Wikipedia:Articles for deletion/Genome-wide complex trait analysis


 * The following discussion is an archived debate of the proposed deletion of the article below. Please do not modify it. Subsequent comments should be made on the appropriate discussion page (such as the article's talk page or in a deletion review).  No further edits should be made to this page.

The result was keep. Although it is clear from the discussion that improvement is needed.  Sandstein  13:20, 9 December 2018 (UTC)

Genome-wide complex trait analysis

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This is page is an astounding work of original research and synthesis, assembling a bunch of primary sources and unsourced content into a review article. To make this a Wikipedia article it would have be completely done over. It reflects a ton of work and kudos for that, but it doesn't belong here per WP:OR and WP:NOT. Maybe Wikiversity.

I am also nominating the following page, for the same reason:

-- Jytdog (talk) 10:23, 2 December 2018 (UTC)


 * Note: This discussion has been included in the list of Medicine-related deletion discussions. Jytdog (talk) 10:25, 2 December 2018 (UTC)


 * Keep. I am the primary author of these two articles. Jytdog is engaged in a hostile nomination due to my comments on his other genetics AfD, Articles for deletion/Designer baby (2nd nomination). (We have never interacted before that I can recall, but he has a history of this sort of thing.) His comments here are no more correct than his claims on that AfD; if you look at the 2 articles, you will see scores of citations of reviews, systematic reviews, textbooks, and meta-analyses and that they are scrupulously cited, to a fault. --Gwern (contribs) 21:12, 2 December 2018 (UTC)
 * I am sorry you feel that it is hostile. These two pages are what they are; there are loads of primary sources per WP:MEDDEF, and these pages don't belong in WP per the nomination. You should publish these pages somewhere else as your own reviews of the field. We will see what others say. Jytdog (talk) 21:46, 2 December 2018 (UTC)
 * Optimistic keep-but-crop-heavily This is indeed an impressive piece of work, but I agree that it is too heavy on the synthesis of primary material to sit well with the sourcing balance that is expected for a WP article. It's a shame because there's easily enough review and meta-analysis material in there to pass muster for a topic - e.g., , , , , . BUT the synthesis, well-referenced as it may be, is very heavy here.
 * Starting from the end, most of the primary source overkill is located in the "Traits" section - that, I believe, is really out of scope, what with pulling together almost 200 (!) primary research results. Personally I quite like having this available - looks like a great resource; but the arguments against it do have grounding in policy. - Sections "Benefits", "Disadvantages" and "Interpretation" seem well reasoned, but they are reasoned - they consist of conclusions drawn by the author from an assembly of primary material. Again, no good for an encyclopedia. Section "Implementations" I don't find troublesome because it just lists available software approaches, and boy do we ever have a tradition of that. "History" I think works because it's mostly a chronological assembly of material, which doesn't really fall under "synthesis". The lede reads well but I assume that much of it would have to be removed if one took away the original reasoning sections.
 * Overall, yes, most of the meat of this article is too synthetic for local consumption. I wish it could be cut down to what's reasonable, though, instead of deleted, because there's a lot of effort and expertise here that would be a shame to just chuck out. If the author could just get this entire thing published as a review article in a journal, then one could go to town with that source... -- Elmidae (talk · contribs) 14:43, 3 December 2018 (UTC)
 * Add: I've only just looked at Genetic correlation, and it's the same in green. Great work, wrong venue, cutting it down would be a lot of effort but may be worth it.


