Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Archive 10
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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.
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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.
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MediaWiki message delivery (talk) 13:23, 21 August 2018 (UTC)
Expert attention
This is a notice about Category:Molecular and Cell Biology articles needing expert attention, which might be of interest to your WikiProject. It will take a while before the category is populated. There might be as few as one page in the category, or zero if someone has removed the expert request tag from the page. — Mr. Guye (talk) (contribs) 22:31, 9 September 2018 (UTC)
- @Mr. Guye: Thanks! I've just also found two other categories. how easy would these be to merge?
- T.Shafee(Evo&Evo)talk 23:59, 9 September 2018 (UTC)
- @Evolution and evolvability: Probably not easy, but I really don't know. Maybe nominate them for merging at CfD, and ask for help there. — Mr. Guye (talk) (contribs) 00:04, 10 September 2018 (UTC)
Nonglobular Protein Taskforce
There was an editathon at the recent NGP-Net conference for nonglobular protein science, which is affiliated with a European consortium/scientific society. There was interest from the student network in sponsoring regular editathons and curating some pages from our topic area. Many of the pages that were identified as needing improvement are within the bounds of WP:MCB (or occasionally
Some other projects have the concept of a task force (
Example topics to include would be intrinsically disordered proteins, protein tandem repeats, amyloid, low-complexity_regions, and methods for investigating such topics.
-- Quantum7 07:17, 14 September 2018 (UTC)
- @defensins) are also in a sorry state. T.Shafee(Evo&Evo)talk13:41, 14 September 2018 (UTC)
Circulating mitochondrial DNA
I have just created a stub on circulating mitochondrial DNA, which is a topic with over 800 Google Scholar hits and a breathless writeup on September 13 in Scientific American. If anybody want to improve my terrible stub, please do. Abductive (reasoning) 20:34, 20 September 2018 (UTC)
Disambiguation links to Adhesin
Can anyone on this wikiproject help with the disambiguation links to Adhesin. It is a specialist topic and I don't have the expertise to fix the list here.— Rod talk 16:01, 26 September 2018 (UTC)
- I think that the dab page needs to be turned into a ) 16:42, 26 September 2018 (UTC)
Pyruvate kinase
The article on pyruvate kinase says that "In Archaean oceans, phospho-enolpyruvate may have been present abiotically." I doubt that phosphoenolpyruvate is stable in water. Wouldn't it hydrolyze immediately to phosphoric acid and pyruvic acid?? I didn't want to edit the article because I'm not sure of this but it sounds suspicious to me. This was the only place I could find to leave a comment. And I will sign my post with four tildes, if that's what you want.
The mark of the anonymous commenter: 169.229.232.53 (talk) 21:37, 26 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.
 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.
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MediaWiki message delivery (talk) 17:57, 30 September 2018 (UTC)
Removal of 3DMet data from {{Chembox}}
3DMet ID (P2796) (see uses)
At the moment, the article about
If and when this article is deleted, it follows that the {{Chembox}} data row (|3DMet= in {{Chembox}}) should be removed too (we should not link or point to an irrelevant and not-notifyable database). Today, some 126 articles use parameter |3DMet=: [1].
Action needed: The only way to save this information is to prove notability of 3DMet by adding secondary sources (read the AfD though for an investigation already made into this: few sources are sound). -DePiep (talk) 07:23, 19 October 2018 (UTC)
- Huh? WP:N has nothing to do with infoboxes. That an article isn't notable by the particular definition used in notability policies does not mean it isn't useful in chemboxes. Jo-Jo Eumerus (talk, contributions) 14:07, 19 October 2018 (UTC)
- If the 3DMet database is not noteworthy in Wikipedia, then referring/linking to it is not noteworthy either. How can an irrelevant database be relevant in infoboxes? -DePiep (talk) 14:50, 19 October 2018 (UTC)
- Or, the other way around: if there is a useful application of 3DMet data in literature (for some compound), that would be a supporting reference for 3DMet. -DePiep (talk) 14:53, 19 October 2018 (UTC)
- "Relevant" in the sense of an infobox and "relevant" in the sense of WP:Notability are not the same thing at all. For example, if the database is frequently used by chemists but seldom discussed. Jo-Jo Eumerus (talk, contributions) 15:07, 19 October 2018 (UTC)
- Yes, that is the point: if its usage & virtues are not ending up in sources (publications), it is clearly not relevant. Not the database, not the application wrt a compound. If the database would add really something to some research issue, that creates relevance. In the end: Why have a redlink i.e. nonexistant "3DMet" in the lefthand side of {{Chembox}}, with data (ID) in righthandside? -DePiep (talk) 15:30, 19 October 2018 (UTC)
- "Relevant" in the sense of an infobox and "relevant" in the sense of WP:Notability are not the same thing at all. For example, if the database is frequently used by chemists but seldom discussed. Jo-Jo Eumerus (talk, contributions) 15:07, 19 October 2018 (UTC)
Advice on new article: Ragulator-Rag complex
I just added a new article by my class (Ragluator-Rag complex) and was wondering what to do to get it noticed and properly indexed or catagorized.137.142.46.79 (talk) 19:38, 24 October 2018 (UTC) Sorry, I wasn't logged in, Jparcoeur (talk) 19:40, 24 October 2018 (UTC)
- @Jparcoeur: You came to the right place. I've made some edits and suggestions on the article's talk page. T.Shafee(Evo&Evo)talk 11:08, 25 October 2018 (UTC)
Heterosaccharide
Does this need to be its own article, or can it be redirected to something else, like
09:00, 26 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.
