Wikipedia talk:WikiProject Molecular Biology/Genetics/Archive 3

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)

@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 ([2]). Adrian J. Hunter^{(talk•contribs)} 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^{(talk•contribs}

) 05:44, 23 January 2017 (UTC)

I boldly converted it to a disambig. Adrian J. Hunter^{(talk•contribs)} 06:46, 23 January 2017 (UTC)

@Adrian J. Hunter: Thank you DennisPietras (talk) 02:19, 24 January 2017 (UTC)

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)

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 (talk • contribs) 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! Thank you 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)

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! 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)

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)

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

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^{(talk•contribs}

) 12:10, 10 February 2017 (UTC)

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 ). 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

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)

@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.

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)

@

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

@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)

@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)

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. 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)

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)

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. Thank you DennisPietras (talk) 01:20, 16 February 2017 (UTC)

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 (

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)

Thank you to all! I'm feelng better today. DennisPietras (talk) 03:40, 23 February 2017 (UTC)

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^{(talk•contribs)} 06:10, 13 March 2017 (UTC)

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)

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)

There is a page

A merge would be better as each article has unique content, and per

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... 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 (talk • contribs) 03:11, 25 March 2017 (UTC)

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)

Greetings to the Genetics project members! Kindly note my assessment in

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 Molecular Biology/Genetics/Archive 3/Popular pages with a list of the most-viewed pages over the previous month that are within the scope of WikiProject Molecular Biology.

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 Molecular Biology, 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)

Hello WikiProject Genetics. I am here regarding the article

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)

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 (talk • contribs) 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)

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)

Hi! I found that Wikipedia has almost no articles about

Hi

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^{(talk•contribs}

) 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.

talk

) 03:27, 21 November 2017 (UTC)

Wikidata could be a perfect unifying database for this sort of thing (

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^{(talk•contribs)} 23:30, 22 November 2017 (UTC)

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

I think this is a good idea, and I've been intending to dome something with

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.

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)

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^{(talk•contribs)} 01:42, 4 December 2017 (UTC)

Thanks.— Rod ^talk 08:01, 4 December 2017 (UTC)

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([email protected]) 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)

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)

Human Disease Modifier Gene

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.

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)

Links to DAB pages

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).

• BC200 lncRNA  Done
• Alternative splicing  Done by a previous editor
• The Monarch Initiative
• DNA (cytosine-5)-methyltransferase 3A  Done by a previous editor
• SH3KBP1  Done
• Razi Vaccine and Serum Research Institute  Done
• IgSF CAM  Done

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)

Telegony (pregnancy)

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)

Facto Post – Issue 10 – 12 March 2018

Facto Post – Issue 10 – 12 March 2018 Milestone for mix'n'match Around the time in February when Wikidata clicked past item Q50000000, another milestone was reached: the mix'n'match tool uploaded its 1000th dataset. Concisely defined by its author, Magnus Manske, it works "to match entries in external catalogs to Wikidata". The total number of entries is now well into eight figures, and more are constantly being added: a couple of new catalogs each day is normal. Since the end of 2013, mix'n'match has gradually come to play a significant part in adding statements to Wikidata. Particularly in areas with the flavour of digital humanities, but datasets can of course be about practically anything. There is a catalog on skyscrapers, and two on spiders. These days mix'n'match can be used in numerous modes, from the relaxed gamified click through a catalog looking for matches, with prompts, to the fantastically useful and often demanding search across all catalogs. I'll type that again: you can search 1000+ datasets from the simple box at the top right. The drop-down menu top left offers "creation candidates", Magnus's personal favourite. m:Mix'n'match/Manual for more. For the Wikidatan, a key point is that these matches, however carried out, add statements to Wikidata if, and naturally only if, there is a Wikidata property associated with the catalog. For everyone, however, the hands-on experience of deciding of what is a good match is an education, in a scholarly area, biographical catalogs being particularly fraught. Underpinning recent rapid progress is an open infrastructure for scraping and uploading. Congratulations to Magnus, our data Stakhanovite ! Links Wikipedia goes 3D allowing users to upload .STLs for digital reference, Beau Jackson for 3dprintingindustry.com, February 22 2018 WikiCite report (video) Formal publication and announcement of ISBN citation dataset, see Twitter post, February 23 2018 Plotting the Course Through Charted Waters, workshop on data visualization literacy from Mikhail Popov, Wikimedia Foundation Using Wikidata to build an authority list of Holocaust-era ghettos, Nancy Cooey, United States Holocaust Memorial Museum, February 12 2018 Why Should You Learn SPARQL? Wikidata! Mark Longair, blogpost November 29 2017 Back to the future: Does graph database success hang on query language?, George Anadiotis for Big on Data, March 5 2018 To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see below. Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 12:26, 12 March 2018 (UTC)

