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Archive 5 | ← | Archive 7 | Archive 8 | Archive 9 | Archive 10 | Archive 11 |
I recently removed all of the image text from File:ISSN HMB statement Fig 1.jpg and replaced it with wikitext. The background image file is likely going to be changed to an svg format soon. Consequently, I'm open to restructuring the background image and repositioning/resizing the annotations based upon feedback from this project.
The original image file that this diagram is based upon was uploaded from a CC-BY-SA 2.0-copyrighted journal article about β-hydroxy β-methylbutyric acid (HMB), hence why there's a lot of emphasis on HMB in this image (note that there are a few minor differences between this image and the original). Unfortunately, the enzymes that catalyze the reactions HMB ↔ HMB-CoA and HMB-CoA ↔ HMG-CoA aren't currently known. Also, some very minor metabolites of leucine aren't shown in this image (L-Leucine → β-Leucine via leucine aminomutase, and β-Leucine → β-ketoisocaproic acid → β-Ketoisocaproyl-CoA → acetyl-CoA via a sequence of uncharacterized enzymes). This textbook diagram illustrates that tertiary pathway. Seppi333 ( Insert 2¢) 19:01, 2 December 2017 (UTC)
Given that the HMB article has been renominated at FAC for the 4th time after a 12 month wait, further feedback on changes to this diagram for the svg version would be very much appreciated. If you think some part of this diagram should be drawn, depicted, or annotated in a different manner, please say so. I'm looking for both general/non-specific feedback as well as specific feedback on one technical and one cosmetic point:
For additional context/information on the pathway being depicted in this diagram, it would probably help to read the article text in Leucine#Metabolism in humans. Seppi333 ( Insert 2¢) 08:22, 21 January 2018 (UTC)
@ Boghog: I'm creating the SVG diagram right now, but I just noticed something. Since MC-CoA→HMB-CoA requires H2O as an input and both HMB-CoA→HMG-CoA and MC-CoA→MG-CoA require CO2 as an input, wouldn't the MG-CoA→HMG-CoA reaction catalyzed by MG-CoA hydratase also require H2O as an input? If so, I should illustrate that in the diagram. Seppi333 ( Insert 2¢) 10:40, 28 January 2018 (UTC)
@ Boghog: The current version of the annotated SVG diagram is transcluded from the template talk page into the collapse tab below. I've finished re-annotating most of it, but the annotations with an orange background need to be repositioned. Logging off for now. Let me know if you have any feedback. Seppi333 ( Insert 2¢) 13:00, 28 January 2018 (UTC)
@
Boghog: I've finished annotating the new svg diagram below. Unless you have any suggestions for further revision, I'm going to replace the current {{
Leucine metabolism in humans}}
template with this one. I can work on splitting this diagram into two tomorrow if
Galobtter thinks it would be best to move the biosynthesis section out of the
beta-Hydroxy beta-methylbutyric acid#Pharmacology section.
Seppi333 (
Insert 2¢)
12:36, 29 January 2018 (UTC)
Annotated SVG version of the diagram
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Reflist for
{{
Leucine metabolism in humans}} |
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Beta-Hydroxy beta-methylbutyric acid recently became a good article, so I renominated it FAC for the 4th time: Wikipedia:Featured article candidates/Beta-Hydroxy beta-methylbutyric acid/archive4.
I really need more editors to comment at this nomination and review it against the WP:Featured article criteria. For those who haven't reviewed an article at FAC before, this is the "FAQ" page for reviewing articles at FAC. Seppi333 ( Insert 2¢) 03:46, 2 February 2018 (UTC)
Figured that folks may be interested in this discussion. Jo-Jo Eumerus ( talk, contributions) 14:29, 4 February 2018 (UTC)
There is a discussion at the above link. Your input is most welcome. Boghog ( talk) 17:39, 11 February 2018 (UTC)
Hello there! I just came across this article ( Cooperative antigen transfer) and I was wondering if an expert could take a look at it? I know little about the topic. -- TheSandDoctor ( talk) 20:20, 12 February 2018 (UTC)
Please see the latest discussion at Talk:Sex, which proposes to restrict the scope of the article. -- EncycloPetey ( talk) 16:52, 18 February 2018 (UTC)
Please share your views here: Talk:Umami#This really should be called savory
Anna Frodesiak ( talk) 01:06, 24 February 2018 (UTC)
Facto Post – Issue 10 – 12 March 2018
Milestone for mix'n'matchAround the time in February when Wikidata clicked past item Q50000000, another milestone was reached: the mix'n'match tool uploaded its 1000th dataset. Concisely defined by its author, Magnus Manske, it works "to match entries in external catalogs to Wikidata". The total number of entries is now well into eight figures, and more are constantly being added: a couple of new catalogs each day is normal. Since the end of 2013, mix'n'match has gradually come to play a significant part in adding statements to Wikidata. Particularly in areas with the flavour of digital humanities, but datasets can of course be about practically anything. There is a catalog on skyscrapers, and two on spiders. These days mix'n'match can be used in numerous modes, from the relaxed gamified click through a catalog looking for matches, with prompts, to the fantastically useful and often demanding search across all catalogs. I'll type that again: you can search 1000+ datasets from the simple box at the top right. The drop-down menu top left offers "creation candidates", Magnus's personal favourite. m:Mix'n'match/Manual for more. For the Wikidatan, a key point is that these matches, however carried out, add statements to Wikidata if, and naturally only if, there is a Wikidata property associated with the catalog. For everyone, however, the hands-on experience of deciding of what is a good match is an education, in a scholarly area, biographical catalogs being particularly fraught. Underpinning recent rapid progress is an open infrastructure for scraping and uploading. Congratulations to Magnus, our data Stakhanovite! Links
Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from
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MediaWiki message delivery ( talk) 12:26, 12 March 2018 (UTC)
Hi. I have been thinking over an issue and would appreciate a second opinion.