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. 
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MediaWiki message delivery (talk) 15:01, 29 October 2018 (UTC)
Featured quality source review RFC
Editors in this WikiProject may be interested in the
Infobox gene changes
Yep, still on this old horse. Have posted at Wikiproject Medicine: Wikipedia_talk:WikiProject_Medicine#Help_needed_improving_gene_infobox_(alternate_title:_Tom_(LT)'s_annual_gene_infobox_whinge) --Tom (LT) (talk) 10:39, 12 November 2018 (UTC)
Draft:C3orf67 review
Could somebody take a look at
- Protein-coding genes are considered notable by default but the format is odd. I'd point the author to TBR1 as a template seeing as that is a good article. Jo-Jo Eumerus (talk, contributions) 17:48, 13 November 2018 (UTC)
Infobox gene changes
Yep, still on this old horse. Have posted at Wikiproject Medicine: Wikipedia_talk:WikiProject_Medicine#Help_needed_improving_gene_infobox_(alternate_title:_Tom_(LT)'s_annual_gene_infobox_whinge) --Tom (LT) (talk) 10:39, 12 November 2018 (UTC)
Draft:C3orf67 review
Could somebody take a look at
- Protein-coding genes are considered notable by default but the format is odd. I'd point the author to TBR1 as a template seeing as that is a good article. Jo-Jo Eumerus (talk, contributions) 17:48, 13 November 2018 (UTC)
Topic Page on Selfish genetic element
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)
Large genetics class off the rails
Please see Wikipedia:Education_noticeboard#Large_genetics_class_off_the_rails and the pages linked there, which need checking. Jytdog (talk) 20:11, 18 November 2018 (UTC)
Help with draft on Ferlin proteins
There is a new editor looking for help with a draft,
Thank you User:onel5969 for your time and suggestions, and for submitting the draft for me. I included your suggestions in the newest version and also added a new figure which I meant to add earlier. --Sam orbital (talk) 23:19, 18 November 2018 (UTC)Sam orbital
ZNF385D infobox
I just created ZNF385D and for some reason the infobox isn't working... is it just a lag fetching stuff from Wikidata? Jytdog (talk) 03:14, 21 November 2018 (UTC)
- A mapping between ZNF385D and the Wikidata item d:Q18046323 needed to be added . It is unclear to me if there is a bot that is supposed to do this automatically. Boghog (talk) 05:42, 21 November 2018 (UTC)
Facto Post – Issue 18 – 30 November 2018
Facto Post – Issue 18 – 30 November 2018
MediaWiki message delivery (talk) 11:20, 30 November 2018 (UTC) |
Facto Post – Issue 19 – 27 December 2018
Facto Post – Issue 19 – 27 December 2018
MediaWiki message delivery (talk) 19:08, 27 December 2018 (UTC) |
Hello friends, another headache biology article I'm hoping you all can help with. Is endoexocytosis different than endocytosis/exocytosis, or has someone gone and conflated the two? I can't make heads or tails of it. ♠PMC♠ (talk) 13:53, 5 January 2019 (UTC)
- It's possible that it's another term for diacytosis. Natureium (talk) 20:07, 5 January 2019 (UTC)
- Not a conflation, but it seems like this is terminology with very limited uptake (groan... pun somewhat intended ;) Looking at the main source for the article (Nickel et al 2008), it seems to be a self-conscious coinage by the authors of that paper. From the discussion section,
This internalization is thus, an "endoexocytic" process in which a decision must be made as to which cell will incorporate the internalized pentilaminar membranes.
