User talk:Boghog/Archive 11

You deserve this

 * . Thanks! Because it was placed in the middle of my talk, I just noticed it.  Sorry about that. I feel a little guilty since the work I have done is relatively minor compared to all great work you have done on getting FA promoted.  In any case, thanks again! Boghog (talk) 20:30, 4 January 2017 (UTC)

Observation
There appears to be a bit of contention going on right now at Silicon Alley, and as an outsider looking in I would caution you to be careful not to cross the edit warring threshold - whether or not there is consensus behind your position reverting the edit that many times does not seem to be helping the situation. Garchy (talk) 17:46, 9 January 2017 (UTC)

Reference errors on 11 January
Hello, I'm ReferenceBot. I have automatically detected that an edit performed by you may have introduced errors in referencing. as follows: Please check this page and fix the errors highlighted. If you think this is a false positive, you can [//en.wikipedia.org/w/index.php?action=edit&preload=User:A930913/RBpreload&editintro=User:A930913/RBeditintro&minor=&title=User_talk:A930913&preloadtitle=ReferenceBot%20–%20&section=new report it to my operator]. Thanks, ReferenceBot (talk) 00:24, 12 January 2017 (UTC)
 * On the SLC7A11 page, [//en.wikipedia.org/w/index.php?diff=759520558 your edit] caused a redundant parameter error (help) . ([ Fix] | [//en.wikipedia.org/w/index.php?title=Wikipedia:Help_desk&action=edit&section=new&preload=User:ReferenceBot/helpform&preloadtitle=Referencing%20errors%20on%20%5B%5BSpecial%3ADiff%2F759520558%7CSLC7A11%5D%5D Ask for help])

Silicon Alley Biotechnology RFC closed
I have closed a RFC you participated heavily in here. The result was that biotechnology should be excised from the article on Silicon Alley completely. If you have any questions or concerns about this closure, please feel free to discuss them with me on my talk page. Thank you. Tazerdadog (talk) 13:02, 19 January 2017 (UTC)

organoids and pseudogenes
Hi! As I do more and more editing, I keep seeing you pop up on talk pages of articles I'm interested in. I wonder if we are long-lost half-sibs from my (our?) father as he made his way through North Africa and Italy during WWII. You should probably be afraid...very afraid...8-) The latest Science has a review about organoids. So, I looked at the wp page and found that it has a section "Basic research with organoids". If you remember, you removed a section reminiscent of that from the pseudogene article. Do you think there is a place for a section like that in articles about basic science? That is, a section where editors could mention recent findings they think are interesting without shoving them into the "heart" of an article. The section of organoids isn't really being used that way, but I get the impression that if anybody has seen such a section it would be you. Can you point me to an example? Thanks, DennisPietras (talk) 22:20, 19 January 2017 (UTC)

Thanks: It's going to be a bright sunshiny day!
Hey Boghog — My eyes thank you for agreeing to the color change (Seppi333 pinged you about). #FFCC66 has better contrast with lettering while retaining good contrast with the white background. — βox73 (৳alk) 03:51, 29 January 2017 (UTC)

Protein sequencing
Hi Boghog, The "mass spectrometry" section I revised as "Protein identification and characterization by mass spectrometry" is a complete alternative to "Edman degradation", not a sub-section of it. It should be promoted one level. I agree that a shorter section title is desirable. "mass spectrometry" in paragraph 2 will need to link to this new title. Regards, ChiBetaChiBeta (talk) 04:44, 30 January 2017 (UTC)


 * Sorry, my mistake. I restored the level of the mass spec section. Thanks for your additions!  Cheers. Boghog (talk) 05:35, 30 January 2017 (UTC)


 * Thanks for that! There are a few other parts of the article that need to be brought up to date. I'll try to keep my section headings succinct and any references in the existing format. Thanks for tidying up the page. ChiBeta (talk) 07:00, 30 January 2017 (UTC)

