Wikipedia talk:WikiProject Genetics

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WikiProject Genetics (Rated Project-class)
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Wikipedia:WikiProject Unique Identifiers[edit]

So, there's a new project which may be of interest to some here. It arises out of Wikipedia:Village_pump_(proposals)#UID_interface_to_Wikipedia, a proposal to make wikipedia articles available by their UID - for instance by their UNIPROT number. Umm. For reasons which should be all to obvious to anyone interested in computational aspects of genetics. And those two pages are all I have to show you, but I live in hope of input from you to take it all further. --

Gene cluster article[edit]

Eight months ago, I wrote

In mid-March, two students announced on the talk page of the Gene cluster article, that they were planning to improve the article, as a college project. They requested other editors not to edit the article until their project was assessed, om May 7th. They then made many changes to the article, adding a lot of new material.
Other editors praised their efforts. I criticised them, as I believed they were incorporating errors and misunderstandings into the article. They accepted some of my criticisms, and made some corrections.
Their deadline is now a week past, and I assume that their project is over, though they and their professor have given no feedback on it. I believe that they have made many improvements to the article, most notably the addition of material about Hox genes and the Homeobox family. But I also believe that some of the errors they introduced are still there, and should be removed.
However, I believe that I am not the best person to clear up the errors. While I believe I am technically competent to do it, I feel some "commitment" to the article, which must be a bad thing. I would prefer another editor to take a lead here. I have already stated many of my views on the errors, on the article's talk page, and can provide further details if asked. Maproom (talk) 11:19, 15 May 2014 (UTC)

No-one responded (and today, coincidentally, my request was archived). I am planning to work on the article myself soon. I shall copy this to its talk page.

While the students made many improvements to the article, they added a long section on formation, discussing various theories about the origin of gene clusters. But this is absurd; the origin of gene clusters (by duplication and divergence) was known in 1972, and is not in doubt. This is acknowledged in the second sentence of the article "A gene cluster is part of a gene family": The gene family article starts "A gene family is a set of several similar genes, formed by duplication of a single original gene."

I will replace the long "formation" section by a much shorter historical section, mentioning the various pre-1970 conjectures. Maproom (talk) 11:01, 19 January 2015 (UTC)

Yes check.svg Done Maproom (talk) 16:08, 14 April 2015 (UTC)

A thorough review of the gene article[edit]

Transcluded from Talk:Gene/Review

To WP:MCB, WP:GEN, WP:BIOL and WP:EB

The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo)talk 09:49, 31 March 2015 (UTC)

It appears the main reason gene was delisted as a GA was sourcing (see Talk:Gene/GA1). The following free textbook is probably sufficient to document most basic facts about genes:
a second one is even more relevant, but unfortunately not freely accessed:
I will start working on this as I find time. Boghog (talk) 17:58, 31 March 2015 (UTC)
Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to give it some attention. Opabinia regalis (talk) 19:19, 31 March 2015 (UTC)
I'll probably go through and make all the necessary MOS tweaks for FA status to the article within the next week. Too preoccupied with other articles at the moment to make any substantive content/reference changes though. Seppi333 (Insert  | Maintained) 03:24, 1 April 2015 (UTC)

Glossary[edit]

Snooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. --Squidonius (talk) 21:47, 1 April 2015 (UTC)

Including a glossary could be useful, but I think it should be concise and tailored specifically for this article. Currently {{Genetics glossary}} contains 22 entries and some of the definitions are quite lengthy. A shorter glossary, closer to the size of {{Transcription factor glossary}} or {{Restriction enzyme glossary}}, IMHO would be more effective. Another option is to transclude the {{Genetics sidebar}} which in turn links to {{Genetics glossary}}. Boghog (talk) 06:38, 2 April 2015 (UTC)
...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence. Seppi333 (Insert  | Maintained) 07:25, 2 April 2015 (UTC)
Collapsed or not collapsed, {{Genetics glossary}} is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article. IMHO, a long glossary defeats its purpose. Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse. Boghog (talk) 08:30, 2 April 2015 (UTC)
Fair enough. Might as well make a new one since it's not referenced anyway; imo, glossaries should cite sources, preferably another glossary, because it's article content. Seppi333 (Insert  | Maintained) 08:39, 2 April 2015 (UTC)
Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article genetics glossary. (I'm not really sure we need both.) I agree that the template is way too long, and as constructed is hard to ctrl-F for a term.
I suggest just linking to the MBC glossary as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers. Opabinia regalis (talk) 21:47, 2 April 2015 (UTC)