Behavioural genetics

Behavioural genetics, an article that you or your project may be interested in, has been nominated for a community good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. AIRcorn (talk) 09:48, 20 March 2018 (UTC)

Merger proposal related to

Lábrea fever and Hepatitis D

A discussion is taking place that may be of interest to some members of this project at Talk:Hepatitis_D#Merger_proposal. — soupvector (talk) 13:42, 2 April 2018 (UTC)

Clear Labs

I work at a genomics company called Clear Labs. I have disclosed my conflict of interest on the Talk page of the Clear Labs article and offered a proposed replacement of the article that is much shorter, less promotional, less out-of-date, better-sourced, etc. here. It’s been a couple weeks with no response on the article’s Talk page, so I wanted to see if anyone here had a minute to review my proposed draft and let me know if I was doing anything inappropriate COI-wise. Mark Bajus at Clear Labs (talk) 22:33, 5 April 2018 (UTC)

 Done Natureium (talk) 17:27, 6 April 2018 (UTC)

Draft:Gene Amplification in Paramecium tetraurelia

Any interest in rescuing this abandoned draft? Espresso Addict (talk) 01:25, 9 April 2018 (UTC)

Cleaned it up and moved to main space. As always, could use some more editing. Boghog (talk) 04:35, 9 April 2018 (UTC)

Thank you! Always good to see content assimilated. Espresso Addict (talk) 05:22, 9 April 2018 (UTC)

Well done. I'll also contact a few academics to see if I can convince any to write an article on Paramecium tetraurelia. T.Shafee(Evo&Evo)^talk 07:02, 9 April 2018 (UTC)

Facto Post – Issue 11 – 9 April 2018

Facto Post – Issue 11 – 9 April 2018 The 100 Skins of the Onion Open Citations Month, with its eminently guessable hashtag, is upon us. We should be utterly grateful that in the past 12 months, so much data on which papers cite which other papers has been made open, and that Wikidata is playing its part in hosting it as "cites" statements. At the time of writing, there are 15.3M Wikidata items that can do that. Pulling back to look at open access papers in the large, though, there is is less reason for celebration. Access in theory does not yet equate to practical access. A recent LSE IMPACT blogpost puts that issue down to "heterogeneity". A useful euphemism to save us from thinking that the whole concept doesn't fall into the realm of the oxymoron. Some home truths: aggregation is not content management, if it falls short on reusability. The PDF file format is wedded to how humans read documents, not how machines ingest them. The salami-slicer is our friend in the current downloading of open access papers, but for a better metaphor, think about skinning an onion, laboriously, 100 times with diminishing returns. There are of the order of 100 major publisher sites hosting open access papers, and the predominant offer there is still a PDF. From the discoverability angle, Wikidata's bibliographic resources combined with the text and data mining purposes they highlight. The long tail, or in other words the onion heart when it has become fiddly beyond patience to skin, does call for a pis aller . But the real knack is to do more between the XML and the heart. Links Crossref as a new source of citation data: A comparison with Web of Science and Scopus, CWTS blogpost 17 January 2018, Nees Jan van Eck, Ludo Waltman, Vincent Larivière, Cassidy Sugimoto Citations with identifiers in Wikipedia, figshare dataset Making women more visible online—with Wikidata tools!, Wikimedia blogpost 29 March 2018 by Sandra Fauconnier Village pump discussion, Turn on mapframe? We’re ready if you are reaches conclusions The Power of the Wikimedia Movement beyond Wikimedia, Forbes 28 March 2018, Michael Bernick Tracing stolen bitcoin, blogpost 26 March 2018 by Ross J. Anderson To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see below. Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 16:25, 9 April 2018 (UTC)

Automatic archiving of this page again?

