necessary to include an API column in the list. Boghog (talk) 04:57, 25 July 2023 (UTC)

Maybe the issue of denoting weather a protein have been empericially observed could also be solved by a notion in one of the other columns. Like for example in the Actual Proteins column simply add -'Not yet observed' to all the proteins which are theorised to exist but which he haven't for varies good reasons yet detected or recorded.

I think one of the main purposes of a list like this is to easily visualize how much of the things we consider facts about proteins that is based on concrete observation, and how much is based on simmilar patterns that we have seen elsewhere. So that is is easy to see where the central gabs in our knowlagede base and understanding is, and where one should start if one wanted to improve it. Claes Lindhardt (talk) 11:43, 25 July 2023 (UTC)

Adding columns to tables that are not supported by a reliable source is not a solution. UniProt is generally regarded a reliable source. Even though there are uncertainties associated with "protein existence" in UniProt, UniProt is probably the best single, most reliable source we have to support the existence of a protein. Furthermore UniProt is one of the few sources we have that has coverage over most of the human genome and that a bot can programmatically access to populate a table. Wikipedia's mission is not to increase the accuracy of data, only to report pre-existing data accurately. Boghog (talk) 17:16, 25 July 2023 (UTC)

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