References[edit]

I'm planning on adding some more Molecular Biology of the Cell references to the article using {{rp}} to specify chapter sections. I went to the MBOC 4th ed. online page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for Biochemistry 5th ed. online? Alternatively, maybe there's a more easily refernced online textbook for general citations. T.Shafee(Evo﹠Evo)talk 11:30, 20 April 2015 (UTC)

I had the same train of thought here on the regular talk page. How about something like this? Uses {{sfn}} to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'. Opabinia regalis (talk) 06:09, 21 April 2015 (UTC)
You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful. T.Shafee(Evo﹠Evo)talk 08:06, 21 April 2015 (UTC)
I am not a big fan of {{sfn}} templates. They are more complicated and harder to maintain. Plus they don't directly address the problem of searching Molecular Biology of the Cell. What seems to work is to search for the chapter or subchapter titles in quotes. For example search for "DNA and Chromosomes" provides a link to the introduction of chapter 4. Then one can reference the chapter or subchapter number with {{rp}}. I am busy this week but should have more time this weekend to work on this. Boghog (talk) 12:21, 21 April 2015 (UTC)
I mis-described my own suggestion; it's actually {{efn}} (not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use {{rp}} like this, but I think the links police won't like that. Opabinia regalis (talk) 18:03, 21 April 2015 (UTC)
OK, I now see what you mean. The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
or have separate citations for each chapter where only the |chapter= and |chapterurl= parameters differ:
Boghog (talk) 18:47, 21 April 2015 (UTC)
My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a bit silly. I think I like that idea in combination with {{rp}} chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting. Opabinia regalis (talk) 20:49, 21 April 2015 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat. T.Shafee(Evo﹠Evo)talk 12:24, 22 April 2015 (UTC)

You're the one currently doing the work, so I think that means you get to decide :) Opabinia regalis (talk) 19:01, 22 April 2015 (UTC)

MBOC references[edit]

Article

Genes[1]:2 are numerous[1]:4 and useful[1]:4.1

References

  1. ^ a b c Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. 
Glossary
Ch 2: Cell Chemistry and Biosynthesis
2.1: The Chemical Components of a Cell
Ch 4: DNA and Chromosomes
4.1: The Structure and Function of DNA
4.2: Chromosomal DNA and Its Packaging in the Chromatin Fiber
Ch 6: How Cells Read the Genome: From DNA to Protein
6.1: DNA to RNA
6.2: RNA to Protein
Ch 7: Control of Gene Expression

So {{rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo)talk 01:29, 27 April 2015 (UTC)

I've finished adding MBOC references up to section 3 (gene expression). Also, whoever originally wrote the gene expression section of the article really liked semicolons! T.Shafee(Evo﹠Evo)talk 10:51, 27 April 2015 (UTC)
Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in WP:ACCESSIBILITY so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue. Opabinia regalis (talk) 07:50, 28 April 2015 (UTC)

Wikipedia talk:Articles for creation/International Society for Forensic Genetics[edit]

Dear genetics experts: Here's an old AfC submission which will soon be deleted as a stale draft. Is this a notable organization which should have an encyclopedia article?—Anne Delong (talk) 16:56, 9 April 2015 (UTC)

I took a look at Google and PubMed and I found very few secondary hits. It seems to be a legit international organization, has regular conferences, a journal, publications, and addresses problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods. I DO NOT know the influence it has in the international forensic community, or if it is indeed used to set related international standards. It may be so, but I could not tell. IF the article was to be rescued, I would delete 90% of it, as it seems mostly self-promotion of individuals working there. My gut feeling is burn it. Cheers, BatteryIncluded (talk) 20:58, 10 April 2015 (UTC)
Thanks, BatteryIncluded. I agree about the promotional aspect, and I was prepared to address that issue, but the references are not linked on line and I don't have the knowledge to judge whether they are reliable and appropriate. Since you didn't find much, I will leave the draft to be deleted unless someone else here decides to take it on.—Anne Delong (talk) 02:10, 14 April 2015 (UTC)

Genome engineering v. Genome editing? Distinction within Genetic engineering?[edit]

The pages for Genome engineering and Genome editing seem to overlap quite a bit, with no apparent rationale for the distinction, if any.