Hi folks, it seems like this page used to be automatically archived by lowercase sigmabot III, but that stopped about a year and a half ago when we switched to the sleeker talk page heading at the top. I don't quite understand how the new talk navbox works, but is there a way to set up automatic talk page archiving again (alternatively, is that something folks want?)? Thanks Ajpolino (talk) 18:07, 9 April 2018 (UTC)

I think that the new header should be compatible with lowercase sigmabot III (since the bot creates the archive subpages, and the header just needs to link to the created subpages). I've therefore re-added the {{User:MiszaBot/config}} configuration template. T.Shafee(Evo&Evo)^talk 23:39, 9 April 2018 (UTC)

Proposal: Merge 'Exome' and 'Coding Region' Harveyjamesm (talk) 21:51, 10 May 2018 (UTC)

Exome and Coding region are nearly synonymous. You could argue "coding region" might refer specifically to a single gene whereas "exome" is global, but wouldn't it be more logical to put them both together? I'd personally argue Exome is a more up to date descriptor, plus the exome consists of many coding regions, and is in fact the coding region of the entire genome.Harveyjamesm (talk) 21:51, 10 May 2018 (UTC)

Thanks for the suggestion, but they are not the same concept. An exome is the total set of exons in an organism. An exon is a coding region plus any flanking UTRs. Hence coding regions form an important part of the exome, but are not synonymous with it. --Mark viking (talk) 22:30, 10 May 2018 (UTC)

thanks for clarifying that Harveyjamesm (talk) 08:34, 11 May 2018 (UTC)

I think that the topics are sufficiently different to have separate pages. Protein coding region is most commonly used to refer to regions of individual genes rather than those regions across the whole genome. T.Shafee(Evo&Evo)^talk 10:04, 11 May 2018 (UTC)

Facto Post – Issue 12 – 28 May 2018

Facto Post – Issue 12 – 28 May 2018 ScienceSource funded The Wikimedia Foundation announced full funding of the ScienceSource grant proposal from ContentMine on May 18. See the ScienceSource Twitter announcement and 60 second video. A medical canon? The proposal includes downloading 30,000 open access papers, aiming (roughly speaking) to create a baseline for medical referencing on Wikipedia. It leaves open the question of how these are to be chosen. The basic criteria of Prophylaxis misses the point that gate-keeping will be done by an algorithm. Two well-known but rather different areas where such considerations apply are tropical diseases and alternative medicine. There are also a number of potential downloading troubles, and these were mentioned in Issue 11. There is likely to be a gap, even with the guideline, between conditions taken to be necessary but not sufficient, and conditions sufficient but not necessary, for candidate papers to be included. With around 10,000 recognised medical conditions in standard lists, being comprehensive is demanding. With all of these aspects of the task, ScienceSource will seek community help. Links d:Wikidata:Lexicographical data, Wikidata's multi-lingual dictionary project gets going Ordia tool, a basic search interface for Wikidata lexemes and forms OpenRefine tool 3.0, May update allows wrangling of tabular information into Wikidata d:Wikidata:WikiProject British Politicians pushes ahead with data modelling and imports #1Lib1Ref Returns for a Second Time in 2018, IFLA blogpost 25 May 2018, second chance this year to participate in referencing Wikipedia To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see below. Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. ScienceSource pages will be announced there, and in this mass message. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 10:16, 28 May 2018 (UTC)

Facto Post – Issue 13 – 29 May 2018

Facto Post – Issue 13 – 29 May 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Respecting MEDRS Facto Post enters its second year, with a Cambridge Blue (OK, Aquamarine) background, a new logo, but no Cambridge blues. On-topic for the WP:MEDRS guideline, for the referencing of articles at all related to human health, is applied in typical discussions. Close to home also, a template, called {{ medrs}} for short, is used to express dissatisfaction with particular references. Technology can help with patrolling, and this Petscan query finds over 450 articles where there is at least one use of the template. Of course the template is merely suggesting there is a possible issue with the reliability of a reference. Deciding the truth of the allegation is another matter. This maintenance issue is one example of where ScienceSource aims to help. Where the reference is to a scientific paper, its type of algorithm could give a pass/fail opinion on such references. It could assist patrollers of medical articles, therefore, with the templated references and more generally. There may be more to proper referencing than that, indeed: context, quite what the statement supported by the reference expresses, prominence and weight. For that kind of consideration, case studies can help. But an algorithm might help to clear the backlog. WP:MEDRS Links World Cup scorers bubble chart, by the league in which they play, query run on Wikidata Timeline of discoveries of natural satellites in the solar system, query run on Wikidata 4800 Welsh portraits added to Wikimedia Commons and Wikidata, National Library of Wales blogpost 27 June 2018, by Jason.nlw The "deaditors" of Wikipedia, Hay Kranen blogpost, 15 June 2018 Six dimensions of open access, polemical tweet, 17 June 2018 If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 18:19, 29 June 2018 (UTC)

