Wikipedia talk:WikiProject Genetics

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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)
@Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS." I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view. I tried setting the template parameter expand=true so the box is expanded by default but that made no difference. Maybe better to change to a bulleted or indented list? Adrian J. Hunter(talkcontribs) 10:50, 30 June 2015 (UTC)
@Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in {{Hidden begin}} + {{Hidden end}}, which renders properly on phones (default expanded). T.Shafee(Evo﹠Evo)talk 12:31, 30 June 2015 (UTC)
Yep, that works – thanks! Adrian J. Hunter(talkcontribs) 13:23, 30 June 2015 (UTC)

99 Lives Cat Genome Sequencing Project, at the U. of Missouri[edit]

Homepage: http://felinegenetics.missouri.edu/99lives

Definitely notable, given this level of Google News coverage. I'm working on updating the Manx cat article with info about the loosely affiliated Manx Cat Genome Project, so maybe someone else can take on the larger organization.  — SMcCandlish ¢ ≽ʌⱷ҅ʌ≼  10:26, 3 October 2016 (UTC)

Merge discussion[edit]

Editors may perhaps be interested in Talk:Desirable genetic trait#Merge proposal. --Tryptofish (talk) 23:00, 15 October 2016 (UTC)

Now probably moot – Desirable genetic trait has (rightly, in my view) been deleted. Maproom (talk) 08:05, 16 October 2016 (UTC)
Correct. Thanks anyway. --Tryptofish (talk) 20:37, 16 October 2016 (UTC)

Czechs[edit]

Hello all--I know very little about genetics, but I do know that this Y-DNA haplogroup stuff has been contentious in various articles. With that in mind, I would like to ask some of you to look at this edit: Concus Cretus and ThecentreCZ seem to be getting into it a bit, without the mutual courtesy of talk page discussion. Thank you, Drmies (talk) 15:50, 21 October 2016 (UTC)

That is historical revisionism of Czech National Revival and triggers

as a German-Czech editor and his purposeful look on genetics studies, which is due to compromises at discussions on other articles purely false, and even is not the main indicator of main attributes of any nations.

--ThecentreCZ (talk) 16:37, 29 October 2016 (UTC)

Missing information on RNA expression pattern[edit]

On the Template:Infobox gene there is an "RNA expression pattern", which seems rather informative – see GLUT1 for an example. However, this is currently missing an link to an article on Wikipedia describing exactly what this is, and how to read it. Please, can someone more knowledgeable than me (or rather much more knowledgeable) start such an article? Tony Mach (talk) 15:56, 10 November 2016 (UTC)

Addressed over at Template_talk:Infobox_gene#Missing_information_on_RNA_expression_pattern. Best, Andrew Su (talk) 05:19, 11 November 2016 (UTC)

2016 Community Wishlist Survey Proposal to Revive Popular Pages[edit]

Magic Wand Icon 229981 Color Flipped.svg

Greetings WikiProject Genetics Members!

This is a one-time-only message to inform you about a technical proposal to revive your Popular Pages list in the 2016 Community Wishlist Survey that I think you may be interested in reviewing and perhaps even voting for:

If the above proposal gets in the Top 10 based on the votes, there is a high likelihood of this bot being restored so your project will again see monthly updates of popular pages.

Further, there are over 260 proposals in all to review and vote for, across many aspects of wikis.

Thank you for your consideration. Please note that voting for proposals continues through December 12, 2016.

Best regards, SteviethemanDelivered: 18:00, 7 December 2016 (UTC)

Mitochondrial chromosome[edit]

In the Template:Chromosomes, we can read the list of human chromosomes, with 22 autosomes, and 2 sex chromosomes + the pseudoautosomal region. Do you think we should add the mitochondrial chromosome? This might be done by adding a new line, entitled Mitochondrial chromosome, and linking to mitochondrial DNA. Manudouz (talk) 14:53, 18 December 2016 (UTC)

Please help out merging genome editing & genome engineering[edit]

At Talk:Genome engineering#Merge discussion it was decided that genome editing & genome engineering should be merged. However in November User:Evolution and evolvability asked for a qualified academic to help out with the merge. Maybe someone in here can lend a hand? Please just go ahead and properly merge both articles so that no content is lost.

I guess as there's also a genetic engineering article the most appropriate target to merge to would be genome engineering? What do you think would be the more accurate or popular term?

--Fixuture (talk) 16:44, 27 December 2016 (UTC)

To clarify, I think that genome editing & genome engineering can safely be merged, however genetic engineering is quite a different topic. The genome edit/eng pages both pertain to insertion and removal of multiple genes in a genome, usually in a targeted manner (a process that has been traditionally relatively difficult). Genetic engineering is a much broader term that includes simpler techniques such as addition of plasmids to bacteria, and is often used to indicate the addition of a single gene to a genome. T.Shafee(Evo&Evo)talk 00:38, 28 December 2016 (UTC)
@Evolution and evolvability: Thanks for the explanation. I know it's different topic - or from what I understood at least a superordinate one. What I meant to say is that by that naming convention the target of the page should be genome engineering. But I don't know what the best target for the merge would be. e.g. while I think "editing" is a term more often used in common language and better understood it doesn't really fit it as it's not the usual type of editing as one knows from IT and it doesn't really encompass additions, removals as well as the term "engineering". --Fixuture (talk) 18:06, 29 December 2016 (UTC)
Ah, now I'm with you. "Genome engineering" is the older term, e.g. for adding and optimising whole biochemical pathways into bacteria. "Genome editing" has become popular in the last few years with the advent of comparatively easy nuclease tools (TALON, CRISPR etc). "Editing" has also been used, partly to distance the technology from the public understanding issues in which genetic engineering has become mired. I think "Genome engineering" should probably be the main page, since it's still by far the more commonly used term term. T.Shafee(Evo&Evo)talk 00:23, 30 December 2016 (UTC)

Genetics article ratings are a mess, IMHO[edit]

I'm a new user with considerable experience in genetics. I consulted the table "Genetics articles by quality and importance" on Wikipedia:WikiProject Genetics to find which articles I might help to improve. I would say, IMHO, that the ratings are fubar and should just be ignored, except for the notion I'm entertaing that there must be some way to actually fix the table. Does anybody actually know how to do that? Thanks, Drdfp (talk) 05:25, 2 January 2017 (UTC)

Assessments of of article quality and priority are performed by individual editors, often members of wikiprojects. You are welcome to improve those assessments, according to Wikipedia practice, as you see fit. A rough guide to article class is at Wikipedia:Version 1.0 Editorial Team/Assessment and of article priority is at Wikipedia:Version_1.0_Editorial_Team/Release_Version_Criteria#Priority_of_topic. In what way have you found these assessments to be a mess and fubar? --Mark viking (talk) 05:54, 2 January 2017 (UTC)
Hi Drdfp! Always good to have now biologists join the community. Keeping both the quality and importance ratings up to date is certainly important. The importance ranking of pages tends not to change much over time (although sometimes topics change importance, e.g CRISPR). However, the quality scores do need constant re-evaluation as the information in the pages evolve. Both importance and quality for every page can be updated by any editor. The lower quality levels have quite broad guidelines, whereas "Good" and "Featured" articles have to pass a peer-review process. The Molecular and Cell biology wikiproject has a good summary here. The summary table then automatically updates itself. Is it the importance or quality scores that you reckon need a review? T.Shafee(Evo&Evo)talk 08:39, 2 January 2017 (UTC)
@Mark viking:2 extreme examples of how fubar they are. There are 2044 unassessed articles listed! The central dogma article was rated start class until I changed it to A. That has been discussed on the talk page for the central dogma. Apparently somebody else needs to review my rating, but since there are over 2,000 unassessed articles, I don't think a second review is going to be forthcoming anytime soon. At least now nobody looking to help improve a start-class article will need to look at the central dogma. I'm retired and developing a wikipediaddiction, so I'm going to try to assess articles and change ratings as I get time, but currently, that list is a mess. I've changed my username from Drdfp to DennisPietras (talk) 04:37, 11 January 2017 (UTC)
@Mark viking: I just read "alleles" and moved it from start class to B, because it isn't Crappy and it isn't worthy of an A. That way, somebody who might be interested in alleles but might be intimidated by the work of editing a start class article might more readily work on it. DennisPietras (talk) 04:59, 11 January 2017 (UTC)
@Mark viking: I just read autosome and don't know what to do with it. Very little discussion on the talk page. One person asked for suggestions for what to add. That question beats the heck out of me! I would make a few tiny edits, but why bother? It is rated as start-class. It is a short article, but so what? That shouldn't mean it stays forever as start-class. Comments? And to think that there are over 2000 unassigned articles. I won't live long enough to look at them... DennisPietras (talk) 05:16, 11 January 2017 (UTC)
@DennisPietras: It's great seeing you review the ratings. Even getting through the backlog is an important task, and reassessing the existing ones is just as vital. Autosome is definitely still start-class to my eye. It could do with some history, better organisation headings, some discussion&comparison of other organisms, some evolution info. Some articles (espec low-importance ones) can sit as start or C for ages, and often that's not too much of a problem.
Just a note, I think A class was basically phased out when FA and GA were brought it, so articles can't be above B class unless they've gone though GA or FA peer review. It might be worth either reducing central dogma back to B-class, or submitting it for GA review. I've adapted MCB's rating scale to be more relevant for genetics and added it here. Hope that's helpful. Deinitely worthwhile getting through some of the backlog that's built up! The main thing is consistency across the categories. T.Shafee(Evo&Evo)talk 05:57, 11 January 2017 (UTC)
@Evolution and evolvability and Mark viking:Re:autosomes: I understand that there are things that could be added. My thought would be to show how our chromosome 2 was derived from a fusion of 2 smaller chromosomes still seen in chimps, but that could be better discussed in an evolutionary background, IMHO. We could talk about the chromatin structure of autosomes, but there aleady is a page about that.... and on and on. Autosome to me could be a nearly finished B rated low importance article with more "see also" links. Re: A class phased out: and yet, there stands a row of one A class article, the central dogma, generated by me. Oh, the power! 8-) Maybe somebody will see that and think, "hmmm, maybe with a little effort this could become a GA article", and go for it. DennisPietras (talk) 00:35, 12 January 2017 (UTC)

To do list comments[edit]

To do list

   Ensure that all of these categories are within Category:Genetics
   Confirm that the hierarchy of Category:Genetics and List of basic genetics topics are what a typical reader would expect. An example Genetics hierarchy is here.