I gather that Genetic engineering is a broader topic than Genome engineering, but the distinction is not apparent (to me) in the articles. For example, the intro sentences:

  • Genetic engineering: "Genetic engineering, also called genetic modification, is the direct manipulation of an organism's genome using biotechnology."
  • Genome engineering: "Genome engineering refers to the strategies and techniques developed in recent years for the targeted, specific modification of the genetic information – or genome – of living organisms."

Perhaps add these to your list of things to look at? I don't have the expertise to do that myself. Thanks! -- Bassomatic (talk) 15:20, 10 April 2015 (UTC)

I agree with you that they look like they could be merged. I'm currently busy with the gene article but I'll have a look at it when I'm done. For the moment I've added a merger discussion section and merger tags to the articles. T.Shafee(Evo﹠Evo)talk 00:00, 15 April 2015 (UTC)

This is slightly tangential, but should there be an article on epigenetic engineering (e.g., this summary paper which discusses another paper where the authors made use of engineered transcription factors and modulate transcriptional activation/repression through histone modification) at some point, or would that topic be better suited for coverage in the genetic engineering article? Seppi333 (Insert ) 01:48, 15 May 2015 (UTC)

CDKN2A disambiguation page[edit]

I previously posted this in October 2014, but didn't receive a response. It is still an issue.

Over at Wikipedia:Disambiguation pages with links, we're having trouble disambiguating links to CDKN2A. It isn't apparent from context whether they should go to p16 or p14arf. Would it be possible for someone to go through the articles on the "What links here" page and correct the links appropriately? Otherwise, if CDKN2A should have an article of its own then some more information could be added and the {{Letter-NumberCombDisambig}} tag could be removed. Nick Number (talk) 14:28, 13 April 2015 (UTC)

GScholar produces 29,900 hits for the term CDKN2A. This gene plays a role in cancer and looks quite notable. Looking at the history, there was some information on added to the page, then reverted as spam, but it didn't look like spam to me. This single gene encodes both proteins. There is also a p19ARF homolog in mice. --Mark viking (talk) 17:35, 13 April 2015 (UTC)
@Mark viking: So you'd support restoring some of the deleted content and making it into a full article about the gene rather than a disambiguation page? Nick Number (talk) 19:48, 13 April 2015 (UTC)
I'd support this. A quick search reveals the secondary sources: a review article, a page from the NIH, and a section from the NCI. GeneCards has some good information and there are quite a few references at the WikiGenes article. --Mark viking (talk) 20:03, 13 April 2015 (UTC)
@Mark viking: Ok, I've converted it to a stub using those references. If you have a chance, please look it over. I am not a geneticist, and AP Bio was a long time ago, so I may have misstated something. Nick Number (talk) 15:45, 14 April 2015 (UTC)

Annotated image policy[edit]

If anyone has an interest in interactive annotated images, I've made a post on WP:IUP to discuss when wikilinked image annotation is appropriate. T.Shafee(Evo﹠Evo)talk 02:22, 19 April 2015 (UTC)

Chinese study using CRISPR on human embryo[edit]

Protein & Cell published a paper on CRISPR/Cas9 use for gene therapy in human embryos. An article in Nature states the paper looks "set to reignite the debate on human-embryo editing" - and the experiments are facing a backlash

Discussion on ITN: Wikipedia:In the news/Candidates § Human embryos genetically modified for the first time

-- Aronzak (talk) 23:43, 23 April 2015 (UTC)

There's also an excellent Ars Technica article on it. More generally, the genetic engineering, genome engineering, gene targeting and CRISPR pages need a bit of an update. T.Shafee(Evo﹠Evo)talk 00:21, 24 April 2015 (UTC)
SEE below for my request for a separate article on crisper-cas9.Mercurywoodrose (talk) 16:20, 15 May 2015 (UTC)

