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question for experienced editor

Resolved

Hello everyone. Protein O-GlcNAc transferase has an infobox with a diagram that seems, from the infobox, to illustrate the stucture of O-GlcNAc transferase. In fact, if you look at the file description (which does not appear in the infobox) the image is of only one of a repeating unit that is only part of O-GlcNAc transferase and not even its active site. I'm a newbie, but I think that including the image in the infobox, which implies to the reader that it is the structure of the protein, is disinformation. The best figure for the struture of the entire molecule comes from this figure (from this review, but those images are not OK for The Commons, if I understand correctly. Is anybody else bothered by this "disinformation"? If so, what should be done? Thank you. JeanOhm (talk) 19:56, 9 May 2017 (UTC)

Hi JeanOhm, I agree that the image is misleading. As described at Wikipedia:Disinfoboxes, sometimes problems can arise when contributors force things into infobox fields when they don't quite fit. In this case, I think the easiest solution would be to add a  | caption =  field to the infobox (which {{infobox enzyme}} supports), and state exactly what the image depicts. Adrian J. Hunter(talk•contribs) 11:23, 10 May 2017 (UTC)
@Adrian J. Hunter: Thank you. Done. JeanOhm (talk) 01:55, 11 May 2017 (UTC)

incredibly easy citation tool

Hello everyone. I want to inform everyone who may not know about the tool at http://tools.wmflabs.org/citation-template-filling/cgi-bin/index.cgi?ddb=&type=pubmed_id&id=&add_param_space=1&add_ref_tag=1&full_journal_title=1

It makes adding references incredibly easy. Maybe everybody knows about this, but as a newbie,I was stunned. From the page "Enter a DrugBank ID, HGNC ID, ISBN, PubMed ID, PubMed Central ID, PubChem ID, or URL and press submit to fill out an appropriate template that can be pasted into a Wikipedia article". Thanks to Boghog for pointing this out to me! JeanOhm (talk) 19:40, 11 May 2017 (UTC)

Nice! An equivalent for doi references is this link. They can be pretty useful if VisualEditor's reference function isn't available. T.Shafee(Evo&Evo)talk 23:36, 11 May 2017 (UTC)

Elizabeth Cavert Miller and James A. Miller - one article or two?

I was thinking of writing WP entries for Elizabeth Cavert Miller and James A. Miller, two married biochemists who conducted research on carcinogens at UW-Madison. I don't think I have ever written a single article about a couple before, so I thought I might get some more advice before I charged ahead with this. I'm not a biochemist and I would be creating this entry just based on the info I can find in reliable sources.

Several things make me think that a joint article might be the right approach. They conducted research as a team, were elected to the NAS in the same year, and share a joint NAS Biographical Memoir; the memoir states it was their desire to share one. I do notice that the German WP has separate pages for them (here and here) and that both look like Start-class articles. Does anyone have an opinion? EricEnfermero (Talk) 21:39, 26 March 2017 (UTC)

Given the joint nature of their work, a single article seems appropriate. I note there is a lot of overlap between the two German WP pages. ChiBeta (talk) 02:22, 31 March 2017 (UTC)
As per ChiBeta, if their work is largely as a team, I suspect a single page would make more sense. If might however be a good idea to create redirect pages on their seperate names since people will search for them. Leopardtail (talk) 13:38, 13 May 2017 (UTC)

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Transactivation domain

What importance rating should this article be assigned with respect to our project's talk page banner (i.e., on Talk:Transactivation domain)? Transcription factor is rated high importance, so I'm guessing this should either be low or medium, but I'm not sure which. Seppi333 (Insert 2¢) 03:22, 26 May 2017 (UTC)

I think a low importance rating for this very specialized topic is appropriate. Boghog (talk) 05:26, 26 May 2017 (UTC)
Alright, I've rated it as you've suggested. Seppi333 (Insert 2¢) 05:34, 26 May 2017 (UTC)

Request for comments to determine consensus regarding external cell bio image usage.

Hello everyone. Please don't sit this one out. I/we are fortunate to have many great images available to help explain/illustrate aspects of cell biology that are in "open" publications, either initially or after a 6 or 12 month wait. However, many of these are licensed NC, and so are not appropriate for uploading to the commons. It is possible to construct prose in a wp article that allow readers, with one simple click, to view those images. Here's an example:

  • The GRASP65 protein crystal struture has been determined. It can form a hexameric superhelix, with a small portion of the C-terminal end of Golgi Matrix Protein GM130 bound to each GRASP65 subunit, as shown in this figureref#

I can cite wp policy guidelines that allow that sort of external link in the prose of an article. Other editors cite wp policy against it. Since wp policy is decided by the community, not individual editors, and since the wp policy (whatever it really is) was agreed upon before the proliferation of open publications, I hope that all of you will write an opinion about the use of external links as I described above. Perhaps it is important to note that this sort of external link in prose would not be used to replace citations, nor would it be used to link to uncited work. It is simply a way to give readers who want to the option of viewing an external supplement without needing to search for it. So, I am going to start this survey of opinions.

Strong support. BTW, the relevant policy I read is at the restrictions on linking guideline which states, in bold, in the lead section, that "These external-link guidelines do not apply to citations to reliable sources within the body of the article." JeanOhm (talk) 02:21, 24 May 2017 (UTC)

  • There are no guidelines that promote/allow external links in prose. Repeating what I previously wrote:
  • WP:EL which states These external-link guidelines do not apply to citations to reliable sources within the body of the article in turn refers to WP:CITE which states that inline citations should appear as footnotes using <ref>...</ref> markup so that the citations appear in a "References" section at the end of the article. As a consequence, any external link contained in a citation is displayed in the "References" section and not in the prose. WP:CITE further states Embedded links should never be used to place external links in the content of an article. Also per WP:LINKDD: Don't put external links in article prose.
  • If a graphic is critical to understanding a subject, then a graphic with a compatible license should be displayed directly in the article. Forcing the reader to switch back and forth between external sources and Wikipedia is not good style.
  • Concerning the figure that you want to link to, I have already created a figure of the monomer (File:PDB 4REY.png). Using PyMOL, I should be able to create a picture of the superhelix with a compatible license that I will upload to commons hence completely removing the need to link to the external figure. I don't have time right now to finish this, but I should have time over this weekend. Boghog (talk) 03:19, 24 May 2017 (UTC)
First installment of helix: File:4REY side helix.png Boghog (talk) 19:04, 24 May 2017 (UTC)  Done Boghog (talk) 07:12, 25 May 2017 (UTC) :