Problems:

1. clicking "these categories" gives a 404 Not Found response

2. in "List of basic genetics topics"

"craniosynostosis" is not something typical reader would expect, IMHO
"Jurassic Park (genetics of)" doesn't exist
"List of human genetic disorders" seriously, why not just link to the online medelian inheritance in man?

instead of trying to maintain such a list independently? https://www.omim.org/

"non-directiveness" doesn't exist
"patent" If somebody wanted to create a page about biological patents, sure, but not just the generic patent page Same for "technology transfer".

DennisPietras (talk) 04:21, 11 January 2017 (UTC)

How to organize the workforce[edit]

Folks, I'd like to see genetics articles get needed attention. I am going to throw out some suggestions and see if any stick. I'm a newbie, so this may be totally inappropriate, but whatcha gonna do, fire me?

1. Delete the "To do list" section. Has anybody but me ever commented on the links? Who is it that is responsible for eliminating things like "patent" from this project? Just do it.

2. Realize that there are about 100 people who have signed up for the project. I suggest that whoever is leading this project (if anyone?) compose a "ping list" (manually, if needed) of those users and send out a message asking each member to assess 20 of the 2044 unassessed articles over the next month. Explain how to do it. Explain that they are free to assess whatever articles they wish. If all goes well, by March we'll have a much better idea of what we are dealing with.

3. if all doesn't go well and there are still 1984 unassessed articles come March, just forget about the project. Seriously.

Note: I do NOT have the people skills to be a leader. If nominated, I will not campaign. If elected, I will not serve. DennisPietras (talk) 00:59, 12 January 2017 (UTC)

I would attach little significance to who is "signed up".
When I first started to edit Wikipedia, I signed up for several projects, becasue they looked interesting, or because someone recommended them to me. I soon lost interest in most of them. I didn't unsign as I probably should have; and now I can't remember what they were. I think my behaviour is quite typical: I suspect most signed-up members of most projects have contributed nothing for years. Maproom (talk) 22:28, 12 January 2017 (UTC)
The todo list should ideally contain a general list of useful tasks that can be done by new members, but I agree, it's a neglected currently. WP:MCB has a more general 'Goals' section that performs a similar function. A slightly better metric of who is active in the WP:GEN community is this automated list. I agree that updating the rankings is highly useful, so happy to do my part to work though the backlog (although wikiprojects perform useful functions in addition to page rating). Most (all?) WikiProjects are non-hierarchical - they act like communal meeting places for editors with a particular interest to coordinate and update each other. T.Shafee(Evo&Evo)talk 02:01, 13 January 2017 (UTC)
Heh, this is a big of a chicken-and-egg problem because of people like me who notice that the assessments are often dated and crappy, and therefore never bother to update assessments... ;) Good to see someone is interested in tackling the problem. If some of the articles have assessments from other projects that could be reasonably inherited, I believe there's a bot that will do that. I'll try to be less bad at this! Opabinia regalis (talk) 07:56, 13 January 2017 (UTC)
To help in the effort, I've also added the tracking log of all assessment changes to the WP:GEN statistics page! Should be nice to see what's getting reclassified. T.Shafee(Evo&Evo)talk 10:21, 13 January 2017 (UTC)

Gene of uncertain significance[edit]

This new article needs some help, the principal author, Dpaulbick, is new to WP. Roger (Dodger67) (talk) 17:45, 12 January 2017 (UTC)

That article reads like a rambling incoherent essay, sometimes with little relationship to its lead. Its point seems to be that there are genes that we don't know what they do. Maproom (talk) 18:13, 12 January 2017 (UTC)
The subject of this article I think is more subtle. We know what many of these genes do, but we don't know the impact of mutations in these genes have on patients. This is more of a medical than scientific article. This should be explained better in the lead. Without further clarification, the article is very confusing. Boghog (talk) 19:54, 12 January 2017 (UTC)
The main source in this article is PMID 25741868. In closer reading of the source, it appears what is really meant by gene of uncertain significance (GUS) is gene variant of uncertain significance (GVUS). Boghog (talk) 20:02, 12 January 2017 (UTC)
Aren't gene variants normally known as "alleles"? Maproom (talk) 22:03, 12 January 2017 (UTC)
Yes, but variant indicates an allele different from the reference genome, as in a VCF file. In clinical sequencing, we talk of variants and variants of unknown significance (VUS). Genes of unknown significance aren't really talked about, because depending on position, variants within a gene can have different effects on the phenotype. It is the variant that is medically significant and gene-level annotations, while useful, are not determinative. --Mark viking (talk) 22:23, 12 January 2017 (UTC)
Thanks for the link to Variants of unknown significance. Perhaps Gene of uncertain significance should be merged into it. Boghog (talk) 06:41, 13 January 2017 (UTC)
@Maproom: I noticed that you took care of the winkler index issue at the helpdesk. VUS is the way I knew this concept, and I believe that is true for the vast majority of people who know about it. Why not just change the name of Gene of uncertain significance to "Variant of uncertain significance"? That way, both this article and the article Mark viking pointed us to can coexist. Since Variants of unknown significance is such a stub, let's have the longer gene article overwhelm it. BTW, to my eye the longer article isn't so bad. It needs work, but I'd be willng to help. DennisPietras (talk) 21:06, 15 January 2017 (UTC)
@DennisPietras:: I am fairly sure I understand what the Winkler index article is about, so I checked some sources and went ahead with the move. I am less confident about the Variants of unknown significance material. It doesn't need any special power to move (rename) an article, you just need to be an autoconfirmed editor. If you feel confident that the move is justified, you can do it yourself: go to the cryptically named "More" menu at the top of the article, select its only item "Move", type in the new name, amd give your reason. Maproom (talk) 21:28, 15 January 2017 (UTC)

────────────────────────────────────────────────────────────────────────────────────────────────────done DennisPietras (talk) 04:14, 16 January 2017 (UTC)

@Maproom, Boghog, Mark viking, and Aspro: I found a YouTube video made by a genetic counselor about VUS. She is speaking without a script, trying to educate people about VUS. To me, she made at least one mistake, but so be it. This topic is going to be a huge societal issue, and I think people need to hear it. It's here https://www.youtube.com/watch?v=cPFaAw4lSpU What I'd like to do is put some line of wikicode at the start of the article like [[Play_This_URL|as a right side thumbnail]]. Is that even possible? Would that be a violation of YouTube copyright? Do you think it is a good idea? If you think it's a good idea, possible, and not a violation, do any of you know what the real wikicode is? Thanks, DennisPietras (talk) 15:22, 17 January 2017 (UTC)
There's more than one serious mistake in that video. Wikipedia ought be be able to do better. Maproom (talk) 16:51, 17 January 2017 (UTC)
Yes, I agree that there are more mistakes, but would a poet who just got notice of a VUS notice them? The poet could benefit from actually hearing a voice repeating that it's not actionable and they need to keep in contact with their health care professional. Plus, I can't find a better shorter one! The ironic thing is that one of my former students is a genetic counselor, and she's let me down by not having such a video...8-( ..no I'm not going to contact her. — Preceding unsigned comment added by DennisPietras (talkcontribs) 18:57, 17 January 2017 (UTC)
So there's such a thing as a VUS notice? That surprises me. Any two people (who aren't identical twins) must have hundreds of gene differences with some observable phenotypic effect, and thousands without. Maybe I've misunderstood something. Maproom (talk) 09:21, 18 January 2017 (UTC)
@Maproom: Sit down for this: in your genome there are about 70 mutations that were not present in your parents' DNA! https://www.ncbi.nlm.nih.gov/pubmed/22345605 Off the top of my head, I believe I recall that each new whole genome sequence reveals something like 30 million basepair differences from the reference genome! Each of us have dozens of homozygous loss-of-function mutations! This is why it is so bloody difficult to make sense of variants that are found. If you have 25 minutes, watch, for example, https://www.youtube.com/watch?v=fC9rYghqUTo to get a feel for what medical professionals have to deal with! It may be the most amazing 25 minutes of yor life. With the cost of whole genome sequencing now at about $1,000 per individual, the flood of information is going to be overwhelming. Drinking from a full-open fire hydrant doesn't quite give an accurate feel. But the important question is whether any one of these changes has any phenotypic effect. That's why it is going to be so important to educate the public to understand that they don't need to freak out about VUS's. How did you feel when you just learned that you have dozens of homozygous LOF mutations? For me, it was comforting: I could blame my genes for all of my problems! But what about a 20 something planning on having a family? DennisPietras (talk) 13:53, 18 January 2017 (UTC)
Ok, so its millions, not thousands. I can't say I'm surprised. But that makes it even more extraordinary that there should be such a thing as a VUS notice.
@Maproom:I should have made my discussion clearer. For example, consider a woman with a first degree relative having breast cancer. The woman may decide to have her DNA sequenced to determine if she is at elevated risk for cancer from one of the know pathogenic BRCA gene mutations. She will get a lab report which will hopefully state that she does not have one of the known pathogenic mutations, and she will initially be overjoyed, but then go on to read the VUS notice (which I think/hope the lab is legaly required to provide) that she has a mutation in the gene that hasn't been linked to cancer development. The important thing is to educate the woman that she shouldn't focus on feeling "I've got a mutation in my BRCA1 gene" but to simply remember that and to keep her health care professionals aware of it and maybe keep herself up-to-date about the status of that variant, if she doesn't want to trust her health care professionals to keep track of the flood of VUS's that are a'comin'. DennisPietras (talk) 19:08, 18 January 2017 (UTC)
Indeed. If she receives such a notice, everything possible should be done to encourage her to ignore it, and to convince her that it is the outcome of misguided bureaucracy. By "everything", I include explanations in WIkipedia articles. Maproom (talk) 23:20, 18 January 2017 (UTC)