Facto Post – Issue 14 – 21 July 2018

Facto Post – Issue 14 – 21 July 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Plugging the gaps – Wikimania report Officially it is "bridging the gaps in knowledge", with Wikimania 2018 in Cape Town paying tribute to the southern African concept of ubuntu to implement it. Besides face-to-face interactions, Wikimedians do need their power sources. Facto Post interviewed Jdforrester, who has attended every Wikimania, and now works as Senior Product Manager for the Wikimedia Foundation. His take on tackling the gaps in the Wikimedia movement is that "if we were an army, we could march in a column and close up all the gaps". In his view though, that is a faulty metaphor, and it leads to a completely false misunderstanding of the movement, its diversity and different aspirations, and the nature of the work as "fighting" to be done in the open sector. There are many fronts, and as an eventualist he feels the gaps experienced both by editors and by users of Wikimedia content are inevitable. He would like to see a greater emphasis on reuse of content, not simply its volume. If that may not sound like radicalism, the Decolonizing the Internet conference here organized jointly with Whose Knowledge? can redress the picture. It comes with the claim to be "the first ever conference about centering marginalized knowledge online". Links ScienceSource focus list (shortcut WD:SSFL on Wikidata), project to tag a first-pass open access medical bibliography on Wikidata, and also overcome the systematic biases in the medical literature by curation. Wikimedia Foundation and Kiwix partner to grow offline access to Wikipedia, Wikimedia Foundation blogpost 18 July 2018. Wikipedia's upcoming Cape Town conference will tackle the issue of diversity, Jamie Matroos, 2 July 2018. VideoWiki, a video version of Wikipedia. Search Full-Text within 4M+ Books, by MEK, The Open Library Blog, 14 July 2018 More than 5,000 German scientists have published papers in pseudo-scientific journals, NDR, 19 July 2018. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 06:10, 21 July 2018 (UTC)

Facto Post – Issue 15 – 21 August 2018

Facto Post – Issue 15 – 21 August 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Neglected diseases Côte d'Ivoire To grasp the nettle, there are genetic diseases . A major aspect of neglect is found in tracking WHO's neglected diseases, where snakebite , a "neglected public health issue", is on the list. From an encyclopedic point of view, lack of research also may mean lack of high-quality references: the core medical literature differs from primary research, since it operates by aggregating trials. This bibliographic deficit clearly hinders Wikipedia's mission. The ScienceSource project is currently addressing this issue, on Wikidata. Its Wikidata focus list at WD:SSFL is trying to ensure that neglect does not turn into bias in its selection of science papers. Links Wikipedia, Wikidata, and citations, a census, August 2 2018, blogpost by Magnus Manske The rise of Wikidata as a linked data source August 6, 2018, by Karen Smith-Yoshimura on OCLC Research blog Where do Mayors Come From: Querying Wikidata with Python and SPARQL, August 1 2018, Parametric Thoughts blog Newspapers On Wikipedia Update: Initial Wikidata Pass 9 August 2018, Mike Caulfield Google Scholar, Web of Science, and Scopus: a systematic comparison of citations in 252 subject categories Alberto Martín-Martín, Enrique Orduna-Malea, Mike Thelwall, Emilio Delgado López-Cózar, arxiv.org, submitted on 15 August 2018 If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 13:23, 21 August 2018 (UTC)

Request for comments

This is a request for comments regarding the relevance of Denny (hybrid hominin) as it relates to human interspecies breeding. The link to the discussion is at: Talk:Human evolution#A curious discovery, but not really on-topic. Cheers, Rowan Forest (talk) 16:37, 26 August 2018 (UTC)

Sex determination material at the Sexual differentiation in humans article

Opinions are needed on the following:

talk

) 21:24, 31 August 2018 (UTC)

RfC being planned

Please see WP:Reliable_sources/Noticeboard#Primary_genetics_studies. Jytdog (talk) 23:40, 6 September 2018 (UTC)

This is an interesting article with reliable sources SebaSebaBukh (talk) 21:24, 9 September 2018 (UTC)