 * -- Elmidae (talk · contribs) 14:47, 3 December 2018 (UTC)
 * User:Elmidae would you be open to draftification rather than deletion? That would be OK with me; this should not be in mainspace until it is cleaned/done over... Gwern what do you think? Jytdog (talk) 15:58, 3 December 2018 (UTC)
 * That would seem reasonable to me, but would of course depend on Gwern's interest in reworking the articles. -- Elmidae (talk · contribs) 16:40, 3 December 2018 (UTC)
 * Obviously, I disagree. There would be no point to attempting to get this published as it is merely compiling what has already been published; everything is drawn from the provided references, whether that's Neale's textbook, Plomin's textbook, Lee's review, the many phenome papers, the Cheverud's conjecture papers, and so on and so forth. It's all heavily cited, to a fault. Everyone here is freely claiming that this is 'all synthesis' or OR, and yet, no one is giving examples of what they think the OR is.
 * As far as Vrie0006's comment goes: we already discussed it, and I support moving the trait references out to the relevant trait articles as part of their genetic coverage. The information about the genetic heritability or correlations about most traits on WP is in terrible shape, and that's part of why I was compiling the section, as a draft for adding to other articles. I do not have time now to do so myself (and even less time if I must deal with spurious AfDs launched to retaliate against me for my comments on another AfD); Vrie was, however, less interested in helping with this and more interested in deleting them wholesale, and of course I did not support that idea. --Gwern (contribs) 16:50, 4 December 2018 (UTC)
 * , as a concrete example - the start of the "Interpretation" section:
 * GCTA estimates are often misinterpreted as "the total genetic contribution", and since they are often much less than the twin study estimates, the twin studies are presumed to be biased and the genetic contribution to a particular trait is minor.[35] This is incorrect, as GCTA estimates are lower bounds.
 * A more correct interpretation would be that: GCTA estimates are the expected amount of variance that could be predicted by an indefinitely large GWAS using a simple additive linear model (without any interactions or higher-order effects) in a particular population at a particular time given the limited selection of SNPs and a trait measured with a particular amount of precision. Hence, there are many ways to exceed GCTA estimates - followed by examples based on half a dozen primary studies, finished off with an apparently novel example calculation. That is your synthesis, and your original composition of previously unrelated material into an argument structure. Which is fine for a journal article, but not for a Wikipedia article. -- Elmidae (talk · contribs) 17:18, 4 December 2018 (UTC)
 * This definitely seems at first glance to be a synthesis and analysis, which would be very concerning in a Wiki article - but chasing down the sources, the article cited here, "Still Chasing Ghosts," itself makes the point that GCTA estimates are often misinterpreted, in exactly the way described by Gwern. That source is a secondary source, and the summary in the text of the wiki entry which seems to obviously be analysis is basically distilling the points made in that article. So the analysis in the wiki article seems to be exactly the type of tertiary summary of secondary analyses that we want on wikipedia. The following examples are, it seems, largely taken from that source, but the points are in "Chasing ghosts" and are cited to other appropriate secondary sources. Perhaps it is bad form to even cite the primary sources in the wiki article, but again, this isn't synthesis of primary sources, it's detailing the syntheses done elsewhere in several secondary sources, with examples from primary sources. If the primary sources themselves are a problem, they could simply be removed, instead of requiring significant re-editing. Davidmanheim (talk) 07:04, 5 December 2018 (UTC)
 * I agree that it would be nice if the article could be put into shape in situ rather than anything more drastic, as the material is good and well-presented. As noted above, quite a number of reviews and meta-analyses are already used as sources, and if those could be substantially emphasized over the primary sources that should do it. But I suspect that requires a fair amount of insight into the research and where it's buried, and thus would really best be undertaken by the original author if they are willing. (Re primary sources, they are certainly wanted in science articles - for a start we would lose many thousands of taxonomy articles/stubs if they weren't! - but they shouldn't form the skeleton of anything resembling an argument structure, plus WP:MEDRS is particularly leery of them.) -- Elmidae (talk · contribs) 08:20, 5 December 2018 (UTC)
 * Perhaps some of these concerns could be addressed through relatively moderate phrasing modifications, such as including statements like "a 2015 meta-analysis by Polderman et al. found that..." in appropriate places. XOR&#39;easter (talk) 18:06, 5 December 2018 (UTC)