WikiBlame is great![edit]

If I am using it properly, the first 2 topics on the to do list

Ensure that all of these categories are within Category:Genetics
Confirm that the hierarchy of Category:Genetics and List of basic genetics topics are what a typical reader would expect. An example Genetics hierarchy is here.

were added in May 2008 by a user, GregManninLB, who was not signed up on the list of participants at the time and is not now, as far as I can see. I'm deleting them. DennisPietras (talk) 19:11, 17 January 2017 (UTC)

the forlorn 19[edit]

There were 19 articles listed as stub quality and NA importance. Almost all of them were redirect pages, and I decided to be bold and just remove the genetics project banner from those pages. In the "can you believe it" category, one of the pages that was redirected to was site directed mutagenesis, which didn't have a mention of CRISPR on it! So much to do, so little time. The 19 are still there as I write this, because the bot doesn't work in real time. DennisPietras (talk) 19:15, 18 January 2017 (UTC)

I also hopefully took care of the forlorn 12 rated start quality and NA importance. — Preceding unsigned comment added by DennisPietras (talkcontribs) 19:40, 18 January 2017 (UTC)
Good work. I've been working through the '???' importance rating category. T.Shafee(Evo&Evo)talk 23:33, 18 January 2017 (UTC)
@DennisPietras: I can absolutely recommend the "Rater" plugin by Kephir. Just go to your Special:MyPage/common.js and add the text importScript('User:Kephir/gadgets/rater.js'); // [[User:Kephir/gadgets/rater]]. It allows you to edit the class and importance of a page from the Article (without having to switch back and forth to the talk page), and auto-fills an edit summary describing the change so that it's easier to see when people look back through the history tab. T.Shafee(Evo&Evo)talk 11:14, 25 January 2017 (UTC)
@Evolution and evolvability: Remarkably (to me - I don't know how you folks get to know all these things) I actually did get "rater" to appear to the left of "more" on my page. I click on it, and a box opens that appears to indicate that it is a beta version, but, in any case I'm lost about how to actually use it. This may beyond my comprehension, and I'm fairly comfortable doing the ratings the slow way, because I get to see what's up on the talk page. Thanks, DennisPietras (talk) 00:44, 26 January 2017 (UTC)
@Evolution and evolvability: DUH Now I see how to use it wen I'm on the page I want to rate!
  1. REDIRECT Template:WikiThanks DennisPietras (talk) 00:48, 26 January 2017 (UTC)

────────────────────────────────────────────────────────────────────────────────────────────────────@Evolution and evolvability: Much to my delight, I find that rater gives me the option to rate pages importance=bottom. I've been using that for books, etc. However, when I go back to look at the list you generated for me, the "bottom" articles are still listed. I'm going to go ahead and keep using that bottom rating at least until the "bot" (or whatever) problem we've been talking about is fixed. But, I'm wondering if the table "Genetics articles by quality and importance" needs to be modified to have a "bottom" row? DennisPietras (talk) 19:48, 26 January 2017 (UTC)

WikiJournal of Medicine promotion[edit]

WJM Poster (hyperlinked).pdf
WikiJournal of Medicine logo.svg

The WikiJournal of Medicine is a free, peer reviewed academic journal which aims to provide a new mechanism for ensuring the accuracy of Wikipedia's biomedical content. We started it as a way of bridging the Wikipedia-academia gap.[1] It is also part of a WikiJournal User Group with other WikiJournals under development.[2] The journal is still starting out and not yet well known, so we are advertising ourselves to WikiProjects that might be interested.

Engaging Wikipedians

  • Original articles on topics that don't yet have a Wikipedia page, or only a stub/start
  • Wikipedia articles that you are willing to see through external peer review (either solo or as in a group, process analogous to GA / FA review)
  • Image articles, based around an important medical image or summary diagram

Engaging non-Wikipedians

We hope that an academic journal format may also encourage non-Wikipedians to contribute who would otherwise not. Therefore, please consider:

  • Printing off the advertisement poster and distribute in tearooms & noticeboards at your place of work
  • Emailing around the pdf through contact networks or mailing lists (suggested wording)

If you want to know more, we recently published an editorial describing how the journal developed.[3] Alternatively, check out the journal's About or Discussion pages.

  1. ^ Masukume, G; Kipersztok, L; Das, D; Shafee, T; Laurent, M; Heilman, J (November 2016). "Medical journals and Wikipedia: a global health matter". The Lancet Global Health. 4 (11): e791. doi:10.1016/S2214-109X(16)30254-6. 
  2. ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15. 
  3. ^ Shafee, T; Das, D; Masukume, G; Häggström, M. "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine. 4. doi:10.15347/wjm/2017.001. 
WikiJournal of Science logo.svg

Additionally, the WikiJournal of Science is just starting up under a similar model and looking for contributors. Firstly it is seeking editors to guide submissions through external academic peer review and format accepted articles. It is also encouraging submission of articles in the same format as Wiki.J.Med. If you're interested, please come and discuss the project on the journal's talk page, or the general discussion page for the WikiJournal User group.
T.Shafee(Evo&Evo)talk 10:33, 19 January 2017 (UTC)

Z-gene[edit]

@Akshaykatyura: Hi! I'm currently working my way from Z down to reclassify the unassigned articles. The Z-gene article https://en.wikipedia.org/wiki/Z-gene is a stub about the lac z gene, which should be converted to a redirect to the lac operon, IMHO. Any objections? DennisPietras (talk) 03:58, 23 January 2017 (UTC)

Agreed. Good catch. Ajpolino (talk) 04:59, 23 January 2017 (UTC)
A disambiguation page would be better, as "Z gene" could also refer to Protein Z or to an unrelated gene involved in avian sex determination ([1]). Adrian J. Hunter(talkcontribs) 05:40, 23 January 2017 (UTC)
Also if someone who knew anything about the lac operon were to type "Z-gene" into the search box, they'd presumably be looking for Beta-galactosidase rather than lac operon. Adrian J. Hunter(talkcontribs) 05:44, 23 January 2017 (UTC)
I boldly converted it to a disambig. Adrian J. Hunter(talkcontribs) 06:46, 23 January 2017 (UTC)
@Adrian J. Hunter:
  1. REDIRECT Template:WikiThanks DennisPietras (talk) 02:19, 24 January 2017 (UTC)

PIC and mediator[edit]

Hi! I've noticed that there are separate Transcription preinitiation complex and Mediator (coactivator) pages. I think that based on a 2015 review, http://www.nature.com/nrm/journal/v16/n3/box/nrm3951_BX3.html the pages should be merged. Comments? Thanks, DennisPietras (talk) 03:30, 25 January 2017 (UTC)

It may not need to be fully merged. We have separate pages for TFIIA etc. The mediator complex seems to be a well-defined group of proteins, but absolutely needs to be mentioned as a key component of the PIC on the Transcription preinitiation complex page. T.Shafee(Evo&Evo)talk 03:36, 25 January 2017 (UTC)
I agree with Thomas. The review article states that the mediator coactivator complex has roles in addition to being a component of the preinitiation complex. Hence I think it is better to keep the two articles separate while mentioning that mediator is a component of PIC. Boghog (talk) 04:29, 25 January 2017 (UTC)

genetics of cancer redirect to oncogenomics[edit]

@FourViolas: I've disccovered that there is a page "genetics of cancer" which is only a "start" quality article. Meanwhile, "Oncogenomics" is B quality. I propose making genetics of cancer a simple redirect to oncogenomics. Comments, especially from FourViolas, who appears to be the only one recently watching c.o.g? Thanks, DennisPietras (talk) 20:40, 30 January 2017 (UTC)

No objections on the genetics of cancer talk page for more than a week, so I made the redirect. DennisPietras (talk) 02:00, 14 February 2017 (UTC)

Expressomics redirected to Transcriptome[edit]

There is a page expressomics that was created by Jongbak in 2007. Transcriptomics is the current term, but transcriptomics is a simple redirect to transcriptome. I propose that expressomics become a simple redirect to transcriptome. Any objections? DennisPietras (talk) 21:39, 1 February 2017 (UTC)

A merge would be better as each article has unique content, and per WP:PRESERVE, we usually try to preserve verifiable content. For instance, the expressomics article has a section on assay techniques mostly missing from transcriptome--indeed the scope section in transcriptome is completely unsourced.. --Mark viking (talk) 19:48, 2 February 2017 (UTC)
Yes, of course, merge first. Remember, I'm a newbie...I wonder how much longer I'll be able to use that excuse for my brain cramps... Emojione 263A.svg DennisPietras (talk) 22:28, 2 February 2017 (UTC)

Good idea. I added this proposal to each page. Discuss Talk:Transcriptome#Merge Expressomics page into Transcriptome — Preceding unsigned comment added by MangoldOrganizer (talkcontribs) 03:11, 25 March 2017 (UTC)

Is there a way to get a list of genetics article sorted by their average page views?[edit]

Hi! I know where/how to get page view statistics for individual articles, but that would be frustrating, to say the least, for all artcles. Is there a way to produce a list of all articles in the genetics project sorted by page views, hopefully with number of page views listed next to the articles? I have a vague feeling that a SQL search could generate such a list, but my knowledge of SQL ended in the 1990's. Thanks, DennisPietras (talk) 17:30, 2 February 2017 (UTC)

There is the script at User:Dsimic/Traffic stats calculation that given a list of articles, produces page views. But I haven't tried it myself. --Mark viking (talk) 20:01, 2 February 2017 (UTC)
I just looked at that script, and it is waaaayyyy over my head. What I was really hoping for by starting this topic was to nudge Thomas into doing it for us! Emojione 263A.svg DennisPietras (talk) 22:35, 2 February 2017 (UTC)
The WP:GEN assessment page has a list of the top 500, but that's still pretty minimal dataset. What you probably want is the MASSVIEWS wikimedia foundation tool that allows you to view the stats for all articles in any category. E.g. Here is the one for everything in Category:WikiProject Genetics articles (don't forget to check the "use subject page" tickbox). You could similarly do one for just articles in specific imporance/class categories (e.g. Category:C-Class_Genetics_articles or Category:Top-importance_Genetics_articles). T.Shafee(Evo&Evo)talk 01:02, 3 February 2017 (UTC)
Wow! Right under my nose, so to speak. I'm going to have to stop using the newbie excuse soon... Thanks Thomas! DennisPietras (talk) 03:38, 3 February 2017 (UTC)
Absolutely no problem! There can be a lot to get used to on Wikipedia. I'm still learning things after years here. T.Shafee(Evo&Evo)talk 12:04, 3 February 2017 (UTC)

proposed change to "to do list"[edit]

Hi! Currently, the task is:

   Please help to assess the importance and quality of these unassessed articles

which is almost done. So, looking ahead, I suggest that the to do list read:

"There are currently 7 articles rated as stub-class and high-importance. They are, with the average daily number of page views listed after them

TATA box 355
coding strand 235
coding region 174
germline mutation 102
Pribnow box 81
gene delivery 28
Nuclear gene 18

If you are interested in editing, please help improve these pages! Even if you are new to editing, don't worry about making mistakes. People will be watching and helping as needed."