Overall, I'm not a fan of external links in the main text. External images/text can't be edited, improved or integrated with other Wikipedia content, and external links often contains extraneous detail that's not what's trying to be shown in the Wikipedia article. There are a few alternatives that are better:

  • For specific extra information, a normal citation is fine
  • For general useful info, the External links section can include subheadings for videos, links, interactive tutorials etc.
  • For figures from non creative commons sources there are a few options of different efforts
    1. Email the author to ask for a version (I've had a 100% hit rate on this, since they often have a version they use for presentations)
    2. Make a copy (This is the most labour intensive, and may not yield as good results unless you're handy with the relevant programs)
    3. Use the {{External_media}} template (sparingly).

I definitely see how you've tried to use dois to free-read papers to mitigate risks of external links e.g. links breaking when websites reorganise their urls (e.g. journals), links to content that can change over time (e.g. faculty websites). However, overall, I think the benefits of alternative methods outweigh the costs. That said, all solutions have a time requirement, so I absolutely don't want to discourage you from editing. T.Shafee(Evo&Evo)talk 00:22, 25 May 2017 (UTC)

@Evolution and evolvability: Thomas, I don't understand what you wrote. "Make a copy (This is the most labour intensive, and may not yield as good results unless you're handy with the relevant programs)". It would be easy for me to copy an image, convert it to grey-scale and lower resolution, put it on the commons, insert it into an article as a thumb, and have a caption describing it, with a superscripted reference and an EL to the original image in the caption. That to my mind would be the equivalent of the EL in the external media template, with more info about what the EL actually is. However, in an answer to a different question I asked at some help desk or other, I was told that copying and modifying a non-free image, even if not a single pixel is the same color, was still a violation of copyright. Was that bogus info?
Also, I am uncomfortable about asking authors for permissions for this basic reason: If an image is in a journal, it is not, if I understand it correctly, the authors who own the copyright, but rather the journal. Of course, as we both know, presenters show images of both their own copyrighted work and others' copyrighted work with a minimal credit in barely readable font at the bottom, post it on YouTube or elsewhere on the web, and nobody complains, but the wp requirements are so strict that I can't believe it is really acceptable for the commons. sigh. JeanOhm (talk) 05:39, 26 May 2017 (UTC)
@JeanOhm: Ah, yes, I was pretty ambiguous! When I saaid copy, I meant non-copyright violating recreation. For example, this image is a recreation of one from this paper. I emailed the authors of the paper, asking for the PDB file then made the image again myself. Similarly, I published a figure in this book, but I had a slightly different version that I'd previously made for presentations that I then uploaded as this image. Indeed, authors often have a dozen similar figures that never ended up being published that they might be interested in contributing. T.Shafee(Evo&Evo)talk 11:17, 28 May 2017 (UTC)
An advantage of {{External_media}} is that enthusiastic Wikipedians could search for WP:MCB-tagged articles that transclude that template, then find or create replacement images as they are able. Come to think of it, that template should support a |date= parameter that gets automatically populated by a bot, similar to {{citation needed}}, so that when the template has been in use for five years or whatever people would know to make a fresh search for free alternatives. Adrian J. Hunter(talk•contribs) 05:53, 26 May 2017 (UTC)

Orphan help: BLCAP

Hey all! Can anyone help de-orphan BLCAP? It appears there has been much more published on it since the article was generated (see for example here and here), but I can't figure out how to de-orphan it. Double-bonus points if someone can improve the article as well. It's a bit dated and could use some more readable prose. Thanks a bunch and happy editing! Ajpolino (talk) 04:04, 1 June 2017 (UTC)

PROD notification

Hey all! Just wanted to notify the project that I WP:PRODed Cellome. It's an OMICS term I hadn't encountered before and after poking around I don't think an article can be built on the topic. Happy to be proven wrong. As always, feel free to object to the PROD by removing the tag. Happy editing! Ajpolino (talk) 14:56, 6 June 2017 (UTC)

I support removing the article. JeanOhm (talk) 16:07, 6 June 2017 (UTC)

Please review Draft:Golgi matrix

Hello. @Robert McClenon: asked me to request a review of my terrific (I may be biased) new article Draft:Golgi matrix. BTW, I know that once it is moved to mainspace I should make a note at the top of Matrix (biology)#Golgi matrix. Thank you, JeanOhm (talk) 17:23, 1 June 2017 (UTC)

I've left what (I hope) are some useful comments. Overall, the content is good. There are a couple of stylistic and referencing points to fix, but should pass AfC when those are done. T.Shafee(Evo&Evo)talk 05:00, 2 June 2017 (UTC)
I've gone ahead and accepted it. The stylistic and reference issues can be dealt with in article space. It is better than most of the crud that gets into article space (although that doesn't say much). Robert McClenon (talk) 17:34, 6 June 2017 (UTC)

AfD notification

Sorry, me again. This time its an AfD of Chronic cellular dehydration, here. Thoughts and comments from interested parties would be appreciated. Thanks! Ajpolino (talk) 16:56, 7 June 2017 (UTC)

Facto Post – Issue 1 – 14 June 2017

Facto Post – Issue 1 – 14 June 2017
Editorial

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

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

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

Links
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MediaWiki message delivery (talk) 09:33, 14 June 2017 (UTC)

Assessment of class and importance

Hi. I recently started assessing unassessed articles tagged with WP:MCB. So far I have reduced the backlog from about 1.800 to 1.250. However, since I normally do most of my work on anatomy and medicine related articles I find it very hard to asses importance for MCB articles, so at the moment I am only assessing class and NOT importance. If anybody is interested in helping (so class and importance can be rated simultaneously) I can recommend the Rater gadget and unassessed articles for our project can be found here and if you only would like to rate by importance have a look here. Kind regards JakobSteenberg (talk) 14:53, 13 May 2017 (UTC)

@JakobSteenberg: I'll try to lend a hand this week. I should be able to do a couple of hundred. T.Shafee(Evo&Evo)talk 00:18, 15 May 2017 (UTC)
If anyone else would be happy to tackle a few of these, I'd gladly accept the help. I've got through a few hundred (of the ~2000 total). Most of them are low-importance stub/starts like enzymes and metabolites. Note: Enzymes don't need to be tagged for WP:CHEMS, but metabolites should. T.Shafee(Evo&Evo)talk 14:06, 16 June 2017 (UTC) (Gentle ping Boghog, Seppi333, Adrian J. Hunter, Jytdog, JeanOhm)

Transfer "Light-independent reactions" to another project?