 * Keep - Notable topic and more than enough references. ♟♙ (talk) 21:49, 3 December 2018 (UTC)
 * Thanks for entirely missing the point, mate. Truly a "drive-by" comment. -- Elmidae (talk · contribs) 08:07, 4 December 2018 (UTC)
 * Thanks for the unhelpful attitude. ♟♙ (talk) 22:49, 4 December 2018 (UTC)
 * Draftify. Per Elmidae and Jytdog's discussion. GREML (at intro of article) does get used in genetic analyses like genome wide association mapping to the point I even recognize it from skimming papers, but the state of the article just isn't ready for mainspace. The topic can have very concise content and be notable, but I also can't vote keep due to all the synthesis, etc. mentioned above. Kingofaces43 (talk) 03:53, 4 December 2018 (UTC)
 * Note: This discussion has been included in the list of Science-related deletion discussions. Kingofaces43 (talk) 03:56, 4 December 2018 (UTC)


 * Draftify. I'm not sure what that means but FOR SURE this page should not be merged with Genome-wide Complex Trait Analysis for many reasons. First and foremost, genetic correlations should not be equated in any way with GCTA. GCTA is a software tool, not a scientific concept. Genetic correlations can be calculated in many, many ways including pedigrees, twins, adoptees, GCTA, and others still. However, and as I've said on the talk page, the article as written leaves much to be desired. For example, the lists of trait pairs, as much work as it represents, should be entirely deleted IMO, with perhaps a few notable examples. The original research on this page is not a resource for the field, and such a resource is not effective as a wikipedia page. I offered to help in the past but found the page's primary author was highly protective, which is understandable. Vrie0006 (talk) 14:53, 4 December 2018 (UTC) P.S.: Sorry, missed the point here that there was no discussion of merge, but rather that both pages were nominated for deletion. I would still say draftify, but draftify here means deleting tons of content. I'm OK with that. Vrie0006 (talk) 14:54, 4 December 2018 (UTC)
 * Draftify both per Elmidae's comments above. These look to be the start of a viable review article, but that's not what we publish. However, the problem may not be intrinsic to the article; that is, it might be remediable through ordinary editing. That editing should take place in the Draft area. In addition, many of the citations appear to be to preprints, which in this case violates WP:MEDRS. Links to preprints (arXiv, biorXiv, faculty websites, etc.) should be provided as supplements to journal versions. XOR&#39;easter (talk) 15:25, 4 December 2018 (UTC)
 * Could you quote the part of MEDRS which bans preprints like Arxiv or Biorxiv, which are increasingly the main publishing venues of these fields? For example, He was urged at the CRISPR conference to upload his article on the CRISPR babies to Biorxiv; which part of MEDRS would ban citing this upload? --Gwern (contribs) 16:50, 4 December 2018 (UTC)
 * Quoting WP:MEDRS, with emphasis added in places: Ideal sources for biomedical information include: review articles (especially systematic reviews) published in reputable medical journals; academic and professional books written by experts in the relevant fields and from respected publishers; and guidelines or position statements from national or international expert bodies. Primary sources should generally not be used for medical content – as such sources often include unreliable or preliminary information, for example early in vitro results which don't hold in later clinical trials. Preprints on arXiv and biorXiv are primary sources that have not undergone peer review. In some circumstances, preprints can be cited as sources for expert opinion (the relevant bit of policy being WP:SPS). In other cases, a preprint might effectively be "reviewed" in secondary sources before it is formally published. I don't think that those exceptions apply here. XOR&#39;easter (talk) 17:16, 4 December 2018 (UTC)
 * That it discussing primary sources for medical outcomes, where it is possible that "unreliable or preliminary information" will be presented. The concern there - that non-peer reviewed information from clinical trials about medicine will be repeated - is not really relevant here. In any case, I'm confused how that section of the rules is relevant for statistical analyses of public data that are increasingly never published in journals. Davidmanheim (talk) 07:16, 5 December 2018 (UTC)
 * I recognize that we're not talking about clinical-trial results here, but the article does concern the scientific study of human beings, which is always cause to tread carefully. And if there's an entire body of research that never gets formally reviewed, then the question of how we could potentially cite that work is a much bigger question than this one AfD. As it stands now, citations to non-reviewed work are generally Considered Harmful. XOR&#39;easter (talk) 18:18, 5 December 2018 (UTC)


