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Human mitochondrial genetics

Hello. There is currently a dispute between myself and Hipal regarding the inclusion of certain links on the Human mitochondrial genetics page. The links in question are to scientific resources for visualising and analysing mtDNA. Ivan (talk) 04:19, 13 June 2024 (UTC)

I'm inclined to think that at least one of these should be included under WP:ELYES #3 (neutral and accurate information, but too much to put it directly in the article – my go-to example of this an online BMI calculator for Body mass index). Someone interested in Human mitochondrial genetics might also be interested in knowing what the gene sequences are. I'm not sure what the different capabilities are for each of these four websites. If they all have basically the same contents, then a smaller number would be appropriate. WhatamIdoing (talk) 16:15, 13 June 2024 (UTC)
Иованъ came here directly without explaining why the links belong.
Thank you, WhatamIdoing, for giving us an argument for inclusion.
The links are:
  1. ISOGG YBrowse: A genome browser.
  2. mitoWheel: A mitogenome browser.
  3. mtDNAprofiler: An mtDNA sequence analysis tool.
  4. mtDNAtool: Tom Glad's mtDNA analysis tool.
The subject matter seems far more complicated than BMI. I'm concerned that we're adding links that would be helpful to few at best. I suspect that people familiar enough with the topic to use such tools wouldn't be coming to the Wikipedia page at all, but instead would be working from far better materials. --Hipal (talk) 16:59, 13 June 2024 (UTC)
I will do my best to provide objective information for your assessment.
  • ISOGG YBrowse is the only online resource of its kind. It is a linear mitogenome browser, which among other things breaks the mitogenome into individual genes. There is a learning curve, but it is rather mild for most applications and the resource is aimed at laypeople. Everyone who has been interested in mitochondrial genes themselves has used this tool at one point.
  • mitoWheel is a simpler, graphically more intuitive, but far less capable mitogenome visualiser. No learning curve, but limited functionality.
  • mtDNAprofiler and mtDNAtool are two resources that can take "raw" sequences and determine an mtDNA clade (and more) from it, each compatible with different formats. I suspect that people familiar enough with the topic to use such tools wouldn't be coming to the Wikipedia page at all, but instead would be working from far better materials. Genetic genealogy is a large branch of citizen science. None of these tools are geared towards professionals (any more). Excluding these links on the grounds that they would be too complicated to use is like excluding a link to eBird from a birdwatching page just because there is a learning curve to reporting a sighting reliably. Ivan (talk) 18:06, 13 June 2024 (UTC)
Thank you for the descriptions. Based upon them, I'd lean toward #2 as the sole link to add of the four, if we add any. --Hipal (talk) 01:51, 14 June 2024 (UTC)
Whereas I would lean towards deleting #3 and #4, if we delete any. Unless you write a separate article on YBrowse, an article on human mitochondrial DNA without an external link to it is like an article on free software without a link to Github. Ivan (talk) 02:02, 14 June 2024 (UTC)
It sounds like having both of the last two would be a little redundant. WhatamIdoing (talk) 15:38, 14 June 2024 (UTC)
Would you agree on the inclusion of the first two, then? Ivan (talk) 15:41, 14 June 2024 (UTC)
I think all four are permissible per the guideline, but that all four aren't necessary. I could agree to have all four, but I think that three or fewer would be sufficient to meet the goal (i.e., to provide readers with more information/resources than we can put directly into the Wikipedia article itself).
If we decided to have three, I'd exclude one of the last two. If we decided to have two, I'm not sure whether it makes more sense to have one of the first pair plus one of the more complex ones, or just the two first/simpler ones. If we decided to have only one, I'd suggest one of the first two. WhatamIdoing (talk) 16:07, 14 June 2024 (UTC)
Alright, I will delete the link to mtDNAprofiler and reinsert the remaining three. Thank you. Ivan (talk) 16:10, 14 June 2024 (UTC)
In this edit, Hipal just removed both ISOGG YBrowse and mtDNAtool from the External Links section with the summary if we have any consensus, it's only for one. Since your wording included I think all four are permissible per the guideline but also if we decided to have three, I'd exclude one of the last two, I combined that with my own support for all but mtDNAprofiler (in retrospect not a good external link), for a 2:1 majority opinion. Would you prefer Hipal's reduction to 1 source or my reduction to 3 sources? Ivan (talk) 17:32, 14 June 2024 (UTC)

Hang on please. Do the last two do anything without the user providing data? --Hipal (talk) 16:47, 14 June 2024 (UTC)