Comments? Objections? DennisPietras (talk) 15:50, 3 February 2017 (UTC)

Asp294His merge into MC1R[edit]

@Fnielsen: et al. Does anybody object to me merging Asp... into MC1R and then making Asp... into a redirect to MC1R? DennisPietras (talk) 02:31, 5 February 2017 (UTC)

Haha, definite merge. I'm not convinced that ever warranted its own article. V600E shoudl also be merged into BRAF and C957T could even be merged into DRD2. In fact, the only article on a specific gene mutation that I've ever seen done well is ΔF508, which has a lot of information that usefully expands on the Cystic fibrosis article. T.Shafee(Evo&Evo)talk 00:53, 6 February 2017 (UTC)
You can merge it, but let the Wikidata item stay. Another (half) example: Factor V Leiden is written as a genetic disorder, but has the "Infobox single nucleotide polymorphism". — fnielsen (talk) 15:04, 7 February 2017 (UTC)
@Fnielsen and Evolution and evolvability:Wow, I've opened a nice can of worms! I'm learning so many more things about MCR1 that I'm intending to make major additions to that article. So, now what I want to do specifically with Asp294His is to just move it to "MC1R Asp294His". Any objections? Thanks, DennisPietras (talk) 19:24, 7 February 2017 (UTC)
@DennisPietras: Given that it's so short, I would have through ti could just be a section of the Melanocortin_1_receptor page, perhaps in a section titled "single nucleotide polymorphisms". However if you are happy to expand it sufficiently to justify its existence, I'd go for Melanocortin_1_receptor D294H as a title, to include the protein's full name, and use the shorter notation for the mutation. However, as you've noticed, we've not really any strong precedents for these sorts of SNP articles, since there are so few, and they're a tiny fraction of the possible notable SNPs. T.Shafee(Evo&Evo)talk 03:26, 8 February 2017 (UTC)
@Evolution and evolvability:I think you misunderstood. I left the snp article untouched, and just finished a distressingly long process of beefing up the MC1R article. Off to bed. DennisPietras (talk) 06:27, 8 February 2017 (UTC)
@Fnielsen and Evolution and evolvability: I just moved it to Melanocortin 1 receptor Asp294His DennisPietras (talk) 03:39, 10 February 2017 (UTC)

With a general remark: It seems that science beginning perhaps in the 1990s had great optimism regarding individual SNPs to explain a variety of behaviour and diseases. I have not so much followed the topic for the past years but it seems to me that "SNP-blaming" is not so much in fashion anymore. Later meta-analysis studies may have squashed hopes. Perhaps it is me that is not up to date? Should articles such as Melanocortin 1 receptor Asp294His be regarded as a fad of the 00s? — fnielsen (talk) 08:49, 10 February 2017 (UTC)

@Fnielsen: A good point. There are certainly a few SNPs that have been shown to have large enough effects even on their own, so I think it is conceivable that there could be sufficiently notable SNPs to justify their own article. However I don't know enough about the topic to know if those actually match up with the handful of SNP articles that currently exist. In general I favour merging into parent gene articles since I suspect that otherwise readers don't find them anyway. T.Shafee(Evo&Evo)talk 10:47, 10 February 2017 (UTC)
@Fnielsen and Evolution and evolvability: et al. Judging from the number of GWAS studies, I don't think snips are a fad, but I do agree with Thomas that they should generally be merged into the parent gene article. DennisPietras (talk) 21:35, 10 February 2017 (UTC)

I guess this proves that I'm a masochist - in the asexual sense[edit]

So, the page https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Genetics/Assessment gives guidance about how to rate the importance of articles. I wonder if we should let the community of wikipedia readers rate the importance of articles. That is, if a page averages more than 17 page views/day it becomes rated at least high importance. I set the level at 17 so that nuclear gene would stay at high importance. Heterogeneous ribonucleoprotein particle is a stub currently rated at mid importance, but it has 43 views/day. By my suggestion, it would become high importance, even though I don't think it qualifies by the current guideline of "High school students may have some familiarity, or else early undergraduate students should be very familiar with the subject." Believe me, I realize that this reclassification would be a lot of work, but the one person who has adopted gene delivery for a school project has re-energized me for the task. Comments? DennisPietras (talk) 04:19, 10 February 2017 (UTC)

@DennisPietras: Sorry to be a dampener on this, but I think that the importance ranking and reader traffic are separate statistics. Firstly, traffic can stats fluctuate a lot over time depending on what's in the news, and I don't think it's useful for the importance rating to keep up with that. Also, importance can be different to different WikiProjects, e.g. Axolotl is high-importance to WikiProject Amphibians and Reptiles, but the genetics components of that page are only of low importance to WP:GEN. Finally, I think it's also useful to keep more-or-less in line with other WikiProjects. I don't mean to be overly-negative! I think that the current ratings guidelines are reasonably sensible, even if their implementation is still quite variable and subjective. I totally agree with your move of CRISPR to "High" though! T.Shafee(Evo&Evo)talk 11:25, 10 February 2017 (UTC)
I'm not sure Nuclear gene should be high priority. It's really just a term that needs to be defined... The relevant info mostly belongs at Gene, Mitochondria, etc. 17 views per day is tiny compared to, say, Genome or Dominance (genetics), each at ~900 views per day. I think setting a 17 view per day cutoff would lead to a huge number of high-importance articles, which would defeat the purpose of the rating. Adrian J. Hunter(talkcontribs) 12:10, 10 February 2017 (UTC)

Mediator (coactivator)[edit]

Hi again folks. I'm starting to gather up the references and courage to tackle improvements to Mediator (coactivator), which gets 63 views/day. I have 2 separate concerns.

Does anybody object to me moving the article to "Mediator complex (molecular biology)"?
The article has had very few recent edits. Boghog is by far the most recent human editor (presuming that her/his username isn't reflective of his/her species identity Emojione 263A.svg). What I would prefer to do is copy the code of the page into my sandbox, work on it there, and then transfer the whole thing back into the mediator page when I'm done. That's what I did at https://en.wikipedia.org/wiki/User:DennisPietras/sandbox3 before transfering it into the Proximity ligation assay page, and I liked that much more than tryiing to work on an article when it is "live". Is that the way major edits are usually done? I wouldn't suggest it, except that Boghog now knows my intentions and there is little other editorial interest. Should I put an "under construction" sign on mediator even though I'm working on it in my sandbox? Any suggestions? Thanks, DennisPietras (talk) 15:06, 10 February 2017 (UTC)
Since there is another article called Endogenous mediator, renaming Mediator (coactivator) as Mediator complex (molecular biology) would not be appropriate as it would be too general. Even if these two articles were merged, I still not sure the rename would be appropriate. Wikipedia generally does not disambiguate article names based on the field. For example, the disambiguations for Mercury are Mercury (element), not Mercury (chemistry) and Mercury (planet), not Mercury (astronomy). Generally there is no need to work on an article in your sandbox and in fact reasons not to, especially if the article is actively being edited by others. Also if you completely restructure an article in your sandbox and then apply those changes in one edit to the live article, others might object. It is better to make smaller edits one at a time and see how others react. While there is no requirement to do so, if you plan to completely restructure an article, it would be prudent to briefly outline the changes you plan to make on the article's talk page before your make those changes to see what others think. Boghog (talk) 19:58, 10 February 2017 (UTC)

Transcription factor and General transcription factor[edit]

Hi again folks. Transcription factor gets about 700 views/day. General tf about 100. Is there any traction out there for merging the 2 articles? I came across those 2 while updating mediator (which is far from finished), and then clearly preinitiation complex is next for me. DennisPietras (talk) 02:42, 14 February 2017 (UTC)

The term "general transcription factor" is frequently used in the literature and hence is independently notable and consequently deserves its own article. I see no advantage of merging these two articles. Boghog (talk) 06:35, 15 February 2017 (UTC)
I agree with Boghog. They're distinct enough topics that they warrant being separate. Also the Transcription factor article is already pretty long. T.Shafee(Evo&Evo)talk 23:03, 15 February 2017 (UTC)

Mediator explanatory footnotes[edit]

Hi again folks. I'd appreciate feedback on how I'm using enf's in Mediator (coactivator), particularly how I used it in enf d to direct folks to be able to see a reasonably-sized version of a copyrighted image that I can't put on the commons. Actually, I'd most appreciate some "way to go's", but if I'm violating wp community standards, it's better to know now. Thanks, DennisPietras (talk) 20:48, 14 February 2017 (UTC)