I can't find any other significant usage of the term; other search hits are mostly things like "endo/exocytosis", and the articles citing Nickel mostly don't seem to pick it up either. (The only other usages I could find also have Murray as the senior author.) Also, the other citations in our article are just a subset of the papers cited in Nickel. So our article is pretty much an abstract of this one decade-old primary source. I'd prod it, with no prejudice toward re-creation if the term does eventually catch on. (No shame in that... when I came back to WP a few years ago, I prodded one of my own decade-old stubs created to explain a term that had gone obsolete in the meantime...) Opabinia regalis (talk) 21:57, 5 January 2019 (UTC)
We suck
Somehow this survived over a year and 800,000 pageviews on Cellular respiration. I've no idea how I didn't catch it at the time, but I guess the take-home message is that we need more people watching articles. Adrian J. Hunter(talk•contribs) 08:03, 16 January 2019 (UTC)
- @Adrian J. Hunter: Yeesh, I hate finding ones that have been long-standing like that. A lot of these sorts of issues would be improved with growing the editor base for watching and spot-checking articles, but that's been an ongoing priority for years! Even rating all the backlog of unrated pages last year lead me to some errors that have been around for over a decade. T.Shafee(Evo&Evo)talk 01:31, 21 January 2019 (UTC)
MINAS
Could someone have a look at MINAS to see if it's notable? Thanks in advance. – Uanfala (talk) 00:48, 21 January 2019 (UTC)
- @MMDB and no more notable than metalPDB (which doesn't have a page). However I'm probably an inclusionist when it comes to these databases so I think that it is sufficiently notable to stay in as a stub. I'd probably draw the line at FREP though, which has only been cited 11 times since 2004, and has been offline for a few years now. T.Shafee(Evo&Evo)talk01:42, 21 January 2019 (UTC)
Could someone who knows the topic take a look at these two diffs, [2] and [3], and tell me if they seem promotional/suspicious? I don't know enough to know if what they're writing is legitimate science or promotion. The reason I'm suspicious is because the account seems to edit very intermittently, making occasional huge additions to random, totally disparate topics, and it just feels off to me. ♠PMC♠ (talk) 04:53, 21 January 2019 (UTC)
- @Premeditated Chaos: The edits to Dielectrophoresis seem reasonable to me, since dielectrophoretic cell sorting is a notable application. I'm not keen on referring to it by a particular brand of machine, but then we do the equivalent in the Illumina dye sequencing article. The Single-cell analysis edits are definitely unbalanced. Dielectrophoretic cell sorting is pretty niche, so definitely the lead now over-emphasises it, but the rest of the edits are more reasonable. T.Shafee(Evo&Evo)talk 06:51, 21 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.
Recently Jimmy Wales has made the point that Coptic ?).
Android phone 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.
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MediaWiki message delivery (talk) 10:53, 31 January 2019 (UTC)
Facto Post – Issue 21 – 28 February 2019
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MediaWiki message delivery (talk) 10:02, 28 February 2019 (UTC) |
GAI (Arabidopsis thaliana gene)
GAI (Arabidopsis thaliana gene) is tagged with this project so I thought I'd ask here. The article has two infoboxes, one {{Infobox nonhuman protein}} and another is a manually created infobox inside the article for "Gene ontology". Is there an already existing infobox that does what the "Gene ontology" one does? --Gonnym (talk) 08:48, 20 March 2019 (UTC)
- Find sources: Google (books · news · scholar · free images · WP refs) · FENS · JSTOR · TWL
- Candida blankii (edit|talk|history|links|watch|logs|google) AfD discussion
Our favorite yeast? Probably not. But no pretense of compliance with
Facto Post – Issue 22 – 28 March 2019
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MediaWiki message delivery (talk) 11:46, 28 March 2019 (UTC) |
Facto Post – Issue 24 – 17 May 2019
Facto Post – Issue 24 – 17 May 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.
Two dozen issues, and this may be the last, a valediction at least for a while. It's time for a two-year summation of ContentMine projects involving TDM ( text and data mining ).
Wikidata and now Structured Data on Commons represent the overlap of Wikimedia with the Semantic Web. This common ground is helping to convert an engineering concept into a movement. TDM generally has little enough connection with the Semantic Web, being instead in the orbit of machine learning which is no respecter of the semantic. Don't break a taboo by asking bots "and what do you mean by that?" The Wikipedia referencing guideline MEDRS. Where WikiFactMine set up an API for reuse of its results, ScienceSource has a SPARQL query service, with look-and-feel exactly that of Wikidata's at query.wikidata.org. It also now has a custom front end, and its content can be federated, in other words used in data mashups: it is one of over 50 sites that can federate with Wikidata.