Reference errors on 7 February
Hello, I'm ReferenceBot. I have automatically detected that an edit performed by you may have introduced errors in referencing. as follows: Please check this page and fix the errors highlighted. If you think this is a false positive, you can [//en.wikipedia.org/w/index.php?action=edit&preload=User:A930913/RBpreload&editintro=User:A930913/RBeditintro&minor=&title=User_talk:A930913&preloadtitle=ReferenceBot%20–%20&section=new report it to my operator]. Thanks, ReferenceBot (talk) 00:24, 8 February 2017 (UTC)
 * On the Time perception page, [//en.wikipedia.org/w/index.php?diff=764168767 your edit] caused a redundant parameter error (help) . ([ Fix] | [//en.wikipedia.org/w/index.php?title=Wikipedia:Help_desk&action=edit&section=new&preload=User:ReferenceBot/helpform&preloadtitle=Referencing%20errors%20on%20%5B%5BSpecial%3ADiff%2F764168767%7CTime perception%5D%5D Ask for help])

Melanocortin 1 receptor
Hi! We are going to meet again! Please keep an eye on me: I'm near to starting significant additions to the article. It turns out to be involved in a lot more than red hair! DennisPietras (talk) 20:19, 7 February 2017 (UTC)
 * Removing redundant URL's...That's all???? Either you are getting soft, or I'm improving! This has given me the courage to ask if you'd please look at Polysome Profiling to see if there are any problems. DennisPietras (talk) 02:27, 9 February 2017 (UTC)

Reflist columns
Hi Boghog. I saw your edit about the references column width at the GMO food controversies page. The reason that I had reduced the column width is that, on my approx. 18-inch display, the references display as a single, very long column, and the column only goes part way across the screen. My intention was to make it more likely to show two columns instead of one. With such a very long reference list, I feel like having a single column is undesirable. Oddly, the standard 30em setting always displays as two columns for me, except at that one page. I suppose one approach would be to simply omit the column width and make a single screen-wide column for all reader displays, but as I said, I'd rather have two columns. Given that two columns apparently only display for that page on large desktop screens, I wonder if there could be an alternative solution, so I'm asking you about it. --Tryptofish (talk) 18:10, 14 February 2017 (UTC)


 * Hi Tryptofish. I initially suspected that there was something strange with Genetically modified food controversies. I have done some experimenting with mobile view, and I find that other pages that also use only display in one column. This was not previously the case.  Has something changed with the Wikipedia rendering engine?  I am stumped. Boghog (talk) 18:44, 14 February 2017 (UTC)


 * I just did some looking around, and for my display, all the other 30em pages are displaying two columns as they usually do for me. I would have thought from that, that it's specific to that page, but you seem to be finding it now on other pages. So that at least is a difference between your display and mine. I don't know. I guess another possibility is a change in browser software (I use Firefox). The GMO page does have that "refs=" parameter, and I wonder if that interferes with the columns parameter. Beyond that, I'm baffled. I could ask at Village Pump Technical, if you think it's a good idea. --Tryptofish (talk) 18:56, 14 February 2017 (UTC)
 * I just tried removing the defined refs, so it was simply with no other parameters, but it still showed up as a single column for me. --Tryptofish (talk) 19:02, 14 February 2017 (UTC)

With great thanks to, the solution (at least for that page) was a simple matter of putting the "clear" template at the end of the section just before the references. Apparently, the "see also" section was bleeding an override of the column width into the references section, because there was a portal link alongside the see also. --Tryptofish (talk) 19:37, 14 February 2017 (UTC)
 * It's just me, your friendly neighborhood gnome. HTH. – Jonesey95 (talk) 19:48, 14 February 2017 (UTC)
 * Ah, OK. Thanks Tryptofish for your #persist(ance) and Jonesey95 for your #solution.  Learn something new everyday :-) Boghog (talk) 20:16, 14 February 2017 (UTC)

Note of thanks
Hi. I just wanted to thank you for your input on the interactive gene structure diagrams. I put you in the acknowledgements in the recent WikiJournal article (here)! T.Shafee(Evo &#38; Evo)talk 10:09, 25 January 2017 (UTC)

Me too. Thanks for some help on nomenclature and organic chem over the past few weeks. --Smokefoot (talk) 19:46, 23 February 2017 (UTC)

Template
You know how to fix this warning:

"Warning: Page using Template:Infobox medical condition with unknown parameter "complications" (this message is shown only in preview)."

You get it when you hit "previous" on articles like this.