Hello. I started a discussion at Talk:Light-independent reactions about transferring the whole article "Light-independent reactions" to a sister project, like either Wikiversity or Wikibooks. I realized that whoever would request an importation on the whole article should work on the article. Because I can't be the one working on it or requesting a transfer, I hope that someone else interested can go to v:Wikiversity:Import and/or b:Wikibooks:Requests for import and work on an imported copy at either Wikiversity or Wikibooks. Anyone interested? Thanks. --George Ho (talk) 16:46, 28 June 2017 (UTC)

brcaexchange.org

Do folks feel like brcaexchange.org is a valuable addition to the 3 BRCA articles? An IP keeps trying to force it into WP. I have been removing it, and also cleaned the ELs on those articles today as they had become all crufted over. Jytdog (talk) 19:36, 11 July 2017 (UTC)

I think it is probably appropriate for BRCA mutation as a database of variants. I don't really know the difference between that database and e.g. the universal mutation database or the brca database. For BRCA1 and BRCA2, I'd probably leave the cancer.gov link too. In general, I think that a long article can supprt 4-8 external links if they are distinct from one another (e.g. scientific database, patient information, etc). T.Shafee(Evo&Evo)talk 00:43, 12 July 2017 (UTC)

Tris

Could someone fix this part of the Tris page?

I can't tell what it's trying to say!

Thanks DemandAmbition (talk) 09:53, 21 July 2017 (UTC)

I've had a go. Hopefully the wording is a little clearer now. T.Shafee(Evo&Evo)talk 11:24, 21 July 2017 (UTC)

Vitamins - specifically B vitamins articles

Hi, please help! I came across Vitamin B3 which redirects to Vitamin B3 complex a barely started stub of a thing that doesn't reflect the depth of knowledge here on Wikipedia on such topics. Looking at the history of Vitamin B3 redirect it's unclear what the approach has been to creating articles about the human interest in essential micronutrients vs articles about chemical compounds which don't care about humans or metabolic pathways. Can someone help or advise where to start to sort this out? I'm not in this project or even a layperson in biochem so will message some of you individually too. Thanks so much. Donama (talk) 00:55, 11 August 2017 (UTC)

Btw you will see from my last edit on vitamin B3 complex what aroused my interest. When folks trying to find out more about whether they should take B3 because they're pregnant or thinking of it, they need to get better than that landing page! We do have an obligation to not be completely useless to non-experts! Donama (talk) 00:55, 11 August 2017 (UTC)

Facto Post – Issue 3 – 11 August 2017

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.

Internet-In-A-Box

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

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

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

  • Plaudit for the Medical Wikipedia app, content that is loaded into Internet-In-A-Box with other material, such as per-country documentation.
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MediaWiki message delivery (talk) 10:55, 12 August 2017 (UTC)

AfD Notification for ED1

Hello all, an AfD that may interest some group members is here. Comments would be appreciated. Happy editing! Ajpolino (talk) 00:01, 28 August 2017 (UTC)

Which infobox for merger?

From what I can see, the articles Porphobilinogen_synthase and Delta-aminolevulinic_acid_dehydratase should be merged. Since they use different infoboxes, does anyone know if there is any preference for which to include in the merged version? T.Shafee(Evo&Evo)talk 02:56, 17 September 2017 (UTC)

Photosynthesis equation correction

Somewhat ridiculously for such a core piece of biochemistry, an IP editor has just noted on Talk:Photosynthesis that the light and dark reaction equations may be incorrect as written. Currently, the Calvin Cycle net reaction is written as follows:

Current version =  3 CO2 + 9 ATP + 6 NADPH + 6 H+ → C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O (looks balanced, but water consumed by ATP hydrolysis not shown)

However hydrolysis/condensation of ATP consumes/produces H2O. I had a quick look in MBOC and Biochemistry. MBOC uses a vaguer version of the equation. Biochemistry uses an explicit version that looks very different to ours[1][2]

Vague version =  3 CO2 + 9 ATP + 6 NADPH + 6 H+ Water→ C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O (as found in MBOC 4; corrected 11:01, 18 September 2017 (UTC))
Explicit 6-Carbon =  6 CO2 + 18 ATP + 12 NADPH + 6 H+ 12 H2O → 2 C3H6O3-phosphate C6H12O6 + 18 ADP + 18 Pi + 12 NADP+ + 3 H2O 6 H+(as found in Biochemistry)

If you use the 3-carbon and include the water molecules consumed by hydrolysis, the eqn ends up looking unbalanced because of the water disappearing to become 'hidden' in ATP:

Explicit 3-Carbon =  3 CO2 + 9 ATP + 6 NADPH + 3 H+ 6 H2O → 2 C3H6O3-phosphate + 9 ADP + 8 Pi + 6 NADP+ + 3 H2O 3 H+ (water produced by ATP condensation now shown, but makes the eqn look weird)

Note that this is a net production of water, not consumption as in the original. Am I missing something obvious? Second opinions? If it does need to be changed, what do people reckon is the ideal solution? T.Shafee(Evo&Evo)talk 12:38, 17 September 2017 (UTC)