The human factor comes to bear through the front end, which combines a link to the HTML version of a paper, text mining results organised in drug and disease columns, and a SPARQL display of nearby drug and disease terms. Much software to develop and explain, so little time! Rather than telling the tale, Facto Post brings you ScienceSource links, starting from the how-to video, lower right.
The review tool requires a log in on sciencesource.wmflabs.org, and an OAuth permission (bottom of a review page) to operate. It can be used in simple and more advanced workflows. Examples of queries for the latter are at d:Wikidata_talk:ScienceSource project/Queries#SS_disease_list and d:Wikidata_talk:ScienceSource_project/Queries#NDF-RT issue. Please be aware that this is a research project in development, and may have outages for planned maintenance. That will apply for the next few days, at least. The ScienceSource wiki main page carries information on practical matters. Email is not enabled on the wiki: use site mail here to Charles Matthews in case of difficulty, or if you need support. Further explanatory videos will be put into commons:Category:ContentMine videos. 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.
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MediaWiki message delivery (talk) 18:52, 17 May 2019 (UTC)
Facto Post – Issue 23 – 30 April 2019
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MediaWiki message delivery (talk) 11:27, 30 April 2019 (UTC) |
Facto Post – Issue 2 – 13 July 2017
Facto Post – Issue 2 – 13 July 2017
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Most of the articles unintentionally citing retractions are of related to this project. If someone could take a look at those, that would be great.
- @Headbomb: Thanks for the notification! I've checked whether there are non-retracted sources to support the statements in a couple of these and will try help with some more this weekend. Massive thanks to those editors who add
{{retracted}}templates (in particular Rich Farmbrough) - vital work! T.Shafee(Evo&Evo)talk 23:20, 21 February 2019 (UTC)- YOu are welcome, last time I did this was many years ago. Perhaps I can revisit this. All the best: Rich Farmbrough, 09:30, 22 February 2019 (UTC).
- Perhaps some day there will be a way to automate it via a bot. T.Shafee(Evo&Evo)talk 10:29, 22 February 2019 (UTC)
- There is a b} 22:59, 22 February 2019 (UTC)
- Cool! I had no idea this was something we were even trying to track, but it's a really good idea. Opabinia regalis (talk) 06:00, 23 February 2019 (UTC)
- @Headbomb, any updates on this bot? It sounds incredible. Prometheus720 (talk) 00:29, 12 April 2019 (UTC)
- Cool! I had no idea this was something we were even trying to track, but it's a really good idea. Opabinia regalis (talk) 06:00, 23 February 2019 (UTC)
- There is a
- Perhaps some day there will be a way to automate it via a bot. T.Shafee(Evo&Evo)talk 10:29, 22 February 2019 (UTC)
- YOu are welcome, last time I did this was many years ago. Perhaps I can revisit this. All the best: Rich Farmbrough, 09:30, 22 February 2019 (UTC).
I've cleared the backlog of MCB articles with unknown importance--but the page won't update. Help?
Category_talk:Unknown-importance_MCB_articles
I went through every single page. Probably at least a third already had importance assessments. I'd like this to clear fully so that anything which enters it really needs to be assessed. Any tips on what might be happening? Prometheus720 (talk) 20:19, 11 April 2019 (UTC)
- This seems like a good question for the techy people at ) 20:26, 11 April 2019 (UTC)
- It's because those pages are tagged with
{{WikiProject Microbiology|mcb=yes}}without including|mcb_importance=whatever. MCB project tagging should probably just be removed from the micro template and MCB templates added wherever that parameter was previously used. Seppi333 (Insert 2¢) 21:34, 11 April 2019 (UTC)- Curious. I never noticed that "feature" of the micro template. Just removed it from the handful of articles that had it. I'll remove it from the template as well unless anyone feels strongly for its inclusion. I assume it's just a holdover from the olden days. Ajpolino (talk) 22:29, 11 April 2019 (UTC)
- @Ajpolino, I noticed that tag and thought it was weird. So are you saying you are sure it is gone for good from all articles in which it was present? I am for removing it from the template, personally. I think that most tags like that generally create clutter and overhead.Prometheus720 (talk) 00:32, 12 April 2019 (UTC)
- Curious. I never noticed that "feature" of the micro template. Just removed it from the handful of articles that had it. I'll remove it from the template as well unless anyone feels strongly for its inclusion. I assume it's just a holdover from the olden days. Ajpolino (talk) 22:29, 11 April 2019 (UTC)
- It's because those pages are tagged with