Appears to be a faulty warning. Doc James (talk · contribs · email) 15:43, 30 April 2017 (UTC)


 * These templates have become a lot more complicated with wiki data and invoke Lua subroutines. Taking a quick look at the template, it is not at all clear to me where complications is defined.  On one hand, it is rendering a link and on the other, it is throwing an error message. It makes no sense to me.  I am still looking at it to see if I can figure out what is going on.  Boghog (talk) 15:59, 30 April 2017 (UTC)
 * This is over my head. I noticed that you have contributed to this template.  Can you figure out what is going wrong? Boghog (talk) 16:30, 30 April 2017 (UTC)
 * complications was already defined in the template. It needed to be added to the list of "known" parameters in the unknown parameter check at the bottom of the template. I have done that. – Jonesey95 (talk) 18:26, 30 April 2017 (UTC)
 * Thanks for fixing this! Boghog (talk) 18:27, 30 April 2017 (UTC)
 * Looking at it again, it was already fixed, but the parameters were not alphabetized (which is useful only for editors' convenience, not for technical reasons). I have alphabetized the parameters and ensured that what appears to be the canonical version of each parameter name is present in the "check list". I don't know why there are so many capitalized/uncapitalized/misspelled versions of parameters permitted, but I will leave that for other editors to discuss on the template's talk page. – Jonesey95 (talk) 18:39, 30 April 2017 (UTC)
 * Perfect. Thank you both. Doc James  (talk · contribs · email) 19:37, 30 April 2017 (UTC)

Thank you for being one of Wikipedia's top medical contributors!

 * please help translate this message into your local language via meta

Thanks again :-) --  Doc James  along with the rest of the team at Wiki Project Med Foundation 18:08, 3 May 2017 (UTC)

Rating of pages on sodium channel genes
Dear Boghog,

I edited ENaC subunit gene entries on pages SCNN1A, SCNN1B, SCNN1G, and SCNN1D. These pages are currently marked as stubs. I would greatly appreciate if you could review them and rate them, as I would like to remove the stub marking.

Thanks, Genewiki1 (talk) 04:31, 18 May 2017 (UTC)


 * Hi Genewiki1. Great job in expanding these articles! They are reasonably complete and clearly are no longer stubs, so I have promoted them to class B.  Cheers. Boghog (talk) 04:48, 18 May 2017 (UTC)

Thank you very much. You are amazing in the quality and promptness of your replies! Genewiki1 (talk) 04:53, 18 May 2017 (UTC)

HMB FAC 4
Hey Boghog. I've been a little preoccupied with off-wiki matters for the past few weeks, although things have slowed down. I intend to create the 4th HMB FAC soon, so I figured I'd just give you a heads up about that.  Seppi  333  (Insert 2¢) 22:01, 24 March 2017 (UTC)


 * Thanks for the heads up. It might make sense to planned review to publish first.  This would answer some of the concerns from previous FAC reviews. Boghog (talk) 13:11, 25 March 2017 (UTC)
 * Fair enough - I can wait for that. I've renominated it for GA again in the meantime.  Seppi  333  (Insert 2¢) 04:42, 27 March 2017 (UTC)
 * Hey Boghog. I've been a little bit out of the loop on Wikipedia because I recently moved from Potomac/Bethesda, MD to Los Angeles, CA at the end of April.  Anyway, the listed anticipated completion date of the systematic review that you noted was roughly 7–8 months ago.  I noticed that the corresponding author's email address is listed on that page (gupimentel@yahoo.com.br); if you still think we should wait for publication before pursuing the next round at FAC, I can send him an email to inquire about the progress of the review and get an updated estimate on the completion date.
 * I think it's probably worth going through the lengthy wait for someone to take on the GA nomination review before pursuing another round at FAC anyway though.  Seppi  333  (Insert 2¢) 21:47, 14 May 2017 (UTC)
 * That is quite a switch from east to west coasts. I spent a few years in California and throughly enjoyed it.  I hope you like it as well.  It wouldn't hurt to first e-mail the authors of the review to ask them what their time line is and then make a decision of whether to wait or to go ahead with the FAC. Boghog (talk) 05:54, 15 May 2017 (UTC)
 * Alright, I'll send them an email and ask about it. LA seems nice enough; it's quite a bit different compared to the DC suburbs in Maryland though, hehe.   Seppi  333  (Insert 2¢) 21:35, 17 May 2017 (UTC)
 * Their paper is currently being peer-reviewed.  Seppi  333  (Insert 2¢) 16:00, 18 May 2017 (UTC)