Elliot and Elliot's Biochemistry and Molecular Biology tends to be pretty meticulous about these things, and the 2nd ed (2001) gives a different equation again:
E&E 6-carbon =  6 CO2 + 18 ATP + 12 NADPH + 12 H+ + 12 H2O → C6H12O6 + 18 ADP + 18 Pi + 12 NADP+ + 6 H+
To me, that doesn't look balanced. Stoichiometrically, you need 18 water-equivalents to split the ATPs. 12 of them can be water molecules. The remaining 6 water-equivalents can come from the 12 H+ plus 6 of the oxygens from carbon dioxide. The other 6 oxygens balance oxygen in the sugar. The 12 hydrogens in NADPH balance the 12 hydrogens in the sugar. But now there's 6 H+ left over on the products side? Or to put it another way, the reactants have 48 relevant hydrogen atoms (12 from NADPH, 12 free protons, and 24 in water), whereas the products have 54 (12 in the sugar, 36 "hidden" in ADP and Pi, and 6 free protons). But by the same logic, the Stryer Biochemistry version seems to have 36 relevant hydrogens on the left and 54 on the right. So it looks like I'm missing something.
As for your original question about water... I think that our current article is wrong, and that you're misreading MBOC. I'm seeing "water" on the reactants side, not the products side. In case it's for some reason rendering oddly for you, try clicking the image to read the full legend. It says "The entry of water into the cycle is also not shown", implying the Calvin cycle consumes water rather than producing it. A net consumption of 12 waters per 6-carbon sugar by the Calvin cycle makes sense, as combined with 12 waters split at photosystem II and 18 waters produced through condensation of ADP and Pi by ATP synthase, i.e. net 6 water produced by the light reactions, you end up with an overall net photosynthetic consumption of 6 waters per 6-carbon sugar, as expected. Adrian J. Hunter(talk•contribs) 10:14, 18 September 2017 (UTC)
@Adrian J. Hunter: You are right about my misread of MBOC. I just copied it down wrong. I've gone back and corrected my original post just to reduce confusion in a confusing topic. Conceivably the H+ balance could be further complicated by the fact that ATP hydrolysis also produces H+.
ATP-4 + H2O → ADP-3 + Pi-2 + 2H+
T.Shafee(Evo&Evo)talk 11:01, 18 September 2017 (UTC)


References

  1. ^ Alberts, Bruce (2002). "14, Chloroplasts and Photosynthesis". MBOC.
  2. ^ Berg, Jeremy M.; Tymoczko, John L.; Stryer, Lubert (2002). "20.1.4, The Calvin Cycle Synthesizes Hexoses from Carbon Dioxide and Water". Biochemistry.

FPGS in FluoropyrimidineActivity WP1601

I've manually edited {{FluoropyrimidineActivity WP1601}} to disambiguate FPGS to Folylpolyglutamate synthase. Please can someone with a Pathway account make any necessary changes there, in case the template is regenerated? Thanks, Certes (talk) 11:41, 18 September 2017 (UTC)

Facto Post – Issue 4 – 18 September 2017

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 discussion of extinction rates, are the usual topics covered in the media to inform us about this area. But actual data matters.

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

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

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

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MediaWiki message delivery (talk) 14:46, 18 September 2017 (UTC)

Updating templates

Wikipedia cell and molecular biology articles contains some awesome big-picture showing templates comparing prokaryotes and eukaryotes. Such as Template:DNA replication, Template:Transcription and Template:Genetic translation.

However now we know, this prokaryote vs. eukaryote classification is quite an artificial classification, and 3 distinct group, eubacteria (bacteria in new sense), archaebacteria (archaea) and eukaryote works better.

So shouldn't we create 3 fields (total) (1 for bacteria, archaea and eukaryote, each)? Also, in some cases if we have lack of information about archea, we should keep empty place for archaea.

One of the template, Template:Genetic translation (Permalink) shows some rows for archaea; but they used "prokaryote" to mean eubacteria (bacteria of new meaning). But prokaryote does not mean eubacteria. Prokaryote includes both eubacteria (bacteria of new use) and archaea.

So I think it is time to update the templates.


RIT RAJARSHI (talk) 16:01, 9 August 2017 (UTC)

Hi RIT RAJARSHI, I agree that the prokaryotic/archaeal/eukaryotic division in {{Genetic translation}} is less than ideal. The problem is, in the literature, "prokaryotic" is widely used when "bacterial" is really what's meant. For example, the three prokaryotic initiation factors should surely be named "bacterial initiation factors", but we don't get to decide that; I assume they were named before anyone realised how different bacteria and archaea are. As far as I can tell, our understanding of archaean translation is pretty rudimentary. Ideally we'd update all the protein articles linked in the template to clarify whether they really are common in prokaryotes broadly or only in bacteria specifically, and then organise the template accordingly.
For {{DNA replication}} and {{Transcription}}, in the future a three-way split may be appropriate, but per WP:EXISTING we're encouraged to create the articles first. Adrian J. Hunter(talk•contribs) 08:36, 17 September 2017 (UTC)

Thank very much to everyone who responded. @Adrian J. Hunter:. As well, thanks for appreciating the nomenclatural problem, after all it is a problem. However I always write "Bacteria (sensu-stricto)" or "Bacteria (of new use)" to avoid the confusion, because most of the not-too-technical persons treat "prokaryote" and "bacteria" as same thing, yet.

As @Adrian J. Hunter: said, archaeal (former "archaebacteria") genetics and molecular biology is not yet studied elaborately; but in such cases, some "gaps" should be displayed, just like Mendeleev did in his periodic table; not only in wikipedia, but also in textbook charts. RIT RAJARSHI (talk) 16:01, 18 September 2017 (UTC)

Update

I have 2 other related topics to add. But since they are related to the same topic, "template", I've added them here for better categorization. 

   * 1. For all biological structures and processes; a try to give how it is on Eubacteria, Archaebacteria and Eukaryotes. 
   * 2. Smartphones (that shows en.m.wikipedia) DOES NOT SHOW the template, a big-picture. So either make templates visible in mobile view or display a table as an alternative.
  • 1. For all biological structures and processes; a try to give how it is on Eubacteria, Archaebacteria and Eukaryotes. Not only for central dogma, but for all other applicable possible biological structures and functions. For example, in case of a structure, say extracellular matrix, or cell-membrane, or cytosol; or processes like protein degradation or molecular traffiking or say photosynthesis, how it is in eubacteria, archaea and eukaryotes. And if applicable, in organellar-genomes (Plastid-family and mitochondria) and acellular life (virus, viroid, prions).
  • 2. Smartphones (that shows en.m.wikipedia) DOES NOT SHOW the template, a big-picture. So either make templates visible in mobile view or display a table as an alternative. Unfortunately, the mobile view does not show the template appending below the pages. Now the large number of users using mobiles, will be basically be missed from this cool feature. Though it is possible to access desktop view from phones, those people using mobile from beginning/ most-time; will might never know there is such a feature. Also even if people just know about the feature but do not interact or do not get enough scope to try to learn the feature, they will not realize the help / usefulness of this feature. So in my views either the mobile mode should display these templates, at least in compressed (shrinked) form, or as a separate table.