Facto Post – Issue 16 – 30 September 2018

Facto Post – Issue 16 – 30 September 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. The science publishing landscape In an ideal world ... no, bear with your editor for just a minute ... there would be a format for scientific publishing online that was as much a standard as SI units are for the content. Likewise cataloguing publications would not be onerous, because part of the process would be to generate uniform metadata. Without claiming it could be the mythical free lunch , it might be reasonably be argued that sandwiches can be packaged much alike and have barcodes, whatever the fillings. The best on offer, to stretch the metaphor, is the slow food yourself. See Scholarly HTML for a recent pass at heading off XML with HTML, in other words in the native language of the Web. The argument from WikiJournal , and we have the chops to act. Links ImageGrid SPARQL query for the Art+Feminism focus list on Wikidata. Run and then scroll ... The TABernacle tool for Wikidata editing, by Magnus Manske, has been upgraded. Demo with the ScienceSource focus list and main subjects: with a WiDar login you can edit directly in the table cells. Enslaved: People of the Historic Slave Trade, Michigan State University project for a linked open data platform. Quote: "Disambiguating and merging individuals across multiple datasets is nearly impossible given their current, siloed nature." As the Linked Data for Production (LD4P) project finishes its initial two-year cycle and moves into LD4P2, a list of its BIBFRAME and other RDF tools. Machine Learning with and for Semantic Web Knowledge Graphs, detailed slide pack by Heiko Paulheim, University of Mannheim. In Europe, Scientists Need to Share Their Research for Free if They Want Government Funding, Futurism, by Kristin House, 5 September 2018. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 17:57, 30 September 2018 (UTC)

Comment on draft

Your comments on

afc comment|Your comment here. ~~~~}} directly in the draft. Thank you. Sam Sailor

19:06, 28 October 2018 (UTC)

Facto Post – Issue 17 – 29 October 2018

Facto Post – Issue 17 – 29 October 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Wikidata imaged Around 2.7 million Wikidata items have an illustrative image. These files, you might say, are Wikimedia's stock images, and if the number is large, it is still only 5% or so of items that have one. All such images are taken from Wikimedia Commons, which has 50 million media files. One key issue is how to expand the stock. Indeed, there is a tool. WD-FIST exploits the fact that each Wikipedia is differently illustrated, mostly with images from Commons but also with fair use images. An item that has sitelinks but no illustrative image can be tested to see if the linked wikis have a suitable one. This works well for a volunteer who wants to add images at a reasonable scale, and a small amount of SPARQL knowledge goes a long way in producing checklists. It should be noted, though, that there are currently 53 Wikidata properties that link to Commons, of which P18 for the basic image is just one. WD-FIST prompts the user to add signatures, plaques, pictures of graves and so on. There are a couple of hundred monograms, mostly of historical figures, and this query allows you to view all of them. commons:Category:Monograms and its subcategories provide rich scope for adding more. And so it is generally. The list of properties linking to Commons does contain a few that concern video and audio files, and rather more for maps. But it contains gems such as P3451 for "nighttime view". Over 1000 of those on Wikidata, but as for so much else, there could be yet more. Go on. Today is Wikidata's birthday. An illustrative image is always an acceptable gift, so why not add one? You can follow these easy steps: (i) log in at https://tools.wmflabs.org/widar/, (ii) paste the Petscan ID 6263583 into https://tools.wmflabs.org/fist/wdfist/ and click run, and (iii) just add cake. Links Now Wikidata is six, Signpost Special Report Find out how @TheContentMine are attempting to mine scientific and medical literature to improve the accuracy of Wikipedia., Wikimedia UK tweet and video ScienceSource and the Semantic Web sciencesource-pmc-licenses tool by Oravrattas to extract Creative Commons license information from PubMed Central pages, created at the Cambridge Wikidata Workshop Whizzy use of SPARQL to map the London Underground system, whizzed past on Twitter. Wikidata birthday events mapped by SPARQL, too d:Wikidata:Sixth Birthday/Message from dev team If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 15:01, 29 October 2018 (UTC)

Featured quality source review RFC

Editors in this WikiProject may be interested in the

the featured article candidate process (FAC) so that source reviews would need to occur prior to any other reviews for FAC. Your comments are appreciated. --IznoRepeat (talk

) 21:50, 11 November 2018 (UTC)

Request for a second opinion on Cytohet

Hi WP Genetics members, is Cytohet notable enough for its own article in your opinion? Genetics is not my strong point, but it is currently tagged {{notability}}. Thanks! --TheSandDoctor ^Talk 19:25, 12 November 2018 (UTC)