Transactivation domain
What importance rating should this be assigned w.r.t. the WP:MCB project's banner?  Seppi  333  (Insert 2¢) 19:14, 18 May 2017 (UTC)

Lots of students
Hey, the following was originally flagged on WP:Chem but it's more biochem that we're used to. I'm not really sure which bio-wikiprojects are and aren't active (or appropriate) so I thought I'd bring it to you. Wiki_Ed/Hunter_College/Chemistry_378_(Spring_2017) - there are nearly 100 students in it and they've been assigned some very large and well established pages to edit (i.e. DNA, Glycolysis, Chromatography etc). I imagine their activities will be of interest to many. --Project Osprey (talk) 14:42, 22 May 2017 (UTC)

YIPF3
Bit of a surprise to see someone else editing in the quiet backwater of gene stubs. I had a moment of "What?" wondering whatever happened to the underlinked & orphan tags I'd planned to remove after adding the ref. BlackcurrantTea (talk) 20:01, 30 May 2017 (UTC)

Facto Post – Issue 1 – 14 June 2017
MediaWiki message delivery (talk) 09:33, 14 June 2017 (UTC)

Amphetamine figure
Dear Boghog,

Im new to this so not sure if this is the usual way of reaching out. Anyway I found a mistake (same mistake as found in the literature often) in he image File:Amphetamine Friedel-Crafts alkylation.svg [x]

If you look up the reference you cite (202) there you will find the in the end product the Cl on the phenyl ring is still present. One should start from benzene to generate the final product shown in the image.

I hope you appreciate this contribution to make wikipedia a bit better again.

Best wishes

Sander — Preceding unsigned comment added by Solden21 (talk • contribs) 15:31, 21 June 2017 (UTC)


 * – That was certainly embarrassing. I have fixed the error. Thanks for pointing it out. Cheers. Boghog (talk) 16:46, 21 June 2017 (UTC)

Neurobiological effects of physical exercise
Hey Boghog. Is this an article that you'd be interested in working on? There's a fair amount of molecular neurobiology that needs to be covered in more detail, particularly in relation to BBB-permeable neurotrophic myokines (BDNF, VEGF, and IGF-1), a BBB-permeable class I HDAC inhibitor secreted by the liver during endurance exercise (β-hydroxybutyric acid), cortisol (which is BBB-permeable), and non-BBB-permeable neurotransmitters/neuromodulators such as serotonin, dopamine, norepinephrine, epinephrine, acetylcholine, glutamate, GABA, endogenous opioids (particularly β-endorphin), and endocannabinoids (particularly anandamide) that are secreted into peripheral blood plasma or released from CNS neurons during aerobic exercise; this review from March 2017 covers all of these biomolecules.

I figured I'd ask since you since you've been pretty helpful with previous articles and I'm interested in pushing this article through FAC after I get β-hydroxy β-methylbutyric acid promoted to FA status. I've also asked at WT:NEURO for help, but I'm not sure if anyone there is interested in working on this article/topic.  Seppi  333  (Insert 2¢) 06:29, 25 June 2017 (UTC)

Nomination for deletion of Template:PDBsum
Template:PDBsum has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Frietjes (talk) 17:22, 28 July 2017 (UTC)

Facto Post – Issue 3 – 11 August 2017
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 * Facto Post – Issue 3 – 11 August 2017

 

Wikimania report
Interviewed by Facto Post at the hackathon, Lydia Pintscher of Wikidata said that the most significant recent development is that Wikidata now accounts for one third of Wikimedia edits. And the essential growth of human editing. Impressive development work on Internet-in-a-Box featured in the WikiMedFoundation annual conference on Thursday. Hardware is Raspberry Pi, running Linux and the Kiwix browser. It can operate as a wifi hotspot and support a local intranet in parts of the world lacking phone signal. The medical use case is for those delivering care, who have smartphones but have to function in clinics in just such areas with few reference resources. Wikipedia medical content can be served to their phones, and power supplied by standard lithium battery packages.

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

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

Link

 * Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.