RIT RAJARSHI (talk) 17:28, 18 September 2017 (UTC)

Automatic BOT for categorizing and organizing articles into Wikiproject MCB

I often found scattered Wikipedia articles which are not properly categorized and not enroled to an Wikiproject. When I find such article; I add proper categories and wikiprojects if I'm not very busy. But that is a time taking and distracting task. And also often I can't do these small edits when I have scarcity of time

How would it be, if we had a bot that can categorize the articles and assign them in proper wikiprojects accordingly?

With special reference to Project MCB, I often find articles which is enrolled in either Chemistry or Genetics or Pharmacology or Medicine; which also belong very well into the domain of project MCB. One such example was Plasmid copy number . Especially since MCB is an interdisciplinary area, such problems will continue. So we should have a bot, that can trace which articles may fall under scope of MCB, on the basis of hyperlinks with MCB articles and MCB- terms/vocabulary it used. The final step of labelling may be kept on human judgement.

I think this would help in tracing, cataloging, arranging, grouping/mapping and gap-finding in existing MCB articles.

RIT RAJARSHI (talk) 16:39, 18 September 2017 (UTC)

Thanks for the heads up. As you point out, categorization is often a human judgement call, so I am not sure that this is an appropriate job for a bot. WP:GENETICS is very closely related to WP:MCB, so that categorization in the former implies the later. Perhaps we could formalize this by declaring MCB, GENETICS, and BIOLOGY as sister projects. In short, I am being lazy ;-) Boghog (talk) 19:24, 18 September 2017 (UTC)

Creationist "facts" in the laminin article

Pinging @Doc James:@Ozzie10aaaa:@Jytdog:@Boghog:@Rod57:@Miguelferig:

A few weeks ago, an "in popular culture" section that had been gone for over 2 years was re-added to the laminin article. Such section seems to be only activity User:Kjcarrier has on Wikipedia since he added it in 2013, and re-added several times over the years. This is the section:

Some Christian apologists, most notably Louie Giglio, have written about the fact that laminin is shaped like a Christian cross, comparing the role of the cross in theology and laminin's role in the human body. For example, David D. Swanson states: "Our knowledge of truth is most clearly revealed on the cross of Christ. And what holds the human body together? Laminin. And what does it look like? A cross. Coincidence? Some would say yes, but I think it is yet another way God reveals his glory to us. I think God is the one who holds all things together-our bodies-our world-our lives."[1] Fazale Rana, a biochemist and apologist, disagrees with Giglio and instead argues that "Instead of pointing to superficial features of biomolecules such as the “cross-shaped” architecture of laminin, there are many more substantive ways to use biochemistry to argue for the necessity of a Creator."[2]

  1. ^ Swanson, David D. (2012). Learning to Be You. Baker Books. ISBN 1441238492.
  2. ^ Rana, Fazale. "Crossed off the List: Is the Cross Shape of Laminin Evidence for the Creator?". RTB. Retrieved 26 July 2013.

Obviously, quoting the ideas of Christian pastors and creationist advocates from primary sources is not accepted in an article about a protein family. It is simply not encyclopedic. I would appreciate some feedback on this matter. (Since the section has been gone for years the status quo should be to remove until consensus is reached, but I keep being reverted).

Thanks, Neodop (talk) 19:50, 24 September 2017 (UTC)

I keep on thinking this section is apropriate in an article about creationism but not here. It has no scientific references, I mean scientific journal articles.--Miguelferig (talk) 21:00, 24 September 2017 (UTC)::
agree w/ Miguelferig--Ozzie10aaaa (talk) 21:07, 24 September 2017 (UTC)
Like Jytdog says, WP:ONEWAY. We certainly shouldn't be quoting creationist material in an article about a protein. If there are decent sources that discuss these claims from a sociological or psychological perspective, they might be appropriate to cite, so as to have a comprehensive article that covers all aspects of the topic. But I'm not aware of such sources. Adrian J. Hunter(talk•contribs) 12:03, 25 September 2017 (UTC)
I also agree w/ Miguelferig (ie remove from this article) - Rod57 (talk) 13:16, 28 September 2017 (UTC)

An offline app for MolCell biology

Hello everyone,

The Kiwix people are working on an offline version of several Wikipedia subsets (based on this Foundation report). It basically would be like the Wikimed App (see here for the Android light version; iOS is in beta, DM me if interested), and the readership would likely be in the Global South (if Wikimed is any indication): people with little to no access to a decent internet connexion but who still would greatly benefit from our content.

What we do is take a snapshot at day D of all articles tagged by the project (minus Biographies) and package it into a compressed zim file that people can access anytime locally (ie once downloaded, no refresh needed). We also do a specific landing page that is more mobile-friendly, and that's when I need your quick input:

  1. Would it be okay for you to have it as a subpage of the Wikiproject (e.g. WikiProject Molecular and Cell Biology/Kiwix)?
  2. Any breakdown of top-level topics that you'd recommend? (see Wikipedia:WikiProject_Medicine/Open_Textbook_of_Medicine2 for what we're looking at in terms of simplicity)

Thanks for your feedback! Stephane (Kiwix) (talk) 09:38, 10 October 2017 (UTC)