Thanks for your additions. I don't have any strong feeling about footnotes except that they make the article more complicated to read and to maintain. One thing to keep in mind is that graphics are intended to support the text, not the other way around. Also it is assumed that the figures are simplifications of reality and it is not necessary to dwell on their shortcomings. Boghog (talk) 07:15, 15 February 2017 (UTC)
Good work so far DennisPietras. My recommendations are to make sure the lead section only summarises info that's in the rest of the article. Currently the lead seems a bit long. Moving the majority of the information into its own section will also allow more space for the images. As for the footnotes, I think they end up rarely being read, since readers seldom distinguish them from references so don't think to click on most. However there's certainly no harm in them. An alternative strategy for the copyrighted image is to email the author of the paper and ask if they have another version that isn't copyrighted or is under a creative commons license. I've found that people are often very keen to contribute their images once they know what they're being used for. T.Shafee(Evo&Evo)talk 23:01, 15 February 2017 (UTC)
Thanks to both of you. Re: the lead length: it will appear short when I'm done! The reason I put several images in so far is to emphasize the flexibility in structure and associations. That can't be done with just one image, and, yes, I was reluctant to put one on the left, as it is discouarged by wp, but for the foreseeable future I think it will stay there OK. Re: footnotes and readability: I expect that the vast majority of readers won't look at the ref's or efn's, which is why I think putting material in the efn's makes the article more readable. Then, if the article tickles the reader's fancy, they can go back and look at the efn's and/or ref's. Re: image contribution: if I got permission to use more, then I'd have to find a place to put them!!!!!!! If a reader fancies, they can find the images from the info I've given them.
  1. REDIRECT Template:WikiThanks DennisPietras (talk) 01:20, 16 February 2017 (UTC)

Subunit composition section and table[edit]

Hi again. The mediator Subunit composition section begins "The Mediator complex is composed of up to at least 31 subunits in all eukaryotes studied:" which is only true because the editor included "up to" as in advertisements that state up to 75% off.Emojione 263A.svg The main question I have is this: Do we really want to list all of the subunits and include the table? My thought is to put links to subunits that have wp articles in a "see also" section and eliminate the table and "subunit composition" section entirely. I haven't checked completely (nor do I intend to) but the table was added in 2012 and I have to believe it is incomplete. Thanks for any comments. DennisPietras (talk) 21:02, 14 February 2017 (UTC)

The human subunits are already listed in the subunit composition sectdion. The table is a cross-species comparison. Boghog (talk) 07:19, 15 February 2017 (UTC)

Am I alone in my frustration?[edit]

Hi again folks. It seems like everytime I set out to update a genetics article it leads to 2 more that desperately need upgrading! It's like playing Whac-A-Mole for real! sigh. Is this a common experience? Can anybody suggest an alternative treatment to the one I use - eating party peanuts until I forget that I'm frustrated? Thanks, DennisPietras (talk) 20:19, 21 February 2017 (UTC)

yep WP is very uneven -- great in spots, terrible in spots, and mediocre in many; it is a direct result of this being a crowd-sourced beast. There is a ton of work to do, always. You just need to pace yourself and make sure the work you do is very high quality (great sources, neutrally summarized, and overall WEIGHT correct) so that what you actually spend time on sticks, and you can move on to the next problematic article. Jytdog (talk) 20:34, 21 February 2017 (UTC)
I don't think you are alone. It is natural to want to see a field one cares about having lots of solid articles chock full of relevant reliable information, and it is disappointing when most articles fall short. But WP is very much a work in progress--it is a construction site with lots of partially finished articles, some barely started. Rather than feeling frustration, though, I like to see it as a great opportunity to contribute and improve the encyclopedia. With so many articles having potential for improvement, it can be tough to choose which to work on. Jytdog's advice is good here--pick an article in which interests you the most and for which you have the knowledge and resources to add solid content. --Mark viking (talk) 21:02, 21 February 2017 (UTC)
I agree with the comments above. I suspect we've found ourselves lost down editing rabbit holes at some point! I tend to try to set specific and achievable goals (e.g. update a specific article section or make a new image), otherwise it's easy to focus on what's left to do, rather than receive the endorphins due for what you've already done. It think that that is why people often have little trophy cabinets of things they're proud of on their userpages. Every month I leave the world in a slightly better state than I found it. Then again, sometimes I actually enjoy just following a chain of wikilinks, spending 2-5 mins on each article's wording, or reference formatting (WP:WikiGnome), since it requires less brain. Another thing that I find helpful is to occasionally read news about Wiki stuff (e.g. The Signpost and the WMF blog). In part, it just takes practice to find what works best for you! T.Shafee(Evo&Evo)talk 00:56, 22 February 2017 (UTC)
  1. REDIRECT Template:WikiThanks to all! I'm feelng better today. DennisPietras (talk) 03:40, 23 February 2017 (UTC)

Opinions requested[edit]

Opinions are requested at Talk:Expanded genetic code#mouse code about whether certain content is an acceptable use of primary sources. Thanks, Adrian J. Hunter(talkcontribs) 06:10, 13 March 2017 (UTC)

revisions to pioneer factor[edit]

Hi folks! I've been working on revisions to the pioneer factor page on my sandbox, and I am done, IMHO, with the text as I envision it as of 3/14/17. Please review and/or edit User:DennisPietras/sandbox5 if you have time and let's try to reach a consensus on what the wp page should be, before transfering the sandbox to the mainspace. Thanks, DennisPietras (talk) 00:17, 15 March 2017 (UTC)

Proposal of using full size image for RNA expression pattern[edit]

Hello WikiProject Genetics! In infoboxes of gene/protein articles, there are small thumbnail images of RNA expression pattern. I proposed switching these small thumbnail to full size image, because Wikipedia/Mediawiki image system was changed. Since image data are recalled from Wikidata, I post the proposal at Wikidata page (wikidata:Property talk:P692#How about using full size image instead of small thumbnail?). I would like to get your thoughts on that. Thank you. --Was a bee (talk) 06:32, 18 March 2017 (UTC)

Extension of 'Topic Page' review articles from PLOS Computational Biology to PLOS Genetics[edit]

framelss

The journal group PLOS is extending its 'Topic Page' review format that was spearheaded by PLOS Computational Biology to also include PLOS Genetics. In this format, accepted articles are dual-published both in the journal, and as Wikipedia pages (see Wikipedia category).

Suitable topics must either currently lack a Wikipedia page, or have only stub/start class contents. If you you would like to submit such a review article, see these guidelines. If you have any recommendations for topics to be commissioned, feel free to let any of the involved editors know: T Shafee (PLOS Gen), D Mietchen (PLOS Comp Biol).
T.Shafee(Evo&Evo)talk 12:26, 25 March 2017 (UTC)

Exciting! One small bug: the guideline linked to only mentions stub class articles as being suitable. I'd be in favor of including start class articles as suitable as well. --Mark viking (talk) 12:53, 25 March 2017 (UTC)
Well spotted, I've corrected it on the PLOS wiki page. T.Shafee(Evo&Evo)talk 00:37, 26 March 2017 (UTC)
A blog post on the matter is now out. Re the stubs vs. start discussion above, this was intentional when we launched it for Comp Bio but I agree that nothing has come up since that would prevent extension to start class articles. -- Daniel Mietchen (talk) 11:27, 13 April 2017 (UTC)

Russian Domesticated Red Fox[edit]

Greetings to the Genetics project members! Kindly note my assessment in Talk:Russian Domesticated Red Fox#Popular book published in March 2017; further editing needed. I found the Russian Domesticated Red Fox page problematic (see my two edits), though I lack the scientific background to properly improve it. Is it correct that the more extensive description of the experimental project is found on the biographical page of the lead scientist, Dmitry Belyayev? Your help is most welcome, and I look forward to learning from others' further edits. -- Deborahjay (talk) 12:16, 7 May 2017 (UTC)

Popular pages report[edit]

We – Community Tech – are happy to announce that the Popular pages bot is back up-and-running (after a one year hiatus)! You're receiving this message because your WikiProject or task force is signed up to receive the popular pages report. Every month, Community Tech bot will post at Wikipedia:WikiProject Genetics/Popular pages with a list of the most-viewed pages over the previous month that are within the scope of WikiProject Genetics.

We've made some enhancements to the original report. Here's what's new:

  • The pageview data includes both desktop and mobile data.
  • The report will include a link to the pageviews tool for each article, to dig deeper into any surprises or anomalies.
  • The report will include the total pageviews for the entire project (including redirects).

We're grateful to Mr.Z-man for his original Mr.Z-bot, and we wish his bot a happy robot retirement. Just as before, we hope the popular pages reports will aid you in understanding the reach of WikiProject Genetics, and what articles may be deserving of more attention. If you have any questions or concerns please contact us at m:User talk:Community Tech bot.

Warm regards, the Community Tech Team 17:16, 17 May 2017 (UTC)

Facto Post – Issue 1 – 14 June 2017[edit]

Facto Post – Issue 1 – 14 June 2017
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Editorial

This newsletter starts with the motto "common endeavour for 21st century content". To unpack that slogan somewhat, we are particularly interested in the new, post-Wikidata collection of techniques that are flourishing under the Wikimedia collaborative umbrella. To linked data, SPARQL queries and WikiCite, add gamified participation, text mining and new holding areas, with bots, tech and humans working harmoniously.

Scientists, librarians and Wikimedians are coming together and providing a more unified view of an emerging area. Further integration of both its community and its technical aspects can be anticipated.

While Wikipedia will remain the discursive heart of Wikimedia, data-rich and semantic content will support it. We'll aim to be both broad and selective in our coverage. This publication Facto Post (the very opposite of retroactive) and call to action are brought to you monthly by ContentMine.

Links
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Facto Post – Issue 2 – 13 July 2017[edit]

Facto Post – Issue 2 – 13 July 2017
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Editorial: Core models and topics[edit]

Wikimedians interest themselves in everything under the sun — and then some. Discussion on "core topics" may, oddly, be a fringe activity, and was popular here a decade ago.

The situation on Wikidata today does resemble the halcyon days of 2006 of the English Wikipedia. The growth is there, and the reliability and stylistic issues are not yet pressing in on the project. Its Berlin conference at the end of October will have five years of achievement to celebrate. Think Wikimania Frankfurt 2005.