Editor. Please leave feedback for him. 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:Opted-out of message delivery to your user talk page. Newsletter delivered by MediaWiki message delivery MediaWiki message delivery (talk) 10:55, 12 August 2017 (UTC)
 * }

Comment
Hi Boghog have tried to move page Pulmonary surfactant-associated protein B to its original name of Surfactant protein B to be in line with other entries - Surfactant protein A, C and D - on requested moves page it says that the page does not exist - any thoughts - cheers --Iztwoz (talk) 13:44, 25 August 2017 (UTC)


 * Hi Iztwoz. Tough call.  The former is the official HUGO gene name while the later is the recommended UniProt protein name.  Since the former is shorter and is consistent with the current Wikipedia article tiles for other members of the family, I would support renaming as you suggest.  Cheers. Boghog (talk) 18:01, 25 August 2017 (UTC)

Folliculin
Hi, You removed Additional Reading from the Folliculin page, but your explanation was not clear to me. Please explain why? Should we not add additional reading references?? Thanks, Wed1970 (talk) 18:40, 11 September 2017 (UTC)


 * Thanks for your message. In answer to your question, I removed the Baba, et al. citation because it was already included as an in-line reference (link).  There is no need to include the same reference in both the reference and further reading sections. Boghog (talk) 19:46, 11 September 2017 (UTC)

Hi Boghog, Thanks for the explanation-I get it now! SO I can add some additional reading to the Folliculin page as planned. Great! Wed1970 (talk) 16:29, 12 September 2017 (UTC)

additional reading
Hi Boghog, I would like to add several references under additional reading but when I cited 2 new references they wound up under external links. Can you tell me how to correct that? I would like to add another reading or two as well. Thanks Wed1970 (talk) 21:23, 12 September 2017 (UTC)


 * Hi . Short answer: drop the tags (see WP:CITEFOOT). Also where ever possible, please use secondary sources (see WP:SCIRS and WP:MEDRS). We should be citing review articles, not writing them. Boghog (talk) 05:12, 13 September 2017 (UTC)

Hi Boghog, Thanks for fixing the references under Additional Reading. I am editing the FLCN page as part of the GENE_Wiki collaborative effort to update the FLCN Wiki page while simultaneously submitting a FLCN review to the GENE Journal. I thought the purpose was to produce more detailed scientific entries so that was why I included so much primary source detail. There is no review currently available about FLCN function so a secondary source is lacking. Our FLCN review in Gene will correct that! Wed1970 (talk) 16:36, 14 September 2017 (UTC)

Facto Post – Issue 4 – 18 September 2017
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 * Facto Post – Issue 4 – 18 September 2017

 

Editorial: Conservation data
The IUCN Red List update of 14 September led with a threat to North American ash trees. The International Union for Conservation of Nature produces authoritative species listings that are peer-reviewed. Examples used as metonyms for loss of species and biodiversity, and |theoretical discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters. Clearly, conservation work depends on decisions about what should be done, and where. While animals, particularly mammals, are photogenic, species numbers run into millions. Plant species lie at the base of typical land-based food chains, and vegetation is key to the habitats of most animals.

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

Links

 * What Makes a Good Collaborative Knowledge Graph: Group Composition and Quality in Wikidata (paywall)
 * Wikimedia and the free knowledge ecosystem by Maria Cruz
 * Another Year Again: 2017 this time (long), blog by Joe Wass of CrossRef
 * Attack of the 50 Foot Blockchain, blog by User:David Gerard
 * WikiTribune in beta

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 * }

reference error
Hey Boghog, could you take a look at Importin the reference error seems to be due to the two info box templates containing the same reference names I guess. Cheers.CV9933 (talk) 19:06, 8 October 2017 (UTC)
 * Hi CV9933. Thanks for the head up. You are absolutely correct.  The problem is that we have two different gene infoboxes in the same article.  We already have separate KPNA1 and KPNB1 articles that contain the infoboxes. I will replace the two gene infoboxes Importin  with the more compact protein infoboxes. Boghog (talk) 19:44, 8 October 2017 (UTC)

Butyrate-CoA ligase (XM-ligase)
Hey Boghog. Am I correct in thinking that XM-ligase (, ExPASy entry, BRENDA entry) is a family of enzymes that, in humans, comprises the gene products of ACSM1, ACSM2A , ACSM2B, ACSM3, ACSM4 , ACSM5 , and ACSM6 ?