 * Keep and improve with greater stress on the methodological problems of GCTA. --Davidcpearce (talk) 16:31, 4 December 2018 (UTC)
 * Keep I've removed the absurdly long tables of correlations; if there are secondary sources talking about these they would still need to be re-written from scratch to be in a format useful to readers. I don't see any rationale for deleting the rest of the articles. power~enwiki ( π,  ν ) 17:31, 4 December 2018 (UTC)
 * Keep Per the above; also a bad-faith nomination by a user who has since left Wikipedia "under a cloud". Andy Mabbett ( Pigsonthewing ); Talk to Andy; Andy's edits 18:30, 4 December 2018 (UTC)
 * I was wondering when the Jytdog grave-dancers would turn up. This rationale is complete bullshit and lowers my opinion of you a lot, Andy. -- Elmidae (talk · contribs) 18:40, 4 December 2018 (UTC)
 * Even without reviewing the article to decide whether I'm for keeping, draftifying or othering this article, I can tell the above ad hominem comment is in extremely poor taste. You should retract it or expect to have eyes on you for your grave-dancing and personal attacks. Hijiri 88 ( 聖やや ) 22:24, 5 December 2018 (UTC)
 * "eyes"? I'm unmoved by such facile threats. My description of the nomination was accurate; and stands. Andy Mabbett ( Pigsonthewing ); Talk to Andy; Andy's edits 20:27, 6 December 2018 (UTC)
 * Keep and improve as needed. This is typical deletionist overreach (typical of this user, who has by my count nominated 162 articles for deletion!). If something is wrong with an article, fix it instead of culling it. Deletion should only be used for topics that don't meet notability requirements. Genetic correlation and genome-wide complex trait analysis are obviously important scientific concepts that merit good coverage in Wikipedia. Deleet (talk) 18:43, 4 December 2018 (UTC)
 * Hey look, another one. You are entirely wrong, by the way; lack of notability is one of 14 defined deletion criteria. -- Elmidae (talk · contribs) 19:57, 4 December 2018 (UTC)
 * Or, you know, you might just be wrong. ♟♙ (talk) 22:49, 4 December 2018 (UTC)
 * I actually have to agree with Elmidae that some of the recent keep !votes are superficial and not really digging into the actual state of the articles, which basically means they don't get counted in weighing consensus. Not to mention that some are here blatantly violating WP:FOC. They seem to be focused on continuing battleground behavior instead, which is disruptive to the AfD. Plus, simply being notable and sourced does not equal a keep in all cases as demonstrated with the draftify comments. That being said, no one could claim a deletion nomination was bad-faith considering this could just as easily be merged into Genome-wide association study. I wouldn't mind seeing the daughter article myself, hence my !vote, but deleting and fleshing out a little bit of the unique stuff with new secondary sourced content at GWAS is doable too. Kingofaces43 (talk) 01:47, 5 December 2018 (UTC)
 * They "dig into the state of the articles" just fine. The closing admin will determine what is counted and what isn't and your aspersion casting on those with whom you disagree is offensive. Please stop assuming bad faith. ♟♙ (talk) 04:01, 5 December 2018 (UTC)
 * The assumption here (on my part as well) is not of bad faith (in contrast to Andy above, btw) but of lack of understanding of the problem under discussion. The only possible yardstick for that is the content of your contribution. -- Elmidae (talk · contribs) 07:55, 5 December 2018 (UTC)
 * I made no such assumption. Andy Mabbett ( Pigsonthewing ); Talk to Andy; Andy's edits 16:24, 5 December 2018 (UTC)
 * No I was pretty clear that those comments like yours barely even superficially address the issues the most of the draftify !votes were discussing in some detail. Please remember that WP:CON policy requires that such comments are ignored. Also remember not to cast aspersions like you just did either. We already have enough people interjecting their behavior issues into this AfD that's attracting more drama than most science AfDs that come up on my watchlist. Kingofaces43 (talk) 21:08, 5 December 2018 (UTC)