No, it does not. Though to be clear, the data provided does not need to be the user's own. There are public databases that share samples. Ivan (talk) 16:54, 14 June 2024 (UTC)
Thank you. My apologies, but I should have been more specific with my question: The last two require data from outside sources, correct? --Hipal (talk) 17:11, 14 June 2024 (UTC)
That is correct. Ivan (talk) 17:22, 14 June 2024 (UTC)
Thank you. I wanted to make sure I wasn't overlooking something.
The fourth seems far too technical.
As for the third, I'd expect that where ever a person is getting their date from would recommend some analysis tools appropriate for the knowledge level of the person. I don't see a case where a person who could use the tool would actually come to this article without already having awareness of appropriate tools. --Hipal (talk) 17:32, 14 June 2024 (UTC)
I don't see a case where a person who could use the tool would actually come to this article without already having awareness of appropriate tools Since Wikipedia does not support commercial external links, there are very few tools available for analysing so many aspects of one's own or another's mitogenome. Most of these are more haplogroup-focused than mutation-focused. This tool is noncommercial. I don't think that a reader who can get through the Electron transport chain, and humanin section would find copy-pasting data to find mutations daunting, and as an older tool on a website heavily disadvantaged by modern search algorithms, it is unlikely to be discovered by a simple search. It should probably be recaptioned from "An mtDNA analysis tool" to "Retreives mutations from mitochondrial data files". Ivan (talk) 17:49, 14 June 2024 (UTC)
Now that I understand your opposition to mtDNAtool, why did you remove YBrowse? Ivan (talk) 17:52, 14 June 2024 (UTC)
I removed it because it's restoration was premature.
I thank you for taking the time discuss the links. I'd like to hear what others have to say. --Hipal (talk) 21:23, 14 June 2024 (UTC)
Yes, I know you'd like to hear from others, but as of right now there is a 2:1 = 66% consensus for my last edit, so in light of the lack of either a closure process or a minimum participation requirement at ELN, I would appreciate it very much if you took that last revert back. And recaption from the last link from "An mtDNA analysis tool" to "Retreives mutations from mitochondrial data files". Ivan (talk) 00:17, 15 June 2024 (UTC)

For the benefit of the user providing a third opinion, the disputed link is "mtDNAtool: Retrieves mutations from mitochondrial data files." Ivan (talk) 23:34, 18 June 2024 (UTC)

Coming by after seeing WhatamIdoing's post at the Molecular Biology project. The first two links, ISOGG YBrowser and mitoWheel, are good interactive maps of the mitochondrial chromosome and are fine to keep. I find mitoWheel is far better as an educational resource.
By my reading of the mtDNAprofiler site I do not know what need a reader of this article would have for the tools there. They are essentially intended to annotate experimental data, and any scientist gathering this data already has these tools (or can ask a coworker). Nobody else has un-annotated data, unless most databases are storing heaps of un-annotated mtDNA. Though, I don't really see harm in having the link, unless it is unduly highlighting this particular academic group's work.
The last link, mtDNAtool, falls under Ancestry.com's terms and conditions which means that any data you plug into it can, in principle, be recorded by the company (unless I missed something, I didn't read the entire ToS). I find it unlikely that that's happening at that site or that any data plugged into it could be valuable to them, but it really rubs me the wrong way. I wouldn't send a reader there without highlighting that. ― Synpath 07:33, 19 June 2024 (UTC)
I had already struck mtDNAprofiler from the list. After reviewing the ToS I have to agree regarding the last one. I will count that as consensus against inclusion. Thank you for your reply! Ivan (talk) 08:28, 19 June 2024 (UTC)

Internet Archive takedowns

Recently more than half a million books were pulled from the Internet Archive following a lawsuit by book publishers.[1] This means that many of their books are no longer available for borrowing. It is not uncommon for copies of books on the Internet Archive to be linked in citations, so I was wondering if there's a way we can find out which of our articles have been affected by this takedown (i.e. in which articles we link to now-unavailable books). It'd be useful to know how deeply the encyclopedia was affected by this and where we need to remove and/or replace links to pulled books. I was directed here by the help desk, but if there's a more appropriate board to ask about this on, please let me know. --Grnrchst (talk) 09:43, 23 June 2024 (UTC)