I'm asking because I read a review about glycine conjugation that refers to these in the first step of xenobiotic glycine conjugation (full text at ); I'm working on editing the table where glycine conjugation redirects, intend to update the XM-ligase article accordingly, and intend to replace the BRENDA references in template:amphetamine pharmacokinetics with that review.  Seppi  333  (Insert 2¢) 22:33, 8 October 2017 (UTC)


 * Hey . Sorry for not responding sooner, but I have been busy in real life. Best place to look for Enzyme ↔ Gene mapping is ExPASy.  For XM-ligase, the cross-references may be found here which lists ACSM1_HUMAN to ACSM7_HUMAN. Boghog (talk) 19:56, 12 October 2017 (UTC)


 * Alright, thanks for the feedback! I'll expand the XM-ligase page with that information.  Seppi  333  (Insert 2¢) 03:28, 13 October 2017 (UTC)

Facto Post – Issue 5 – 17 October 2017
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 * Facto Post – Issue 5 – 17 October 2017

 

Editorial: Annotations
Annotation is nothing new. The glossators of medieval Europe annotated between the lines, or in the margins of legal manuscripts of texts going back to Roman times, and created a new discipline. In the form of web annotation, the idea is back, with texts being marked up inline, or with a stand-off system. Where could it lead? ContentMine operates in the field of text and data mining (TDM), where annotation, simply put, can add value to mined text. It now sees annotation as a possible advance in semi-automation, the use of human judgement assisted by bot editing, which now plays a large part in Wikidata tools. While a human judgement call of yes/no, on the addition of a statement to Wikidata, is usually taken as decisive, it need not be. The human assent may be passed into an annotation system, and stored: this idea is standard on Wikisource, for example, where text is considered "validated" only when two different accounts have stated that the proof-reading is correct. A typical application would be to require more than one person to agree that what is said in the reference translates correctly into the formal Wikidata statement. Rejections are also potentially useful to record, for machine learning.

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

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

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

Links

 * Jon Udell, blogpost Annotating to extract findings from scientific papers, 15 December 2015
 * TDM and Libraries, Virginia Tech report
 * Magnus Manske, The Whelming: Scaling up Wikidata editing
 * OCLC and Internet Archive collaborate to expand library access to digital collections, metadata and linking exchange
 * GLOW week in November: Wikidata workshops on politician info

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Thanks!
Thank you for picking up and improving my edit. It is appreciated! Pat V patvlegal@juno.com — Preceding unsigned comment added by Patvlaw (talk • contribs) 16:28, 2 November 2017 (UTC)

Help needed
Could you please look at MPST and 3-mercaptopyruvate sulfurtransferase? Are these enzymes the same thing? If so, I will take a stab at merging them. One part that I do not understand, the articles have very different looking databoxes. Thank you, --Smokefoot (talk) 17:13, 8 November 2017 (UTC)
 * Thanks for spotting this. Yes, the two are the same. Best place to look for Enzyme ↔ Gene mapping is ExPASy.  For 3-mercaptopyruvate sulfurtransferase, the cross-references may be found here which lists a single human paralog, THTM_HUMAN.  If there were more than one paralog, in my opinion, the articles should be kept separate.  But in this case, there is a one to one mapping of enzyme and human gene, so it is reasonable to merge the two. Cheers. Boghog (talk) 20:53, 8 November 2017 (UTC)
 * No good deed goes unpunished... I needed to create something on hydroperoxide lyases.  If you get some time, could you give that article a glance through your biochemical lenses?  --Smokefoot (talk) 18:21, 10 November 2017 (UTC)
 * Thanks for creating the article. I have added an enyzme infobox, but because the enzyme is incompletely classified, not all the links work. I don't think there is too much more I can add.  Boghog (talk) 21:53, 10 November 2017 (UTC)
 * Great help. These enzymes are part of the machinery of scent-making in wounded plants.  --Smokefoot (talk) 23:16, 10 November 2017 (UTC)

Facto Post – Issue 6 – 15 November 2017
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 * Facto Post – Issue 6 – 15 November 2017

 