I think it is probably notable, but the proper home for the article is likely "heteroplasmon", rather than cytohet. Canada Hky (talk) 13:46, 13 November 2018 (UTC)

Topic Page on Selfish genetic elements

PLOS Genetics has now joined PLOS Computational Biology in its Topic Pages initiative. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Selfish genetic element wikipedia page. Comments and suggestions welcome! T.Shafee(Evo&Evo)^talk 00:41, 17 November 2018 (UTC)

Facto Post – Issue 18 – 30 November 2018

Facto Post – Issue 18 – 30 November 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. WikiCite issue GLAM ♥ data — what is a gallery, library, archive or museum without a catalogue? It follows that Wikidata must love librarians. Bibliography supports students and researchers in any topic, but open and machine-readable bibliographic data even more so, outside the silo. Cue the WikiCite initiative, which was meeting in conference this week, in the Bay Area of California. In fact there is a broad scope: "Open Knowledge Maps via SPARQL" and the "Sum of All Welsh Literature", identification of research outputs, Library.Link Network and Bibframe 2.0, OSCAR and LUCINDA (who they?), OCLC and Scholia, all these co-exist on the agenda. Certainly more library science is coming Wikidata's way. That poses the question about the other direction: is more Wikimedia technology advancing on libraries? Good point. Wikimedians generally are not aware of the tech background that can be assumed, unless they are close to current training for librarians. A baseline definition is useful here: "bash, git and OpenRefine". Compare and contrast with pywikibot, GitHub and mix'n'match. Translation: scripting for automation, version control, data set matching and wrangling in the large, are on the agenda also for contemporary library work. Certainly there is some possible common ground here. Time to understand rather more about the motivations that operate in the library sector. Links Wikidata and Libraries: Facilitating Open Knowledge, book chapter by Mairelys Lemus-Rojas, metadata librarian and Lydia Pintscher, Wikidata Product Manager, from Leveraging Wikipedia: Connecting Communities of Knowledge (2018) LD4P and WikiCite: Opportunities for collaboration, WikiCite 2018 program abstract, Christine Fernsebner Eslao of Harvard Library Information and Technical Services and Michelle Futornick, Linked Data for Production Program Manager at Stanford University Shell Lessons for Librarians, Library Carpentry lesson At-risk content on Flickr, blogpost 3 November 2018, Andrew Gray Toward an Abstract Wikipedia, recent white paper by Wikidata founder Denny Vrandečić (Google) Account creation is now open on the ScienceSource wiki, where you can see SPARQL visualisations of text mining. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 11:20, 30 November 2018 (UTC)

Request for assessment on MiR-324-5p -Dec 11 2018

The page https://en.wikipedia.org/wiki/MiR-324-5p was developed as part of course on science communication at the University of Cincinnati. It has not been rated yet for importance or quality. It would be great if someone could help with that. thanks! TMorata (talk) 12:27, 11 December 2018 (UTC)TMorata

Topic Page on Micropeptides

PLOS Genetics just published its second Topic Pages article. As with the previous one on selfish genetic elements, it was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Micropeptide wikipedia page. Comments, suggestions, edits and updates welcome! T.Shafee(Evo&Evo)^talk 12:45, 14 December 2018 (UTC)

Facto Post – Issue 19 – 27 December 2018

Facto Post – Issue 19 – 27 December 2018 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Learning from Zotero Center for History and New Media: see Wikipedia:Citing sources with Zotero. It is also an active user community, and has broad-based language support . Besides the handiness of Zotero's warehousing of personal citation collections, the Zotero translator underlies the citoid service, at work behind the VisualEditor. Metadata from Wikidata can be imported into Zotero; and in the other direction the zotkat tool from the University of Mannheim allows Zotero bibliographies to be exported to Wikidata, by item creation. With an extra feature to add statements, that route could lead to much development of the focus list (P5008) tagging on Wikidata, by WikiProjects. There is also a large-scale encyclopedic dimension here. The construction of Zotero translators is one facet of Web scraping that has a strong community and open source basis. In that it resembles the less formal mix'n'match import community, and growing networks around other approaches that can integrate datasets into Wikidata, such as the use of OpenRefine. Looking ahead, the thirtieth birthday of the World Wide Web falls in 2019, and yet the ambition to make webpages routinely readable by machines can still seem an ever-retreating mirage. Wikidata should not only be helping Wikimedia integrate its projects, an ongoing process represented by Structured Data on Commons and lexemes. It should also be acting as a catalyst to bring scraping in from the cold, with institutional strengths as well as resourceful code. Links Zotero Comes to Google Docs, Zotero blogpost by Dan Stillman, 19 October 2018. Category:Wikipedians who use Zotero T115158 Write a Zotero translator and document process for creating new Zotero translator and getting it live in production, long Phabricator thread 2015–17. Zotero Translators, documentation from zotero.org. Home page on GitHub for Zotero translator Javascript Example translator, for Wikisource. m:Structured Data on Commons/Newsletter/2018-12-07 Diversitech, the latest ContentMine grant application to the Wikimedia Foundation, is in its community review stage until January 2. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 19:08, 27 December 2018 (UTC)