Progress must be made, however, on referencing "core facts". This has two parts: replacing "imported from Wikipedia" in referencing by external authorities; and picking out statements, such as dates and family relationships, that must not only be reliable but be seen to be reliable.

In addition, there are many properties on Wikidata lacking a clear data model. An emerging consensus may push to the front key sourcing and biomedical properties as requiring urgent attention. Wikidata's "manual of style" is currently distributed over thousands of discussions. To make it coalesce, work on such a core is needed.

Links[edit]


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Figures at Recombinase-mediated cassette exchange[edit]

Hello WikiProject Genetics. I am here regarding the article Recombinase-mediated cassette exchange, and I'm hoping you can resolve an issue I'm seeing. A friendly reader contacted the Volunteer Response Team the other day (OTRS ticket # 2017071510006261) and pointed out that the two figures in that article are identical and that the caption to Figure 1 doesn't seem to make sense. I took a look and, indeed, the two figures, which have different captions that refer to different things, are both copies of File:RMCE2.PNG.

Now, I looked in the history of the article, and it appears in 2013, the article had another image, the now-deleted image File:RMCE.PNG. This file was deleted on the basis that the original uploader had uploaded an "updated" image, but it appears the "updated" image might have been mistaken to be File:RMCE2.PNG, an unrelated image. Perhaps File:RMCE.PNG should be undeleted and restored as Figure 1 in the article? But why was it removed in the first place? If necessary, I can provisionally undelete the image so that it can be reviewed. Mz7 (talk) 04:11, 17 July 2017 (UTC)

Okay, I contacted the administrator who originally deleted File:RMCE.PNG, and he has now restored it, and I've restored it into the article again. Hopefully this will resolve the reader's concern. Let me know if you guys spot anything. Mz7 (talk) 07:22, 19 July 2017 (UTC)

Genetics and archaeogenetics of Central Asia[edit]

If you search for such subjects you are redirected / sent to Genetics and archaeogenetics of South Asia. Why not make a seperate article? I could start a stub article, but I worry there may be reason for the lack of such a page. — Preceding unsigned comment added by Darokrithia (talkcontribs) 19:27, 7 August 2017 (UTC)

@Darokrithia: I think the redirect is probably there just because of lack of content. It's not really my area, but my suggestion would be to replace the redirect at Genetics and archaeogenetics of Central Asia with a stub on the specific topic and see if anyone reverts it. Remember to put a "See also" section pointing to the South Asia version of the article. You might also want to check with WikiProject Human Genetic History in case they have any ideas. T.Shafee(Evo&Evo)talk 01:40, 8 August 2017 (UTC)

Facto Post – Issue 3 – 11 August 2017[edit]

Facto Post – Issue 3 – 11 August 2017
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Wikimania report[edit]

Interviewed by Facto Post at the hackathon, Lydia Pintscher of Wikidata said that the most significant recent development is that Wikidata now accounts for one third of Wikimedia edits. And the essential growth of human editing.

Internet-In-A-Box

Impressive development work on Internet-in-a-Box featured in the WikiMedFoundation annual conference on Thursday. Hardware is Raspberry Pi, running Linux and the Kiwix browser. It can operate as a wifi hotspot and support a local intranet in parts of the world lacking phone signal. The medical use case is for those delivering care, who have smartphones but have to function in clinics in just such areas with few reference resources. Wikipedia medical content can be served to their phones, and power supplied by standard lithium battery packages.

Yesterday Katherine Maher unveiled the draft Wikimedia 2030 strategy, featuring a picturesque metaphor, "roads, bridges and villages". Here "bridges" could do with illustration. Perhaps it stands for engineering round or over the obstacles to progress down the obvious highways. Internet-in-a-Box would then do fine as an example.

"Bridging the gap" explains a take on that same metaphor, with its human component. If you are at Wikimania, come talk to WikiFactMine at its stall in the Community Village, just by the 3D-printed display for Bassel Khartabil; come hear T Arrow talk at 3 pm today in Drummond West, Level 3.

Link[edit]

  • Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.
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Gene location column added to infobox gene[edit]

New column which shows gene location is added to infobox gene. Feedback welcome at Module talk:Infobox gene#Gene location column added. Thanks! --Was a bee (talk) 11:43, 18 August 2017 (UTC)

Facto Post – Issue 4 – 18 September 2017[edit]

Facto Post – Issue 4 – 18 September 2017
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Editorial: Conservation data[edit]

The IUCN Red List update of 14 September led with a threat to North American ash trees. The International Union for Conservation of Nature produces authoritative species listings that are peer-reviewed. Examples used as metonyms for loss of species and biodiversity, and discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters.

Dorstenia elata, a critically endangered South American herb, contained in Moraceae, the family of figs and mulberries

Clearly, conservation work depends on decisions about what should be done, and where. While animals, particularly mammals, are photogenic, species numbers run into millions. Plant species lie at the base of typical land-based food chains, and vegetation is key to the habitats of most animals.

ContentMine dictionaries, for example as tabulated at d:Wikidata:WikiFactMine/Dictionary list, enable detailed control of queries about endangered species, in their taxonomic context. To target conservation measures properly, species listings running into the thousands are not what is needed: range maps showing current distribution are. Between the will to act, and effective steps taken, the services of data handling are required. There is now no reason at all why Wikidata should not take up the burden.

Links[edit]

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Facto Post – Issue 5 – 17 October 2017[edit]

Facto Post – Issue 5 – 17 October 2017
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Editorial: Annotations[edit]

Annotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead?

1495 print version of the Digesta of Justinian, with the annotations of the glossator Accursius from the 13th century

ContentMine operates in the field of text and data mining (TDM), where annotation, simply put, can add value to mined text. It now sees annotation as a possible advance in semi-automation, the use of human judgement assisted by bot editing, which now plays a large part in Wikidata tools. While a human judgement call of yes/no, on the addition of a statement to Wikidata, is usually taken as decisive, it need not be. The human assent may be passed into an annotation system, and stored: this idea is standard on Wikisource, for example, where text is considered "validated" only when two different accounts have stated that the proof-reading is correct. A typical application would be to require more than one person to agree that what is said in the reference translates correctly into the formal Wikidata statement. Rejections are also potentially useful to record, for machine learning.

As a contribution to data integrity on Wikidata, annotation has much to offer. Some "hard cases" on importing data are much more difficult than average. There are for example biographical puzzles: whether person A in one context is really identical with person B, of the same name, in another context. In science, clinical medicine require special attention to sourcing (WP:MEDRS), and is challenging in terms of connecting findings with the methodology employed. Currently decisions in areas such as these, on Wikipedia and Wikidata, are often made ad hoc. In particular there may be no audit trail for those who want to check what is decided.

Annotations are subject to a World Wide Web Consortium standard, and behind the terminology constitute a simple JSON data structure. What WikiFactMine proposes to do with them is to implement the MEDRS guideline, as a formal algorithm, on bibliographical and methodological data. The structure will integrate with those inputs the human decisions on the interpretation of scientific papers that underlie claims on Wikidata. What is added to Wikidata will therefore be supported by a transparent and rigorous system that documents decisions.

An example of the possible future scope of annotation, for medical content, is in the first link below. That sort of detailed abstract of a publication can be a target for TDM, adds great value, and could be presented in machine-readable form. You are invited to discuss the detailed proposal on Wikidata, via its talk page.

Links[edit]

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Facto Post – Issue 6 – 15 November 2017[edit]

Facto Post – Issue 6 – 15 November 2017
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WikidataCon Berlin 28–9 October 2017[edit]

WikidataCon 2017 group photo

Under the heading rerum causas cognescere, the first ever Wikidata conference got under way in the Tagesspiegel building with two keynotes, One was on YAGO, about how a knowledge base conceived ten years ago if you assume automatic compilation from Wikipedia. The other was from manager Lydia Pintscher, on the "state of the data". Interesting rumours flourished: the mix'n'match tool and its 600+ datasets, mostly in digital humanities, to be taken off the hands of its author Magnus Manske by the WMF; a Wikibase incubator site is on its way. Announcements came in talks: structured data on Wikimedia Commons is scheduled to make substantive progress by 2019. The lexeme development on Wikidata is now not expected to make the Wiktionary sites redundant, but may facilitate automated compilation of dictionaries.

WD-FIST explained

And so it went, with five strands of talks and workshops, through to 11 pm on Saturday. Wikidata applies to GLAM work via metadata. It may be used in education, raises issues such as author disambiguation, and lends itself to different types of graphical display and reuse. Many millions of SPARQL queries are run on the site every day. Over the summer a large open science bibliography has come into existence there.

Wikidata's fifth birthday party on the Sunday brought matters to a close. See a dozen and more reports by other hands.