WikidataCon Berlin 28–9 October 2017
Under the heading rerum causas cognescere, the first ever Wikidata conference got under way in the Tagesspiegel building with two keynotes, One was on YAGO, about how a knowledge base conceived ten years ago if you assume automatic compilation from Wikipedia. The other was from manager Lydia Pintscher, on the "state of the data". Interesting rumours flourished: the mix'n'match tool and its 600+ datasets, mostly in digital humanities, to be taken off the hands of its author Magnus Manske by the WMF; a Wikibase incubator site is on its way. Announcements came in talks: structured data on Wikimedia Commons is scheduled to make substantive progress by 2019. The lexeme development on Wikidata is now not expected to make the Wiktionary sites redundant, but may facilitate automated compilation of dictionaries. And so it went, with five strands of talks and workshops, through to 11 pm on Saturday. Wikidata applies to GLAM work via metadata. It may be used in education, raises issues such as author disambiguation, and lends itself to different types of graphical display and reuse. Many millions of SPARQL queries are run on the site every day. Over the summer a large open science bibliography has come into existence there.

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

Links

 * Wikidata statistics
 * I4OC progress in its first year, with 47% of scientific citation data now open (announced two days ago)
 * The flowering ORCID, Magnus Manske blogpost on identifying authors of scientific papers
 * @querybook, a Twitter feed devoted to SPARQL queries
 * Massive progress on Wikidata coverage of the UK parliament
 * Reminder: WikiFactMine pages on Wikidata are at WD:WFM

Editor. Please leave feedback for him. 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, 15 November 2017 (UTC)
 * }

LFA-1
Hi Boghog,

Could you explain me why you deleted my cit. from LFA-1 related pages?

Best regards, Pulprik


 * Hi Pulprik. Adding the same citation to a large number of articles is suspicious because it often is a result of a conflict of interest (i.e., promoting a citation to which the contributor has a direct connection). Another concern is that the citation in question is primary and per WP:PSTS, should only be used with care:
 * More appropriate secondary sources (review articles) are often available. For example to support the statement that Efalizumab binds to CD11a,  would all be better sources.  I won't revert the addition of this citation if you are a bit more selective where you place it.  Thanks. Boghog (talk) 10:34, 30 November 2017 (UTC)
 * More appropriate secondary sources (review articles) are often available. For example to support the statement that Efalizumab binds to CD11a,  would all be better sources.  I won't revert the addition of this citation if you are a bit more selective where you place it.  Thanks. Boghog (talk) 10:34, 30 November 2017 (UTC)

Help!
Hello, I saw that you had corrected my citations on the MUTYH page, I just added new information and I don't know how to cite the sources the way you did, I'll keep trying, but if I fail to do so, do you mind helping me out again? Thank you! Jonyullo2015 (talk)
 * Hi. Thanks for your message.  I created the citations using the Wikipedia template filling tool (instructions). Given a PMID or PMCID, one can quickly create a fully formatted citation that can be copied and pasted into a Wikipedia article.  Cheers. Boghog (talk) 20:04, 1 December 2017 (UTC)

Facto Post – Issue 7 – 15 December 2017
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 * Facto Post – Issue 7 – 15 December 2017

 

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

Behind this achievement are a technical advance (fatameh), and bots that do the lifting. Much more than dry migration of metadata is potentially involved, however. If paper A cites paper B, both papers having an item, a link can be created on Wikidata, and the information presented to both human readers, and machines. This cross-linking is one of the most significant aspects of the scientific literature, and now a long-sought open version is rapidly being built up. The effort for the lifting of copyright restrictions on citation data of this kind has had real momentum behind it during 2017. WikiCite and the I4OC have been pushing hard, with the result that on CrossRef over 50% of the citation data is open. Now the holdout publishers are being lobbied to release rights on citations.

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

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

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



Links
To subscribe to Facto Post go to Facto Post mailing list. For the ways to unsubscribe, see below. Editor, 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) 14:54, 15 December 2017 (UTC)
 * WikidataCon: Giving more people more access to more knowledge, report by Peter Kraker of Open Knowledge Maps
 * This is a story of my knowledge adventure in New Zealand moths via Wikicommons, Wikipedia and Wikidata, @SiobhanLeachman
 * Wikidata and Arabic dialects, research paper, DOI: 10.1109/AICCSA.2017.115
 * c:Commons:British Library/Mechanical Curator collection/georeferencing status, Mechanical Curator project on Commons hits 50K maps milestone
 * Historical dataset on the provenance of Wikipedia text: Who wrote this?, by Tilman Bayer, WMF blogpost
 * "Anyone can edit", not everyone does: Wikipedia and the gender gap (PDF), journal paper, Heather Ford and Judy Wajcman
 * Alpha Zero’s "Alien" Chess Shows the Power, and the Peculiarity, of AI, MIT Technology Review, by Will Knight, December 8, 2017
 * }