Hey GreenC: are you able to help here? Johnuniq (talk) 09:46, 23 June 2024 (UTC)
I guess we can't use Internet Archive to archive Internet Archive. Agree that it would be interesting to know. Gråbergs Gråa Sång (talk) 15:13, 23 June 2024 (UTC)
This was a caution I had way back when we started to use IA as archive data - unlike Google books that won their suit with publishers, IA's approach hadnt been tested in court, and now we're at this situation. If IA ultimately wins this suit (after all appeals), and the books are back, then we should be fine with using IA as archives. — Masem (t) 15:50, 23 June 2024 (UTC)
I have another "interesting to know" here: half a million books out of how many? It's annoying that these aren't as easily available now, but assuming the WP-cites using them were correctly done, it just means these sources are WP:OFFLINE (or restricted) again. Maybe. Gråbergs Gråa Sång (talk) 18:01, 23 June 2024 (UTC)
The problem is that with the current status of this case, IA should be presumed - for any copyrighted work where there is not clear allowance for its use - to be taken as equivalent to researchgate.net. IA's practice, at the current stage of the trial, has been deemed a copyright violation and while the 500k books removed are those belonging to the 4 publishers that filed suit, one must presume that all the others are copyright violations, unless otherwise indicated. IA is obviously not going to remove those as it fights the suit, only those set by the court, and IA may ultimately win, but we should be avoiding the use of IA for book backup/archive sources since there is a real possibility all such activity by IA will be deemed a copyright violation.
(Again, Google actually won in its suit against the Authors Guild, but their snippet approach practice is far more limited than the IA's approach.) Masem (t) 18:22, 23 June 2024 (UTC)
Sorry, isn't the WP-issue with researchgate.net about user-generated content? Hosting potentially copyvio stuff seems different. Gråbergs Gråa Sång (talk) 18:28, 23 June 2024 (UTC)
Per WP:COPYLINK, if you know or reasonably suspect that an external Web site is carrying a work in violation of copyright, do not link to that copy of the work (emphasis mine). —Compassionate727 (T·C) 22:31, 23 June 2024 (UTC)
The problem is WP:COPYLINK makes no mention or allowance for libraries. Libraries like Internet Archive have their own copyright rules. For example, [2] says "Title 17, section 108 of the U.S. Code permits libraries and archives to use copyrighted material in specific ways without permission from the copyright holder." Copyright is a complex thing. The final ruling of the lower court came up with some complex answers and so Internet Archive is under an injunction which it is legally compelled to follow, as an injunction. What the injunction means for Internet Archive and Wikipedia is explained in the official statement: "What the Hachette v. Internet Archive Decision Means for Our Library". -- GreenC 01:41, 24 June 2024 (UTC)
Then, if I'm told IA removes books when a court tells them they have to, isn't it reasonable to assume they are generally copyright compliant? Gråbergs Gråa Sång (talk) 06:45, 24 June 2024 (UTC)
They have removed the books of the four publishers that won their suit against IA. There may be a large number of books from other publishers that are also being used that would be copyright violations but it would require the publishers of those other works to take action under copyright law. Masem (t) 12:02, 24 June 2024 (UTC)
It's possible, who knows what the future will bring.
There are a lot of exceptions: 1. Many rights holders want their books to have CDL access, so assuming any particular book will taken offline in the future is guesswork. 2. It requires the rights holder to request that it be taken offline. 3. Any book that is out of print is excluded from the injunction, most books on IA are out of print. 4. For books in print, they also need an ebook currently for sale.
To clarify, they "removed", according to the source, CDL access, the "Borrow this book" button at the top of the page. They still offer "short portions of books", per the final ruling of the lower court, and terms of the injunction.
For comparison, we added Google Books links for 10 years while that court case was ongoing. Nobody knew how it would turn out. It was uncertain. Someone could have made the argument the books were "reasonably suspect" because the case was unsettled. But nobody did because so long as Google was in compliance with whatever injunctions were in force at the time, they were not doing anything in violation. The "reasonable suspect" argument could only be made if one was guessing how the case would turn out in the future. -- GreenC 16:26, 24 June 2024 (UTC)
Researchgate allows for people to publish articles bypassing the copyright of the publisher, if the work is not in an open access journal. (The userg aspect is also there too). One could say there's a fair use allowance by the person that did the paper to put it there, but there's no checks and balances like Google Books uses, nor even a checkout system like IA. Masem (t) 02:11, 24 June 2024 (UTC)
Let's assume I inserted this in an article: "Kinser made her first teddy bear in 1976.[1]"
At some point after that IA removes that book. It's annoying for the reader who wish to easily confirm I didn't make that up, but WP:OFFLINE still says it's ok. I could even have skipped the url in the first place. And it may re-appear somewhere else at some point. How is that equivalent to researchgate.net?
Gråbergs Gråa Sång (talk) 18:36, 23 June 2024 (UTC)
Know that many of the taken down books are still available to those who are print-disabled. IA has information about applying for print-disabled access, which takes you to this Google form. You have to be honest on the form, because they are not able to verify your application and must simply take your word for it. It then takes a few days to be approved. Thebiguglyalien (talk) 18:09, 23 June 2024 (UTC)
  • The title of the OPs external link: "Why are so many books listed as Borrow Unavailable at the Internet Archive". "Borrow" means Controlled Digital Lending (CDL), to borrow the entire book ie. flip through cover to cover. This is what the IA court case is mainly about: the entire book. CDL is often irrelevant for Wikipedia citation purposes because we typically link to "short passages" ie. certain pages of a book. This is unaffected by the court case. It is established law (by the Google Books case) that anyone including IA can make available short passages of books and search inside. Internet Archive posted an official statement: "What the Hachette v. Internet Archive Decision Means for Our Library". Their statement:
We may continue to display “short portions” of books as is consistent with fair use—for example, Wikipedia references (as shown in the image above). The injunction does not affect lending of out-of-print books. And of course, the Internet Archive will still make millions of public domain texts available to the public without restriction.
Thus, of those 500,000, most are still available for displaying short portions of books (and search inside). -- GreenC 19:24, 23 June 2024 (UTC)