Links[edit]

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Genetic Engineering Taskforce[edit]

This is a controversial area on Wikipedia as some watching here may know. I have been editing it on and off for seven years and now that the dust has settled from the ARBCOM case I am hoping to get the content in this area organised and improved. I have just got Genetic Engineering to good article status so it is possible. I am happy to plod on by myself, but it is a big and complicated area so any help would be appreciated. There are also a lot of comments to talk pages at multiple venues so having a centralised area for these discussions could be useful. Do editors think a taskforce page would be useful. @Tryptofish, Kingofaces43, Smartse, Lfstevens, Dialectric, and Tsavage: AIRcorn (talk) 07:29, 20 November 2017 (UTC)

I think this is a good idea, and I've been intending to dome something with genome editing/genome engineering for a while. I think it would be sensible to keep the todo list well-defined and manageable so as not to lose steam. The GA blitz on the Gene article a few years back was very effective, so I could imagine a shortlist of articles being possible to overhaul (approx 1 article per 3-5 editors helping out). I can help out with images (and maybe some of the text). One additional feature that could be considered, invitation of experts on genetic engineering to help out, for example by emailing people who have authored good review articles (example), or written about GE in The Conversation (examples). It could be an ideal opportunity to attempt collaboration between experienced Wikipedians and specialist scientists. Also pinging: @Fixuture, Opabinia regalis, Boghog, Adrian J. Hunter, Jytdog, Splette, Samsara, Mark viking, Narayanese, Ettrig, Rjwilmsi, DennisPietras, Dcbennett2, and CatPath:. T.Shafee(Evo&Evo)talk 11:21, 20 November 2017 (UTC)
Good idea. Lfstevens (talk) 15:43, 20 November 2017 (UTC)
Not sure what to do here at this point other than say "hi" and maybe come back later. Samsara 18:11, 20 November 2017 (UTC)
Thanks for the ping! I think it's potentially a very good idea and I wish it well. That said, my experience has been that "just do it" tends to work better than trying to herd cats editors into anything organized. Genetics isn't my strong suit, and I'm frankly sick and tired of the whole GMO thing and eager to spend much less time on it, so I'm going to say no thank you to the invitation. But if there's a particular page where my help would be useful, please do not hesitate to ping me about it. --Tryptofish (talk) 20:17, 20 November 2017 (UTC)
I can't say I would be a lot of help as a primary contributor for the time being either as I'm on a bit of burnout in the subject too, and I usually only have heavy bursts of article editing on the rare occasions I have a good block of time to set aside (though I have a to-do list to tackle on the subject). That being said, I definitely am open to help out where I can for a review of content, etc. as an entomologist in crop protection. I keep up with crop genetics from way back in my grad school training and at scientific meetings still, so I'm happy to act as a subject-matter resource in that topic. If we get a list together of people in the task-force and what areas they would be good to ping on, I'm in for that capacity. Kingofaces43 (talk) 03:23, 21 November 2017 (UTC)

────────────────────────────────────────────────────────────────────────────────────────────────────

Here is a possibly relevant collection of pageview stats on what I think are some of the most viewed genetic engineering articles. T.Shafee(Evo&Evo)talk 11:02, 22 November 2017 (UTC)

Thank you everyone. There is enough interest here that I think it is worth starting this. Will see if and how it evolves. AIRcorn (talk) 08:59, 25 November 2017 (UTC)

Thanks for the consideration. I'm only on here rarely and randomly, lately. As for GE, it took just a refresher look at the language locked into a suite of GM articles by that ARBCOM, for me to want to have zero to do with the topic for the time being -- the consensus process seems too gameable and taxing to make contributing in any way satisfying (maybe later, whenever there are more broadly conclusive developments in the general subject area). Cheers! :) --Tsavage (talk) 13:08, 28 November 2017 (UTC)

SNPs[edit]

Hi! I found that Wikipedia has almost no articles about SNPs (Single-nucleotide polymorphism). Although there are over 140 thousands SNPs in SNPedia, I found only 22 articles in Wikipedia. I categorized them according to their positions on human chromosomes e.g. Category:SNPs on chromosome 1, Category:SNPs on chromosome 11. I think more work should be done on expanding articles about this topic. Here is a list of over 140,000 SNPs, if anyone is interested in creating new SNPs articles. I also suggest starting a special Wikiproject for SNPs expansion. --Brainist (talk) 20:39, 20 November 2017 (UTC)

Hi Brainist, I'm curious to know what others think, but I'm not sure Wikipedia is the best project for this sort of information. Most of these articles seem to be of borderline notability. Wikidata or some dedicated project would be better. There might be a few notable SNPs like rs6265, but even in that case the information would be better contextualised in the article on the parent gene. Btw not everything in dbSNP is really a SNP – eg Rs28363170 is not. Adrian J. Hunter(talkcontribs) 23:39, 20 November 2017 (UTC)
I would have to agree on this. It would be a really high bar for a SNP to be notable, but by then the underlying gene should already be known. An article on a SNP would definitely be an exception rather than an expectation. Kingofaces43 (talk) 03:27, 21 November 2017 (UTC)
Wikidata could be a perfect unifying database for this sort of thing (Andrew Su may have some ideas via their experience with gene wiki). There are very few SNPs that have sufficient info to make an article about. I think that the majority would be better merged into the article on their parent gene. Although there will certainly be a few that are sufficiently notable in their own right (e.g. perhaps the SNP that causes sickle cell anaemia β-globin E7V), but I think they should only get split into their own page if the parent article gets too overwhelmed by content. T.Shafee(Evo&Evo)talk 09:07, 21 November 2017 (UTC)
I agree. If anyone is interested in the wikidata angle, I suggest posting here. Best, Andrew Su (talk) 16:27, 21 November 2017 (UTC)
Chiming in from WikiProject Computational Biology, I agree with the others here: Wikidata would be a better solution for as the majority of SNPs won't be generally notable. I'd definitely be interested in helping out if there's a consensus to migrate info from SNPedia to Wikidata. Thanks, Amkilpatrick (talk) 09:22, 22 November 2017 (UTC)
This isn't a terribly active WikiProject, Amkilpatrick. What you see right here is about as much of a consensus as you're ever likely to get. Adrian J. Hunter(talkcontribs) 23:30, 22 November 2017 (UTC)

Disambiguation links on pages tagged by this wikiproject[edit]

Wikipedia has many thousands of wikilinks which point to disambiguation pages. It would be useful to readers if these links directed them to the specific pages of interest, rather than making them search through a list. Members of WikiProject Disambiguation have been working on this and the total number is now below 20,000 for the first time. Some of these links require specialist knowledge of the topics concerned and therefore it would be great if you could help in your area of expertise.

A list of the relevant links on pages which fall within the remit of this wikiproject can be found at http://69.142.160.183/~dispenser/cgi-bin/topic_points.py?banner=WikiProject_Genetics

Please take a few minutes to help make these more useful to our readers.— Rod talk 15:47, 3 December 2017 (UTC)

All Fixed! The one remaining dablink is intentional. Thanks Rodw! Adrian J. Hunter(talkcontribs) 01:42, 4 December 2017 (UTC)
Thanks.— Rod talk 08:01, 4 December 2017 (UTC)

WikiCV for contributors[edit]

Hi all, I'm a 4th year Computer Science undergraduate student based out of India. I've been selected as an intern for Wikimedia under Round-15 of Outreachy. I'll be building a web tool called WikiCV (under the mentorship of Gergő Tisza and Stephen LaPorte), somewhat similar to your LinkedIn, StackOverflow or Github profile. Before starting with the project, I wanted inputs from users who are my target audience, that is you all! So thought of asking it over the talk page. (My mentors pointed me to this page as here many ardent users are present.)
We came up with this project because we feel that Wikipedia needs a powerful force to draw new editors to the project and allow existing editors to spend more time on it without harming their career; unfortunately, due to the highly collaborative nature of Wikipedia, the value of one's participation is hard to measure for an outsider, which makes it very hard for contributors to take credit for value added to Wikipedia.
Hence, we want to create a contribution summarizing tool which (unlike the existing ones that focus on statistics and are hard to interpret for someone not familiar with Wikipedia editing) highlights contributions in an easy-to-understand manner.

I want your inputs on:
1. What all things would you like to see in your CV for Wikipedia contributions?
2. In what way should we present the data/ contribution summary so that it is understandable by a non-Wikipedia user?
3. What are the benefits/problems of the current tools that summarize the contribution of a user (like Xtools)?
4. The CV will definitely reflect your contribution, but would it be better if it shows your current standing with respect to other users? For example, reputation points in Stack Overflow reflect how good you are relatively. One idea that I thought was - Imagine a tool that tells someone is in the top 1% of editors. Would it be nice? If yes, what would you consider a good basis for that statement?

Also, I prepared a mockup for the CV to give a rough idea as to what we are thinking of. Please check it out as well.
Apart from this, I thought of presenting the contributions in a manner similar to Github. I've prepared a tool for that. Kindly have a look at that as well and give your reviews about it.

My work is largely dependent on your inputs, so please pour in your comments/views. Your help will be quite appreciated!
Anyone can reach out to me through mail(meghasharma4910@gmail.com) as well.
Eagerly waiting for your inputs :)

Meghasharma213 (talk) 15:56, 11 December 2017 (UTC)

@Meghasharma213: This is a great idea. I'm a strong proponent of the idea of being able to raise the profile of Wikipedia as professional service to the community, and this sort of formal recognition framework is extremely useful.[1][2][3][4][5] I've a few thoughts that might help:
  1. Integrate and as much as possible with WikiData and draw ideas from existing tools
    • Scholia - WikiData driven author analytics
    • XTools and dewkin - Overall summary of edits from a very Wikipedian point of view
    • AltMetric reports - An exiting measure of impact outside of narrow academic literature
    • ORCID - Probably the best open standard for unique author IDs, (speak to Andy Mabbett)
    • Whocolour - A great way of indicating an editors contributions to a key article
  2. Different Wikipedians contribute in different ways, consider multiple summary statistics, e.g.:
    • Top 10 articles that the author has contributed to (for authors who contribute to big articles, but are never the dominant editor)
    • Total number of articles where >50% of text is by the contributor (for authors that are the main contributors to a small number of articles)
    • Total number of bytes / words / edits / different articles (for authors who contribute a little bit to a wide array of articles)
    • Number of Good Articles and Featured articles
    • Number of images, or a set of pinned images
  3. Not all edits are equal, different edits can signify very different habits
    • Wordcloud or keywords of topics mentioned in abstracts of the top 20 articles they've edited?
    • Main WikiProjects contributed to (main articles, article talk pages, WikiProject talk pages)
    • Average bytes per edit? (put in percentile context)
    • Average number of images per word? (put in percentile context)
  4. Some final thoughts:
    • Some of these are computationally expensive (e.g. this tool takes ages) so consider ways of making it only need to update a cached version since the last time it was looked at.
    • Avoid semi-3D bar graphs (flat is always better)
    • Avoid stacked bar charts (overlayed line charts are usually better)[6]
    • Make summary data downloadable
    • Make clear when the page's data was last updated
    • Allow users to choose which bits of data are shown
    • For pinned articles, indicate percentage contribution by bytes
    • For pinned articles, perhaps even implement something like WhoColor
    • An area to list all other online presences (again Wikidata integrated) e.g. LinkedIn, ResearchGate, G-scholar, Mendelay, Academia.com, Faculty page, Homepage, Userpage, etc
Best of luck. I hope any of that is helpful, and I look forward to following the project as it develops! T.Shafee(Evo&Evo)talk 09:38, 12 December 2017 (UTC)