 * Keep I have reviewed both the article, and the discussion. It seems clear that the article can be improved and brought more in line with wiki policies on citations and original research - though it is not clear exactly where the issues are. Large parts of the article are clearly not original research, so any issues with original research should be dealt with via discussion about editing the article, not the AfD process. The fact that the discussion is about whether or not specific parts of the article violates specific guidelines, and the exact ways in which it does so, is exactly the reason that Wikipedia policy says that AfD is inappropriate for "Articles that are in bad shape – these can be tagged for cleanup or attention, or improved through editing." Davidmanheim (talk) 07:31, 5 December 2018 (UTC)
 * Keep both GCTA is new but notable – see Genetics, Health, and Society, for example. It is likewise easy to find good sources for the genetic correlation topic too.  The rest is then a matter of ordinary editing, not deletion, per WP:ATD, WP:BITE, WP:IMPERFECT, WP:NOTCLEANUP, WP:PRESERVE, &c. Andrew D. (talk) 08:27, 5 December 2018 (UTC)
 * Andrew... do you ever do ANYthing but plaster "is notable, has sources, some random wikilinks" into these discussions? No-one has ever contested that! I would like it if the article were being kept and cleaned up, but man the knee-jerk superficial !votes are really dispiriting. -- Elmidae (talk · contribs) 09:08, 5 December 2018 (UTC)
 * The nomination complains that the topics in question are unsourced or based on primary sources. The links that I provided point to secondary and tertiary sources such as the Encyclopedia of Genetics.  The argument of the nomination is thereby refuted.  Q.E.D. Andrew D. (talk) 09:30, 5 December 2018 (UTC)
 * If you think that you need read nothing on the page except the nom statement at this stage, that is certainly an explanation. -- Elmidae (talk · contribs) 10:33, 5 December 2018 (UTC)
 * So far, nobody has agreed with the nomination's proposition that these topics should be deleted from Wikipedia and moved to another project such as Wikiversity. Even Elmidae's !vote is a keep and so it's unclear why Elmidae is so intent on insulting other editors who agree with his position.  My !vote stands. Andrew D. (talk) 11:05, 5 December 2018 (UTC)
 * I'm intent on pointing out what a pile of ill-considered !votes results from people a) substituting their dislike of the nominator for sound engagement, and b) phantasizing that pure notability is the only keep/delete criterion in existence. That the direction of these autopilot comments tends to the side I happen to agree with in this case is somewhat incidental. Guess I'm just disappointed - in-depth contributions like those of Davidmanheim above provide a really good basis for coming to a conclusion, and then we get another 50% of... this stuff to muddy the waters. -- Elmidae (talk · contribs) 14:50, 5 December 2018 (UTC)
 * I would agree with the nominator that, as the articles were written at the time of nomination, they were more suitable for another project (e.g., Wikiversity) than for here. I was more optimistic than the nominator about how easily the articles could be brought into compliance with policies (particularly WP:SYNTH). I was somewhat less optimistic than Elmidae was, apparently, since my inclination was that the revisions should go on over in Draft land. XOR&#39;easter (talk) 18:03, 5 December 2018 (UTC)
 * Uh, the nominator eventually said draftify, Elmidae who originally said keep in their initial statement was pretty open to draftify, and a bunch of other editors said the same. That's far from just keeps. Your second to last sentence is violating WP:FOC policy and more or less requires your comments here to be ignored at the close. Editors have been responding to people interjecting their behavior issues into this AfD, so that should be more than enough caution for you to knock off the sniping or try to turn it back on those responding to it. Any more of that really should be dealt with in admin forums at this point since that behavior has functioned to disrupt the AfD already. Kingofaces43 (talk) 21:08, 5 December 2018 (UTC)


 * Keep . The topics clearly pass GNG and problems with the articles are being addressed by various knowledgeable editors. This discussion is getting sidetracked by comments on the nominator and this distracts from the article itself. A keep !vote is not a !vote for or against the nominator’s drama.  Montanabw (talk) 22:06, 6 December 2018 (UTC)


 * The above discussion is preserved as an archive of the debate. Please do not modify it. Subsequent comments should be made on the appropriate discussion page (such as the article's talk page or in a deletion review). No further edits should be made to this page.