Error in Metacycline edit by BogBot
Hi,

There was an error in this edit by BogBot:

https://en.wikipedia.org/w/index.php?title=Metacycline&type=revision&diff=447816017&oldid=443324384

As this: https://medlineplus.gov/druginfo/meds/a682778.html

is for Ferrous Sulfate, not Metacycline. I've removed this entry from the page as Metacycline has no medline plus entry:

https://en.wikipedia.org/w/index.php?title=Metacycline&type=revision&diff=816293357&oldid=798266218

- No identd (talk) 13:04, 20 December 2017 (UTC)

Shocked and astounded
I am not sure why your talk page is not overrun with barnstars because I find your editing history overwhelming. If Wikipedia were a cruise, you would be sitting at the captain's table every single night. EIGHT THOUSAND articles you've created???? ...on topics I can't even begin to understand? Thank you, thank you, thank you. Can I do an interview with you for the Signpost? (the Wikipedia editor newsletter-covering-topics-of-interest-to-editors? Best Regards, Barbara (WVS) ✐ ✉ and Merry Christmas 13:39, 21 December 2017 (UTC)
 * Hi, thanks. However I should point out that many of the articles I created were bot assisted through the auspices of the Gene Wiki project.  I think the guy you really want to interview is  who initiated the Gene Wiki project. My interests broadly span chemistry, pharmacology, and molecular biology.  was an early and prolific contributor to WP:MCB (see Signpost interview), but sadly that project has slowly withered over the years. Several of the remaining editors including myself were previously interviewed by the Signpost.
 * Even though professionals are discouraged from using Wikipedia as a source of information, I think Wikipedia through the hard work of many editors has become a useful initial resource for professionals working in drug discovery and allied fields. As evidence, I point to Derek Lowe (chemist) who writes a blog published by Science Magazine who routinely links to Wikipedia drug and Gene Wiki articles.  Another sign that the scientific community thinks Wikipedia is an important resource is that many of the external scientific databases provide reciprocal links back to Wikipedia.
 * This technical use of Wikipedia sometimes results in a conflict with Wikipedia's broader mission of writing articles that can be written and understood by anyone. But we try to make at least the lead sentence broadly accessible. One of the most contentious issues is trying to find the right balance between making an article broadly accessible while providing enough technical detail to make it of interest to a professional. Another conflict that sometimes arises is the quality of the sources. I initially thought that WP:MEDRS was overly strict, especially when applied to basic biomedical research, but the reproducibility crisis has increased my appreciation of secondary sources.
 * I am more of Wiki Gnome that avoids attracting too much attention to myself. However if you think my rambling thoughts above provides a seed for an interview, I would consider it. Cheers. Boghog (talk) 20:48, 21 December 2017 (UTC)
 * Hi Barbara, while yes, many of Boghog's edits fall loosely under the umbrella of the Gene Wiki project, that in no way should diminish your "shock and astonishment" (and interest!) in the work that he has done. To continue the Wikipedia-as-a-cruise analogy, the Gene Wiki is like an art studio on that ship where we provide some space, some paint, and a few paintbrushes. Boghog is the artist that is converting those raw materials into something beautiful and useful. That he has done this at such a high level over such a long time while also being a great Wikipedia community member is amazing. I would love to read a profile of Boghog's work in the Signpost!  Best, Andrew Su (talk) 22:05, 21 December 2017 (UTC)
 * WP:MCB may be less active than it was several years ago, but definitely not an inactive WikiProject. In any event, I agree with Barbara about your contribution history. Being in the top 1000 in List of Wikipedians by number of edits is quite an accomplishment for content contributors.  Seppi  333  (Insert 2¢) 22:07, 21 December 2017 (UTC)

Merry X-mas
Doc James (talk · contribs · email) 00:56, 24 December 2017 (UTC)


 * Thanks and I wish you a happy holidays and a prosperous New Year. Boghog (talk) 13:41, 25 December 2017 (UTC)