We have an article about cobalamin, which is another name for vitamin B12. The problem is, as such things sometimes are with vitamins (see vitamin B3 complex/ niacin), that it is a group name for a number of compounds that have a certain structure in common, but depending on the ligand attached they have different names, and slightly different properties, as well as some differences in biological functions. And I was wondering maybe it should be a disambig page?
On the one hand, something indeed can be said about cobalamin as a group, on the other hand it rapidly boils down to "if ligand is this, then it is such and such name with such and such properties". So basically, it has a disambig function.
What do you think, what could be put in that article, if it should remain an article? PubChem has a lot of them for reference (as well as vitamin B12) -- Helixitta ( t.) 14:04, 10 March 2018 (UTC)
Adenosine triphosphate, an article that you or your project may be interested in, has been nominated for an individual good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. AIRcorn (talk) 22:42, 26 March 2018 (UTC)
Article review
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To WP:MCB, WP:GEN, WP:BIOL and WP:EB The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo) talk 09:49, 31 March 2015 (UTC)
GlossarySnooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. -- Squidonius ( talk) 21:47, 1 April 2015 (UTC)
ReferencesI'm planning on adding some more Molecular Biology of the Cell references to the article using
I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat.
T.Shafee(Evo﹠Evo)
talk
12:24, 22 April 2015 (UTC)
MBOC referencesArticle Genes [1]: 2 are numerous [1]: 4 and useful [1]: 4.1 References
So {{ rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{ rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo) talk 01:29, 27 April 2015 (UTC)
Collapsed the transclusion. Seppi333 ( Insert 2¢) 04:48, 27 March 2018 (UTC) |
Any interest in rescuing this abandoned draft? Espresso Addict ( talk) 01:27, 9 April 2018 (UTC)
Facto Post – Issue 11 – 9 April 2018
The 100 Skins of the OnionOpen Citations Month, with its eminently guessable hashtag, is upon us. We should be utterly grateful that in the past 12 months, so much data on which papers cite which other papers has been made open, and that Wikidata is playing its part in hosting it as "cites" statements. At the time of writing, there are 15.3M Wikidata items that can do that. Pulling back to look at open access papers in the large, though, there is is less reason for celebration. Access in theory does not yet equate to practical access. A recent LSE IMPACT blogpost puts that issue down to "heterogeneity". A useful euphemism to save us from thinking that the whole concept doesn't fall into the realm of the oxymoron. Some home truths: aggregation is not content management, if it falls short on reusability. The PDF file format is wedded to how humans read documents, not how machines ingest them. The salami-slicer is our friend in the current downloading of open access papers, but for a better metaphor, think about skinning an onion, laboriously, 100 times with diminishing returns. There are of the order of 100 major publisher sites hosting open access papers, and the predominant offer there is still a PDF. From the discoverability angle, Wikidata's bibliographic resources combined with the SPARQL query are superior in principle, by far, to existing keyword searches run over papers. Open access content should be managed into consistent HTML, something that is currently strenuous. The good news, such as it is, would be that much of it is already in XML. The organisational problem of removing further skins from the onion, with sensible prioritisation, is certainly not insuperable. The CORE group (the bloggers in the LSE posting) has some answers, but actually not all that is needed for the text and data mining purposes they highlight. The long tail, or in other words the onion heart when it has become fiddly beyond patience to skin, does call for a pis aller. But the real knack is to do more between the XML and the heart. Links
Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from
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MediaWiki message delivery ( talk) 16:25, 9 April 2018 (UTC)
Talk:GBA_(disambiguation)#Requested_move_13_April_2018 Jytdog ( talk) 02:59, 15 April 2018 (UTC)
Wikipedia:WikiProject Cell Signaling has been inactive for several years, yet its tag is on the talk pages of 295 pages. Should we remove the Cell signalling banner from those pages and replace it with the MCB banner where appropriate? I figure the purpose of the project tags on article talk pages is (1) to help projects keep track of pages their editors are interested in, and (2) to point readers/editors towards a Project that could help address concerns about a particular article. It seems like having the banner from a defunct WikiProject just serves to confuse. Thoughts? I assume a bot could be found to do this task if folks think it's a good idea. Cheers Ajpolino ( talk) 19:28, 24 April 2018 (UTC)