Showcase[edit]

Why is Showcase empty?
aGastya  ✉ Dicere Aliquid :) 23:13, 5 May 2015 (UTC)

Draft:CXorf67[edit]

I've copied the following post that might be of interest over from WT:BIOL. T.Shafee(Evo﹠Evo)talk 10:25, 12 May 2015 (UTC)

Please could someone with knowledge in biology/proteins look at this draft article- due to my lack of subject knowledge, I cannot determine if it's notable enough for Wikipedia or not. Joseph2302 (talk) 15:50, 11 May 2015 (UTC)

I'm not sure about the notability of this one. It's an open reading frame, which has the potential to encode a protein, but not always. They are thousands of open reading frames and most of them are not notable. Of the references currently in the draft, all are reliable but 1-5 are only databases with basic information and not enough to indicate notability. Reference 6 mentions 753 lysine ubiquitylation sites on 471 proteins and makes not specific mentions of CXorf67. Reference 7 goes into some detail but only when its liked to MBTD1 as a fusion gene. Reference 8 is about a large section of chromosome X in general and makes no specific mention of CXorf67. I don't think there is enough significant coverage of this in the literature to distinguish it from the many other open reading frames and establish notability. Sarahj2107 (talk) 13:08, 12 May 2015 (UTC)
I agree with Sarahj2107. There are thousands of ORF and if they code for something, we don't know which protein this one codes for. Although it seems good and standard cell biology research, it is very preliminary and has not reached notability for Wikipedia standards. Also, quoting databases as references is useless because it requires to know the sequence of the oligos input and of ample interpretation. Cheers, BatteryIncluded (talk) 17:22, 12 May 2015 (UTC)
Ref 5 doesn't work and the other refs to databases aren't ideal, since the database content can change and many of them are not versioned in a way that's helpful. That said, I'm inclined to accept these as they come in. I can't see any value in trying to develop a WP:ORF as notability guidelines for open reading frames. IMO if an annotated gene is verifiable it can have a wiki page. (BTW, the mention in ref 6 is in the supplement; it's just an entry in the spreadsheet.) Opabinia regalis (talk) 20:37, 12 May 2015 (UTC)
I fail to see the notability of an uncharacterized protein with unknown function. Cheers, BatteryIncluded (talk) 00:35, 13 May 2015 (UTC)

Wikipedia:Notability (breeds)[edit]

Please see Wikipedia:Notability (breeds) for a draft of a future proposal for a notability guideline on domestic animal breeds. As your wiki-project is involved in this area, I am dropping off an invite to the discussion. Please visit Wikipedia talk:Notability (breeds). Thanks! JTdaleTalk~ 16:17, 14 May 2015 (UTC)

CRISPR-Cas9[edit]

CRISPR-Cas9 is getting a lot of attention now. I think it would be beneficial if all the information on this, and the lawsuit [1] between mit and ucb, was in one place, perhaps in an article on the technique itself, and not scattered between articles. articles containing pieces of it are Jennifer Doudna, Gene drive, David Baltimore, CRISPR, and Cas9. this is a little beyond my scope, otherwise i might be bold and create it. Mercurywoodrose (talk) 16:18, 15 May 2015 (UTC)

Help with a draft article?[edit]

I've declined a draft article that was written by an IP over sourcing issues, Draft:Brain Transcriptome Database (BrainTx) Project. It's a little too good to just leave in the draftspace, so I thought I'd ask here if anyone could help find sourcing. I'd do it myself but I'm really not familiar with genetics beyond the high school level, as interesting as they are. This also needs some slight tweaking for terminology since it does read a little too technical. I was just going to move on to the next AfC draft but I'm afraid of this languishing in the AfC space (since a lot of editors tend to abandon their drafts) and then getting G13'd. It just seems a little too interesting to not try to give it a little bit of extra help. I figure if it doesn't pass then it doesn't pass, but I figured that at the very least I could make you guys aware of it since you'd obviously be more likely to know where to find sourcing for this that I wouldn't. Tokyogirl79 (。◕‿◕。) 10:18, 18 May 2015 (UTC)