@Stephane (Kiwix):. Thanks for the post. very interesting. I don't think anyone would object to you creating a /Kiwix subpage. It might be worth encompassing genetics (WP:GEN) as well, since there is a lot of overlap, and some topics make most sense when both sets are present (as can be seen from our top importance article list. A starting point for the main categories might be these:
  • Cells: organelles, division, important cell types, embryology, viruses (even though they're not cells)
  • Biomolecules: DNA, RNA, protesin, lipids, sugars
  • Metabolism: glycolysis, respiration, photosynthesis
  • Genes: concepts in genetics like genes, chromosomes, genomes, epigenetics, transcription, translation, reculation etc
  • Molecular evolution: duplication, mutation, selection, drift, other key evo topics
  • Techniques: cloning, GM, microscopy, transformation, other important techniques
  • Signalling?: important signalling pathways and concepts. Maybe some developmental biology?
Hope that helps as a start. I think those categories encompass most of the top and high importance articles, though the last one I'm not sure on as it seems narrower than the others. I'd be interested to hear others' thoughts on the categories. T.Shafee(Evo&Evo)talk 04:15, 13 October 2017 (UTC)
This list looks good. One might add Biochemistry and History of Molecular Biology, although if biographies are disallowed, a History section might be compromised. Bioinformatics is important, too, but that might go under techniques. --Mark viking (talk) 05:45, 13 October 2017 (UTC)
Looks good, thank you. We'll probably take bioinformatics as a different content so as to save space : people don't seem too happy with large apps, so we're cutting corners everywhere we can (hence our doing without biographies, except for Wikiproject History). Stephane (Kiwix) (talk) 06:29, 13 October 2017 (UTC)

Does someone mind looking at Cytokinin Signaling and Response Regulator Proteins?

I stumbled across this doing WP:NPP and I would appreciate it if an expert (or anyone with subject knowledge) could look at this article and determine how appropriate for Wikipedia it is. It is too technical for me to review and I could use guidance. Winner 42 Talk to me! 01:59, 13 October 2017 (UTC)

@Winner 42: Well spotted. The content is actually pretty good. Well referenced and reasonably sensibly organised. It doesn't duplicate any content already up that I can find. The Response Regulator Proteins are only mentioned in reference to Cytokinin, and don't have their own pages yet. It therefore probably should just be titled "Cytokinin signaling" though (and could even conceivably be merged into Cytokinin). I'm happy to post this on the article's talk page if useful. T.Shafee(Evo&Evo)talk 03:43, 13 October 2017 (UTC)
At first glance, the article could use wikification and the lede could be written more simply and provide better context, but the content looks OK. Cytokinin signaling is surely a notable topic. There is a mix of primary and secondary sources that are all probably peer reviewed. This is part of Wiki Ed at Wikipedia:Wiki Ed/Mississippi State University/General Biochemistry (Fall 2017) effort. Unlike a lot of student efforts, this student made a good effort to summarize and cite all their facts. For being a new WP editor, a good first effort. --Mark viking (talk) 03:46, 13 October 2017 (UTC)
I also think the article is appropriate for Wikipedia and have made a first effort at wikifying it. Boghog (talk) 06:52, 13 October 2017 (UTC)

Facto Post – Issue 5 – 17 October 2017

Issue 5 – 17 October 2017
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?

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

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

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

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

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

Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 08:46, 17 October 2017 (UTC)

Following this discussion on the Science RefDesk I've been wondering wether the Hepatomegaly article is accurately narrowing to Carnitine palmitoyltransferase I deficiency amongst the several Fatty-acid metabolism disorders, for one of the main possible causes of Hepatomegaly. Reversely, the Fatty-acid metabolism disorder article would be imprecisely describing the class of disorders it seems. Thank you in advance for your advice. --Askedonty (talk) 10:31, 20 October 2017 (UTC)

Cell-cell fusogens article

Hi, a few days ago a new editor came along and blanked the cell-cell fusogens page for being inaccurate. I sent them a note on their talk page to see if I could discuss these changes with the editor, but it came to no avail. TheDragonFire on IRC advised me that I should bring it to some sort of noticeboard, so here I am now after no reply from the blanking editor. I should think the article is alright, but just to check. My name isnotdave (talk/contribs) 08:22, 23 October 2017 (UTC)

Cloning a mammoth

The article Woolly mammoth has a section dealing with current attempts to either clone a mammoth or create a mammoth/elephant hybrid. I have been trying to update both the information and the terminology, but another editor reverts it. He does not understand biology and exhibits an ownership attittude. For example, he writes that "a Japanese team found usable DNA in the brains of mice that had been frozen for 16 years. They hope to use similar methods to find usable mammoth DNA." Unless the mammoth died <16 years ago, it makes no sense. Another jewel is his assertion that building a full set of artificial mammoth chromosomes (all 58) is the easiest way to go forward. His reverts delete the names of the Harvard team and their updated progress, etc. He includes unrelated fluff on goats and mice that have nothing to do with mammoths. I'd appreciate someone taking a look over there. Cheers, BatteryIncluded (talk) 21:37, 1 November 2017 (UTC)

Facto Post – Issue 6 – 15 November 2017

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

WikidataCon Berlin 28–9 October 2017

WikidataCon 2017 group photo

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

WD-FIST explained

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

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

Editor Charles Matthews. Please leave feedback for him.
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MediaWiki message delivery (talk) 10:02, 15 November 2017 (UTC)

Transporter reversal (i.e., Wikipedia's article on neurotransmitter efflux & reverse transport)

This article was nominated for deletion at Wikipedia:Articles for deletion/Transporter reversal. I'm mentioning this here in the event anyone wishes to comment on this topic's WP:notability. Seppi333 (Insert 2¢) 21:59, 30 November 2017 (UTC)

Resolved
 – Closed as keep. Seppi333 (Insert 2¢) 22:36, 30 November 2017 (UTC)
I'm glad it was kept. This mechanism is the basis for antidepressant drugs such as Selective serotonin reuptake inhibitors (SSRIs), a very common type of medication. Why would it be tagged for deletion? It is well explained and referenced thoroughly. BatteryIncluded (talk) 22:56, 30 November 2017 (UTC)