Discussion at RSN on the use of eupedia.com for genetics

It seems to be a one man band, started off as a tourist site and the site owner became interested in genetics. Doug Weller talk 20:31, 10 January 2019 (UTC)

It looks like the link for that discussion is at Wikipedia:Reliable_sources/Noticeboard#Eupedia.com. --{{u|Mark viking}} {Talk} 20:56, 10 January 2019 (UTC)

Facto Post – Issue 20 – 31 January 2019

Facto Post – Issue 20 – 31 January 2019 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. Everything flows (and certainly data does) Recently Jimmy Wales has made the point that Coptic ?). Headlines about data breaches are now familiar, but the unannounced circulation of information raises other issues. One of those is Gresham's law stated as "bad data drives out good". Wikipedia and now Wikidata have been criticised on related grounds: what if their content, unattributed, is taken to have a higher standing than Wikimedians themselves would grant it? See Wikiquote on a misattribution to Bismarck for the usual quip about "law and sausages", and why one shouldn't watch them in the making. Wikipedia has now turned 18, so should act like as adult, as well as being treated like one. The Web itself turns 30 some time between March and November this year, per GIGO, Wikimedians still have a role in its critique. But not just with the teenage skill of detecting phoniness . There is more to beating Gresham than exposing the CC-BY ) standing for the actual license in major repositories. Detailed investigation shows that "everything flows" exacerbates the issue. But Wikidata can solve it. Links Wikipedia:Wikipedia Day for 18th birthday celebrations WMUK video page, with "fake news", Jimmy Wales, Wikidata and more (health warning for those with tune allergy) Why Wikipedia’s Medical Content Is Superior, Stephen Harrison, 28 January 2019, Slate Olivia Colman reveals struggle with Wikipedia over age, Naomi Gordon, 28 January 2019, harpersbazaar.com Making Wikidata visible, Martin Poulter blogpost, 24 January 2019, Bodleian Digital Library Inventory, Magnus Manske blogpost, 24 January 2019, on Wikidata tech support for an image donation by Cleveland Museum of Art If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)

Facto Post – Issue 21 – 28 February 2019

Facto Post – Issue 21 – 28 February 2019 The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page. To subscribe to Facto Post go to Wikipedia:Facto Post mailing list. For the ways to unsubscribe, see the footer. Back numbers are here. What is a systematic review? Systematic reviews are basic building blocks of evidence-based medicine, surveys of existing literature devoted typically to a definite question that aim to bring out scientific conclusions. They are principled in a way Wikipedians can appreciate, taking a critical view of their sources. structured data help? File:Schittny, Facing East, 2011, Legacy Projects.jpg Most likely it would, but the arcana of systematic reviews and how they add value would still need formal handling. The Automatic identification doesn't just happen. Actually these questions lack originality. It should be noted though that WP:MEDASSESS qualifies that indication heavily. Process wonkery about systematic reviews definitely has merit. Links Evidence-Based Practice: Appraise, resources page from Duke University Medical Library & Archives. What should Cochrane do next?, Bad Science blogpost 5 November 2014, Ben Goldacre. Cambridge (UK) Science Festival event, How do scientific discoveries become clinical medicine?, ScienceSource workshop for ContentMine 23 March 2019, with systematic review process diagram. Also on Eventbrite for tickets, taking place in Makespace, 16 Mill Lane. PROSPERO database of PRISMA, for registration of systematic review protocols. Process wonkery thread, wikien-l mailing list, September 2006. Meta-Analysis, xkcd cartoon. If you wish to receive no further issues of Facto Post, please remove your name from our mailing list. Alternatively, to opt out of all massmessage mailings, you may add Category:Wikipedians who opt out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery

MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC)