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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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![]() To grasp the nettle, there are rare diseases, there are tropical diseases and then there are "neglected diseases". Evidently a rare enough disease is likely to be neglected, but neglected disease these days means a disease not rare, but tropical, and most often infectious or parasitic. Rare diseases as a group are dominated, in contrast, by genetic diseases. A major aspect of neglect is found in tracking drug discovery. Orphan drugs are those developed to treat rare diseases (rare enough not to have market-driven research), but there is some overlap in practice with the 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)
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)
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 WP:WCB), so it would make sense organize within this project.
Some other projects have the concept of a task force (example) for organizing sub-communities with shared interests. Technically, this consists of a slightly modified banner on the talk page and a set of categories so that task force members can identify pages requiring improvement. Would this community be supportive of starting a task force relating to nonglobular proteins?
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)
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)
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)
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
![]() The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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![]() 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 meal kit option, in the form of XML. Where scientific papers are delivered as XML downloads, you get all the ingredients ready to cook. But have to prepare the actual meal of 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 real life is a traditional mixture of frictional forces, vested interests, and the classic irony of the principle of unripe time. On the other hand, discoverability actually diminishes with the prolific progress of science publishing. No, it really doesn't scale. Wikimedia as movement can do something in such cases. We know from open access, we grok the Web, we have our own horse in the HTML race, we have Wikidata and WikiJournal, and we have the chops to act. ![]()
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MediaWiki message delivery (talk) 17:57, 30 September 2018 (UTC)
At the moment, the article about 3DMet (one in the Category:Chemical databases (49)), is up for deletion (AfD). Reason is lack of WP:NOTABILITY, as measured by ~not being referenced in secondary (independent) sources. IOW, virtually no sources refer to it as useful etc. or actually use 3DMet.
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)
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)
Does this need to be its own article, or can it be redirected to something else, like saccharide possibly? I don't know enough to tell. ♠PMC♠ (talk) 09:00, 26 October 2018 (UTC)
Facto Post – Issue 17 – 29 October 2018
![]() The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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)
Editors in this WikiProject may be interested in the featured quality source review RFC that has been ongoing. It would change 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) 21:34, 11 November 2018 (UTC)
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)
Could somebody take a look at Draft:C3orf67? I have a basic familiarity with the subject matter, but don't know what our notability guidelines are for these sorts of articles. Should this be moved to mainspace? Please leave your comments on the draft. Thanks. -- RoySmith (talk) 17:26, 13 November 2018 (UTC)
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)
Could somebody take a look at Draft:C3orf67? I have a basic familiarity with the subject matter, but don't know what our notability guidelines are for these sorts of articles. Should this be moved to mainspace? Please leave your comments on the draft. Thanks. -- RoySmith (talk) 17:26, 13 November 2018 (UTC)
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)
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)
There is a new editor looking for help with a draft, User:Sam orbital/sandbox/Ferlin. While from a layman standpoint, there are no issues with the article, and imho it is ready for mainspace, it could probably do with someone from this project taking a look at it. Thanks in advance for your help. Onel5969 TT me 12:25, 18 November 2018 (UTC)
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
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)
Facto Post – Issue 18 – 30 November 2018
MediaWiki message delivery (talk) 11:20, 30 November 2018 (UTC) |
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)
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)
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)
Could someone have a look at MINAS to see if it's notable? Thanks in advance. – Uanfala (talk) 00:48, 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)
Facto Post – Issue 20 – 31 January 2019
![]() The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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Recently Jimmy Wales has made the point that computer home assistants take much of their data from Wikipedia, one way or another. So as well as getting Spotify to play Frosty the Snowman for you, they may be able to answer the question "is the Pope Catholic?" Possibly by asking for disambiguation (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 Tim Berners-Lee. If the Knowledge Graph by Google exemplifies Heraclitean Web technology gaining authority, contra 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 factoid and urban myth, where WP:V does do a great job. Placeholders must be detected, and working with Wikidata is a good way to understand how having one statement as data can blind us to replacing it by a more accurate one. An example that is important to open access is that, firstly, the term itself needs considerable unpacking, because just being able to read material online is a poor relation of "open"; and secondly, trying to get Creative Commons license information into Wikidata shows up issues with classes of license (such as 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)
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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)
Our favorite yeast? Probably not. But no pretense of compliance with WP:Before. 7&6=thirteen (☎) 18:50, 24 March 2019 (UTC)
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MediaWiki message delivery (talk) 11:46, 28 March 2019 (UTC) |
Facto Post – Issue 24 – 17 May 2019![]() ![]() The Editor is Charles Matthews, for ContentMine. Please leave feedback for him, on his User talk page.
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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 ScienceSource project innovates in TDM, by storing its text mining results in a Wikibase site. It strives for compliance of its fact mining, on drug treatments of diseases, with an automated form of the relevant 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)
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MediaWiki message delivery (talk) 11:27, 30 April 2019 (UTC) |
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 {t · c · p · b} 16:25, 21 February 2019 (UTC)
((retracted))
templates (in particular Rich Farmbrough) - vital work! T.Shafee(Evo&Evo)talk 23:20, 21 February 2019 (UTC)
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)
((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)