Template:Tryptophan metabolism by human microbiota

Tryptophan metabolism by human gut microbiota (
)
The image above contains clickable links
This diagram shows the biosynthesis of bioactive compounds (indole and certain other derivatives) from tryptophan by bacteria in the gut.[1] Indole is produced from tryptophan by bacteria that express tryptophanase.[1] Clostridium sporogenes metabolizes tryptophan into indole and subsequently 3-indolepropionic acid (IPA),[2] a highly potent neuroprotective antioxidant that scavenges hydroxyl radicals.[1][3][4] IPA binds to the pregnane X receptor (PXR) in intestinal cells, thereby facilitating mucosal homeostasis and barrier function.[1] Following absorption from the intestine and distribution to the brain, IPA confers a neuroprotective effect against cerebral ischemia and Alzheimer's disease.[1] Lactobacillaceae (Lactobacillus s.l.) species metabolize tryptophan into indole-3-aldehyde (I3A) which acts on the aryl hydrocarbon receptor (AhR) in intestinal immune cells, in turn increasing interleukin-22 (IL-22) production.[1] Indole itself triggers the secretion of glucagon-like peptide-1 (GLP-1) in intestinal L cells and acts as a ligand for AhR.[1] Indole can also be metabolized by the liver into indoxyl sulfate, a compound that is toxic in high concentrations and associated with vascular disease and renal dysfunction.[1] AST-120 (activated charcoal), an intestinal sorbent that is taken by mouth, adsorbs indole, in turn decreasing the concentration of indoxyl sulfate in blood plasma.[1]

This diagram used to just be a jpg image that was published in an open access journal under a copyleft license; recently though, it was reuploaded as an svg image and annotated with wikitext; there's a few differences in this image relative to the original.

Anyway, the reason I've created this thread is to ask if anyone has any constructive feedback or suggestions for changes to the text or diagram itself. Seppi333 (Insert 2¢) 22:05, 5 November 2017 (UTC)

Awesome image! A few ideas:
  • It looks like indole is a derivative of tryptophan, so "(indole and certain derivatives)" in the text should be "(indole and certain other derivatives)".  Done
  • "In the intestine" in the fourth sentence of the description is redundant.  Fixed
  • Unless you think the wikilink is especially valuable, the jargon-word "secretagogue" could be avoided with "Indole itself promotes secretion of...".  Done
  • In the image, "Clostridium sporogenes" should be italicised.  Done
  • Before reading the description, I interpreted the red T-bar as indicating that AST-120 inhibited absorption of indole by the liver. I'd put the label up in the top-right part of the image, and point the T-bar toward indole in the intestinal lumen, rather than indole that's already been absorbed.
  • "DNA damage" in the bottom left could be "DNA damage".  Done
  • Are all the bullet points under, for example, "Neuroprotectant" examples of neuroprotectant activity? If so, I suggest adding colons after "Neuroprotectant" and equivalent headings, or bolding them or otherwise indicating that they're headings.  Done
  • My last idea might be more trouble than it's worth. If I've understood correctly, C. sporogenes itself is an example of a tryptophanase-expressing bacterium. So ideally, the arrow that points toward IPA should come not from tryptophan directly, but from indole. Alternatively or in addition, the third sentence of the description could say something like, "One such bacterium is Clostridium sporogenes, which further metabolises indole...".
Adrian J. Hunter(talk•contribs) 07:12, 6 November 2017 (UTC)
I've marked the entries I've addressed as done/fixed above. From my understanding of the sources I've read, Clostridium sporogenes converts tryptophan to IPA in two steps, with indole being the metabolic intermediate. I could add the change to the caption, but changing the diagram would be more difficult. Seppi333 (Insert 2¢) 19:31, 6 November 2017 (UTC)
Excellent stuff Seppi! I always love seeing more interactive diagrams. Although there will always be an extra technical barrier to creating and editing interactive diagrams, I think that the {{AI4}} template is pretty editable, maintainable, and futureproof. I can't think of any scientific points above what Adrian has already mentioned. I've a few (optional) stylistic points though.
  • If possible it'd be great to get the width down to 500px, since it's at the high end of image sizes, and there's still quite a bit of white space that could be compressed.
  • I tend to think that it's best to only have, at most, two different font sizes in an image to maintain visual consistency.
  • Excellent and thorough caption. I've added a |caption= parameter in the template to allow it be used with a different default if necessary.
Overall, though, great work! T.Shafee(Evo&Evo)talk 10:21, 6 November 2017 (UTC)
Thanks for adding the caption parameter. I can work on the fonts in a bit and see if I can reduce the number of font sizes to 2 or 3. I usually use 600px as the width in a diagram like this, but I think this image could probably be cut down to 550px if the size of the liver is reduced. Seppi333 (Insert 2¢) 19:31, 6 November 2017 (UTC)
Oh, one other thing, when clicking on the background, it would be good if it linked through to a non-interactive, but annotated version of the image (see {{Eukaryote gene structure}} as an example). T.Shafee(Evo&Evo)talk 00:13, 7 November 2017 (UTC)
@Evolution and evolvability: Sorry for the late reply; I implemented your suggestion for the background link. Seppi333 (Insert 2¢) 02:12, 23 November 2017 (UTC)
@Anyone: Is "Lactobacilli" supposed to be italicized or no? Seppi333 (Insert 2¢) 02:12, 23 November 2017 (UTC)
I don't think "Lactobacilli" should be italicised for the reason given here, though we should really explain this at Binomial nomenclature and in the MoS. Btw my earlier comment about the colon after "Neuroprotectant" was meant to refer to all the little headings like that, so Mucosal homeostasis, Maintains mucosal reactivity, Associated with vascular disease, and Associated with chronic kidney disease as well. Adrian J. Hunter(talk•contribs) 04:07, 23 November 2017 (UTC)

@Adrian J. Hunter: My bad. I made the changes you've requested, as the colon in all of those places is appropriate given the relevance of the entries beneath where you've asked me to add them. Also, I do think the MOS and that article should be updated to include when and when not to italicize genera. Seppi333 (Insert 2¢) 05:36, 23 November 2017 (UTC)

Indoxyl sulfate

I'm planning on turning this redlink blue, but I was wondering what others think the new article on this compound should be titled. Based upon PubChem's entry for Indoxyl sulfate, the 2 most appropriate options for the article title IMO would be either Indoxyl sulfate or 3-Indoxylsulfuric acid. Seppi333 (Insert 2¢) 22:13, 10 November 2017 (UTC)

While I'm at it, I suppose I could also create the article on indole-3-aldehyde (denoted I3A in the diagram above); the choices for an article on that compound are Indole-3-aldehyde, 3-Indolecarboxaldehyde, and Indole-3-carboxaldehyde (PubChem's Indole-3-carboxaldehyde entry). I'm more inclined to use one of the latter 2 terms for the article title/page name since they're more complete/descriptive titles. Seppi333 (Insert 2¢) 22:29, 10 November 2017 (UTC)