References

  1. ^ Mullins, Linda (1991). Teddy Bears Past & Present: A Collector's Identification Guide. Hobby House Press. pp. 220–221. ISBN 978-0-87588-384-7.

Sorry if I'm at the wrong place to raise this concern, but when I was attempting to scrutinize the quality of this external link at Vasily Blokhin -- http://pamietamkatyn1940.pl/en/blog/historia_zbrodni/smierc-z-rak-nkwd-2/ -- my browser gives me a warning that the link might be a security risk. Is this something we need to worry about? --ZimZalaBim talk 13:04, 24 June 2024 (UTC)

It is a SSL certificate error which are common due to misconfigurations. So long as you are prepared to view the site without SSL (encrypted), as if it were http and not https, it shouldn't be a problem to bypass the warning screen. Presumably they will repair in time. -- GreenC 16:31, 24 June 2024 (UTC)

Know Your Meme

 You are invited to join the discussion at Wikipedia:Templates for discussion/Log/2024 July 11 § Template:Know Your Meme. 0xDeadbeef→∞ (talk to me) 08:15, 11 July 2024 (UTC)

For articles about a software package, is it acceptable to have a link to the package's downloads page in addition to an official website link? Specifically on Komodo Edit (Talk), an editor added a link to a page to download the software from the publisher (https://downloads.activestate.com/Komodo/) in addition to the "Official website" that already existed. I removed the downloads link as it struck me a breach of WP:ELMINOFFICIAL. The editor who added the link argues that it's helpful since navigating to the downloads page from the main site requires "a circuitous series of click-throughs" (which is true, to be fair). I don't see anything specifically addressing software downloads on the Wiki page for the software in the EL guide, so I'm hoping we can get some guidance here. Thanks!Wburrow (talk) 17:03, 7 August 2024 (UTC)

We're not here to make it easy for people to download software, we're here to discuss encyclopaedically the software. A link to the official site should be sufficient per WP:ELOFFICIAL. Can the download be accessed from the official site? If so then there's no need for a second link. And we already have the repository in the infobox (which is dubious if it falls afoul or not.) Canterbury Tail talk 17:19, 7 August 2024 (UTC)
I agree with Canterbury Tail; also, I add, in case it ever comes up, that a link that autodownloads software (as opposed to one that links to a "Download now" button) would be very unfriendly. WhatamIdoing (talk) 18:01, 7 August 2024 (UTC)

Template:IETF RFC exempt from WP:NOELBODY?

Your opinion is sought at Template talk:IETF RFC#Use in article body, please. fgnievinski (talk) 03:15, 14 August 2024 (UTC)

Since this location was pointed out to me, I wanted to note that I started an external links-related discussion at WP:Village pump (policy)#Formatting of election pages - external links and pseudoheads. I'm happy to move or have it moved here if it is the more appropriate venue. Thanks, Ost (talk) 22:26, 4 September 2024 (UTC)

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