References

  1. ^ Allen, Liz; Scott, Jo; Brand, Amy; Hlava, Marjorie; Altman, Micah (2014-04-17). "Publishing: Credit where credit is due". Nature. 508 (7496): 312–313. doi:10.1038/508312a. 
  2. ^ Narayan, Sneha; Orlowitz, Jake; Morgan, Jonathan T.; Shaw, Aaron (2015). "Effects of a Wikipedia Orientation Game on New User Edits". Proceedings of the 18th ACM Conference Companion on Computer Supported Cooperative Work & Social Computing. CSCW'15 Companion. New York, NY, USA: ACM: 263–266. doi:10.1145/2685553.2699022. ISBN 9781450329460. 
  3. ^ Sugimoto, Cassidy R.; Work, Sam; Larivière, Vincent; Haustein, Stefanie (2017-09-01). "Scholarly use of social media and altmetrics: A review of the literature". Journal of the Association for Information Science and Technology. 68 (9): 2037–2062. doi:10.1002/asi.23833. ISSN 2330-1643. 
  4. ^ Arazy, Ofer; Stroulia, Eleni; Ruecker, Stan; Arias, Cristina; Fiorentino, Carlos; Ganev, Veselin; Yau, Timothy (2010-06-01). "Recognizing contributions in wikis: Authorship categories, algorithms, and visualizations". Journal of the American Society for Information Science and Technology. 61 (6): 1166–1179. doi:10.1002/asi.21326. ISSN 1532-2890. 
  5. ^ Shafee, Thomas; Mietchen, Daniel; Su, Andrew I. (2017-08-11). "Academics can help shape Wikipedia". Science. 357 (6351): 557–558. doi:10.1126/science.aao0462. ISSN 0036-8075. PMID 28798122. 
  6. ^ Rougier, Nicolas P.; Droettboom, Michael; Bourne, Philip E. (2014-09-11). "Ten Simple Rules for Better Figures". PLOS Computational Biology. 10 (9): e1003833. doi:10.1371/journal.pcbi.1003833. ISSN 1553-7358. 


Thanks a lot T.Shafee(Evo&Evo) for your comments. Quite insightful, I must say! Will keep you updated about the project. Meghasharma213 (talk) 14:32, 13 December 2017 (UTC)

@Meghasharma213: Thanks, I'm particularly interested, because I think that it could be applied to the authors of WikiJournal (e.g. in Wiki.J.Med.). T.Shafee(Evo&Evo)talk 22:36, 14 December 2017 (UTC)

Facto Post – Issue 7 – 15 December 2017[edit]

Facto Post – Issue 7 – 15 December 2017
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A new bibliographical landscape[edit]

At the beginning of December, Wikidata items on individual scientific articles passed the 10 million mark. This figure contrasts with the state of play in early summer, when there were around half a million. In the big picture, Wikidata is now documenting the scientific literature at a rate that is about eight times as fast as papers are published. As 2017 ends, progress is quite evident.

Behind this achievement are a technical advance (fatameh), and bots that do the lifting. Much more than dry migration of metadata is potentially involved, however. If paper A cites paper B, both papers having an item, a link can be created on Wikidata, and the information presented to both human readers, and machines. This cross-linking is one of the most significant aspects of the scientific literature, and now a long-sought open version is rapidly being built up.

WikiCite wordmark.svg

The effort for the lifting of copyright restrictions on citation data of this kind has had real momentum behind it during 2017. WikiCite and the I4OC have been pushing hard, with the result that on CrossRef over 50% of the citation data is open. Now the holdout publishers are being lobbied to release rights on citations.

But all that is just the beginning. Topics of papers are identified, authors disambiguated, with significant progress on the use of the four million ORCID IDs for researchers, and proposals formulated to identify methodology in a machine-readable way. P4510 on Wikidata has been introduced so that methodology can sit comfortably on items about papers.

More is on the way. OABot applies the unpaywall principle to Wikipedia referencing. It has been proposed that Wikidata could assist WorldCat in compiling the global history of book translation. Watch this space.

And make promoting #1lib1ref one of your New Year's resolutions. Happy holidays, all!

November 2017 map of geolocated Wikidata items, made by Addshore

Links[edit]


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MediaWiki message delivery (talk) 14:54, 15 December 2017 (UTC)

Human Disease Modifier Gene[edit]

Could someone have a look at Draft:Human Disease Modifier Gene and see if its sourcing is reliable enough for it to be moved to mainspace? Many thanks! – Uanfala (talk) 17:16, 7 January 2018 (UTC)

That draft requires more time than I am willing to donate, but I think the subject is notorious for WP. In particular, the lede section has to be remade and soften the scientific terms to reach high-school-level readers. BatteryIncluded (talk) 18:00, 7 January 2018 (UTC)
I made an attempt to make the lead more accessible. It needs more work, but it may be adequate to move to main space. Boghog (talk) 07:45, 8 January 2018 (UTC)
Good! I'm moving to mainspace then. Thank you for improving it! – Uanfala (talk) 19:58, 9 January 2018 (UTC)

Facto Post – Issue 8 – 15 January 2018[edit]

Facto Post – Issue 8 – 15 January 2018
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Metadata on the March[edit]

From the days of hard-copy liner notes on music albums, metadata have stood outside a piece or file, while adding to understanding of where it comes from, and some of what needs to be appreciated about its content. In the GLAM sector, the accumulation of accurate metadata for objects is key to the mission of an institution, and its presentation in cataloguing.

Today Wikipedia turns 17, with worlds still to conquer. Zooming out from the individual GLAM object to the ontology in which it is set, one such world becomes apparent: GLAMs use custom ontologies, and those introduce massive incompatibilities. From a recent article by sadads, we quote the observation that "vocabularies needed for many collections, topics and intellectual spaces defy the expectations of the larger professional communities." A job for the encyclopedist, certainly. But the data-minded Wikimedian has the advantages of Wikidata, starting with its multilingual data, and facility with aliases. The controlled vocabulary — sometimes referred to as a "thesaurus" as term of art — simplifies search: if a "spade" must be called that, rather than "shovel", it is easier to find all spade references. That control comes at a cost.

SVG pedestrian crosses road
Zebra crossing/crosswalk, Singapore

Case studies in that article show what can lie ahead. The schema crosswalk, in jargon, is a potential answer to the GLAM Babel of proliferating and expanding vocabularies. Even if you have no interest in Wikidata as such, simply vocabularies V and W, if both V and W are matched to Wikidata, then a "crosswalk" arises from term v in V to w in W, whenever v and w both match to the same item d in Wikidata.

For metadata mobility, match to Wikidata. It's apparently that simple: infrastructure requirements have turned out, so far, to be challenges that can be met.

Links[edit]


To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see below.
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MediaWiki message delivery (talk) 12:38, 15 January 2018 (UTC)

Maternal effect and Telegony (pregnancy)[edit]

There appears to be a close relationship between these two articles which probably requires a summary section and wikilinks at both ends. The maternal effect is complex and debatable, and telegony antique, so the situation demands some expertise. I'd be glad of any assistance. Chiswick Chap (talk) 10:19, 22 January 2018 (UTC)

Chiswick Chap: as I understand things, the effects are quite different. The first is supported by evidence, the second is not. Maproom (talk) 14:21, 5 February 2018 (UTC)

Links to DAB pages[edit]

There may be a hundred or so genetics-related articles which contain bad links to DAB pages. User:DPL bot logs them; I can find them; you need do no searching; I think I know enough about genetics to know when not to guess; any help would be appreciated (most of all, by our readers).

In this list, search for "disam" in the text as displayed. If you solve a problem, remove {{dn}} from the article and add {{done}} here. It's possible that some of them may need appropriate redlinking (we all know that there are gaps in Wiki).

That's just an initial batch. Thanks in advance for any help. Narky Blert (talk) 22:49, 24 January 2018 (UTC)

Not sure what to choose for The Monarch Initiative; it seems that all of the mechanisms of 'genetic variant' would apply. Leschnei (talk) 14:43, 3 February 2018 (UTC)

Facto Post – Issue 9 – 5 February 2018[edit]

Facto Post – Issue 9 – 5 February 2018
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m:Grants:Project/ScienceSource is the new ContentMine proposal: please take a look.

Wikidata as Hub[edit]

One way of looking at Wikidata relates it to the semantic web concept, around for about as long as Wikipedia, and realised in dozens of distributed Web institutions. It sees Wikidata as supplying central, encyclopedic coverage of linked structured data, and looks ahead to greater support for "federated queries" that draw together information from all parts of the emerging network of websites.

Mandel zoom 07 satellite.jpg

Another perspective might be likened to a photographic negative of that one: Wikidata as an already-functioning Web hub. Over half of its properties are identifiers on other websites. These are Wikidata's "external links", to use Wikipedia terminology: one type for the DOI of a publication, another for the VIAF page of an author, with thousands more such. Wikidata links out to sites that are not nominally part of the semantic web, effectively drawing them into a larger system. The crosswalk possibilities of the systematic construction of these links was covered in Issue 8.

Wikipedia:External links speaks of them as kept "minimal, meritable, and directly relevant to the article." Here Wikidata finds more of a function. On viaf.org one can type a VIAF author identifier into the search box, and find the author page. The Wikidata Resolver tool, these days including Open Street Map, Scholia etc., allows this kind of lookup. The hub tool by maxlath takes a major step further, allowing both lookup and crosswalk to be encoded in a single URL.

Links[edit]


To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see below.
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Reminder: WikiFactMine pages on Wikidata are at WD:WFM.

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MediaWiki message delivery (talk) 11:50, 5 February 2018 (UTC)