I've created the indoxyl sulfate article. If anyone wants to expand it with the existing references or other citations, feel free to do so. It's really not complete at the moment since I barely covered its clinical significance. Seppi333 (Insert 2¢) 05:57, 16 November 2017 (UTC)

Section reflist

  1. ^ a b c d e f g h i Zhang LS, Davies SS (April 2016). "Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions". Genome Med. 8 (1): 46. doi:10.1186/s13073-016-0296-x. PMC 4840492. PMID 27102537. Lactobacillus spp. convert tryptophan to indole-3-aldehyde (I3A) through unidentified enzymes [125]. Clostridium sporogenes convert tryptophan to IPA [6], likely via a tryptophan deaminase. ... IPA also potently scavenges hydroxyl radicals
    Table 2: Microbial metabolites: their synthesis, mechanisms of action, and effects on health and disease
    Figure 1: Molecular mechanisms of action of indole and its metabolites on host physiology and disease
  2. ^ Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G (March 2009). "Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites". Proc. Natl. Acad. Sci. U.S.A. 106 (10): 3698–3703. Bibcode:2009PNAS..106.3698W. doi:10.1073/pnas.0812874106. PMC 2656143. PMID 19234110. Production of IPA was shown to be completely dependent on the presence of gut microflora and could be established by colonization with the bacterium Clostridium sporogenes.
    IPA metabolism diagram
  3. ^ "3-Indolepropionic acid". Human Metabolome Database. University of Alberta. Retrieved 12 June 2018.
  4. ^ Chyan YJ, Poeggeler B, Omar RA, Chain DG, Frangione B, Ghiso J, Pappolla MA (July 1999). "Potent neuroprotective properties against the Alzheimer beta-amyloid by an endogenous melatonin-related indole structure, indole-3-propionic acid". J. Biol. Chem. 274 (31): 21937–21942. doi:10.1074/jbc.274.31.21937. PMID 10419516. S2CID 6630247. [Indole-3-propionic acid (IPA)] has previously been identified in the plasma and cerebrospinal fluid of humans, but its functions are not known. ... In kinetic competition experiments using free radical-trapping agents, the capacity of IPA to scavenge hydroxyl radicals exceeded that of melatonin, an indoleamine considered to be the most potent naturally occurring scavenger of free radicals. In contrast with other antioxidants, IPA was not converted to reactive intermediates with pro-oxidant activity.

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_Molecular_and_Cell_Biology

Please take a few minutes to help make these more useful to our readers.— Rod talk 17:09, 3 December 2017 (UTC)

Facto Post – Issue 7 – 15 December 2017

Issue 7 – 15 December 2017
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!

November 2017 map of geolocated Wikidata items, made by Addshore
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MediaWiki message delivery (talk) 14:54, 15 December 2017 (UTC)

Facto Post – Issue 8 – 15 January 2018

Issue 8 – 15 January 2018
Facto Post – Issue 8 – 15 January 2018

Metadata on the March

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

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

SVG pedestrian crosses road
Zebra crossing/crosswalk, Singapore

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

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

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MediaWiki message delivery (talk) 12:38, 15 January 2018 (UTC)

Refactoring of the cell line lists

There is a list of cell lines under Cell culture#List of cell lines. Other lists of cell lines can be found under List of contaminated cell lines, List of breast cancer cell lines and List of NCI-60 Cell Lines. New material can be found in several online databases and lists.
Some time in the future I will get around to a) create a lot new pages per cell line b) update the first three above-mentioned lists, possibly adding some lists.

  • Item a) means that some information from the list columns can be moved into the respective cell line pages (No information shall be lost.).
  • Updating List of cell lines would mean that it will become far too large to stay one single table; there are over thousand cell lines around.

One obvious thing is that List of cell lines won't stay in Cell_culture.
Now two questions:

  • What columns should be kept (or added) for the respective tables? Any suggestions (including explanation)?
  • What would be a good way to partition List of cell lines? Each partitioning will mean a loss in sorting capability, but we will need some partitioning. Partitioning by species may not be enough. Any suggestions (including explanation)?
  • One special outcome could be that we move all information but name and classifications into the respective cell line pages. In that case we could replace the lists by categories. How about that?

Tomdo08 (talk) 20:22, 21 January 2018 (UTC)

Note: List of contaminated cell lines too will be too big as one table. Partitioning in principal should be the same like for List of cell lines. Or is there a reason to do it differently? Tomdo08 (talk) 20:34, 21 January 2018 (UTC)
Another note: I won't start on refactoring the lists next week or so, that is months in the future. Tomdo08 (talk) 20:39, 21 January 2018 (UTC)

change the name of the wikipedia page "MIA3" to "TANGO1/MIA3"

We would be interested in changing the name of the page https://en.wikipedia.org/wiki/MIA3 to TANGO1 / MIA3 for the following reasons; I hope you find it interesting to study that possibility. - TANGO1 is identified as a protein required for trafficking of collagens from the ER. Most of the work on this protein is related to its role in collagen export from the ER. MIA3 stands for melanoma inhibitory activity3. There is no evidence that this protein has any function per se in inhibiting melanomas. The term MIA3 is very confusing because the literature also contains MIA and MIA2. So, no one in the scientific community searches for MIA’s, but TANGO1 is a widely searched name and the first paper reporting this protein and its function in 2009 has been cited well over 100 times. The wikipedia by listing TANGO1 as MIA3 in fact lessens the impact of this particular protein. It would be better to list this as TANGO1, but if the editors prefers not to follow this route then please use TANGO1/MIA3. This was everyone will be able to access the information related to the TANGO1 gene. - Also, TANGO1 in google opens only the original publications and not the Wikipedia article. Whereas MIA3 opens the Wikipedia article. So Wikipedia is getting less hits for this error. It would be best to list it as TANGO1/MIA3. Mariaortb (talk) 09:15, 26 January 2018 (UTC)

Facto Post – Issue 9 – 5 February 2018

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

Wikidata as Hub

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

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

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

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Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here.
Reminder: WikiFactMine pages on Wikidata are at WD:WFM.
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MediaWiki message delivery (talk) 11:50, 5 February 2018 (UTC)

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