An article that you have been involved in editing— Vitamin B3—has been proposed for merging with another article. If you are interested, please participate in the merger discussion. Thank you. SusanLesch ( talk) 13:59, 30 April 2018 (UTC)
Hi, I am not a member of your project but do most of my work at Wikiproject Anatomy. At the anatomy project we recently finished classifying our articles and we have just under 1500 articles and redirects related to cells and microanatomy. What I would to know is what is under the scope of your project? Do you include individual cell types such as alveolar cells, osteocytes or melanocytes? If such articles are within your scope please let me know and I will gladly start tagging/adding your project banner to their talk page (in the hope that your project members can find and will work on some of the articles of interest to both wikiprojects). Kind regards JakobSteenberg ( talk) 20:47, 29 April 2018 (UTC)
I just moved Draft:LCHN into mainspace. @ M.Gray97: The infobox_gene template is generating An Error has occurred retrieving Wikidata item for infobox. My template-fu is insufficient to fix this. Could a SME take a look? Thanks. -- RoySmith (talk) 21:17, 6 May 2018 (UTC)
Draft:Comparison_of_DNA_melting_prediction_software I'm a Afc reviewer with cell biology background but still struggling whether this bioinformatics page can be accepted . do give me an opinion. thanks much Quek157 ( talk) 16:22, 8 May 2018 (UTC)
Hey everyone. I'm no wiki expert and there might be internal reasons not to do this, but I thought I'd float it.
There is an excellent+beautiful+open source molecular graphics thing called NGL. It is being developed at UCSD as part of the protein data bank, and I know the person doing it. Some examples: Ribosome https://www.rcsb.org/3d-view/4V4J RNA pseudoknot http://www.rcsb.org/3d-view/2LC8 Dorothy Hodgkin's Insulin https://www.rcsb.org/3d-view/4INS
You can see a (super cool+interactive) presentation on it here http://nglviewer.org/talks/ngl-3dsig/
Adopting ngl would be great for wiki because: -Everything would look super beautiful and make the molecular biology pages more readable -It would allow you to have images of any molecule for which we have a model (= any molecule for which you would want to see an "image") on any page, because you wouldn't need to find a public domain picture. In principle you could just have some markup like <ngl window: "pdbID:4ins"> or whatever and suddenly your webpage has an excellent up-to-date structure
NGL is very cross platform and works well on smartphones. However, it is obviously dependent on webGL.
Using NGL would take more bandwidth. For each structure you'd need to download a pdb file, plus the ngl javascript (which you'd have to do for every page?). That said, I'd like to point out that a 500KB pdb file is smaller than a 1MB animated gif of the same molecule performing a rotation, so a small number of pages would be compressed by this adoption.
NGL is better than the visualizer that proteopedia use http://proteopedia.org/wiki/index.php/Main_Page as you can verify for yourself. — Preceding unsigned comment added by Hamishtodd1 ( talk • contribs) 12:06, 10 May 2018 (UTC)
You are invited to join the discussion at Wikipedia talk:WikiProject Medicine#MicroDNA. – Finnusertop ( talk ⋅ contribs) 22:53, 10 May 2018 (UTC)
Facto Post – Issue 12 – 28 May 2018
ScienceSource fundedThe Wikimedia Foundation announced full funding of the ScienceSource grant proposal from ContentMine on May 18. See the ScienceSource Twitter announcement and 60 second video.
The proposal includes downloading 30,000 open access papers, aiming (roughly speaking) to create a baseline for medical referencing on Wikipedia. It leaves open the question of how these are to be chosen. The basic criteria of WP:MEDRS include a concentration on secondary literature. Attention has to be given to the long tail of diseases that receive less current research. The MEDRS guideline supposes that edge cases will have to be handled, and the premature exclusion of publications that would be in those marginal positions would reduce the value of the collection. Prophylaxis misses the point that gate-keeping will be done by an algorithm. Two well-known but rather different areas where such considerations apply are tropical diseases and alternative medicine. There are also a number of potential downloading troubles, and these were mentioned in Issue 11. There is likely to be a gap, even with the guideline, between conditions taken to be necessary but not sufficient, and conditions sufficient but not necessary, for candidate papers to be included. With around 10,000 recognised medical conditions in standard lists, being comprehensive is demanding. With all of these aspects of the task, ScienceSource will seek community help. Links
Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. ScienceSource pages will be announced there, and in this mass message. If you wish to receive no further issues of Facto Post, please remove your name from
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MediaWiki message delivery ( talk) 10:16, 28 May 2018 (UTC)
The reason I am contacting you is because there are one or more portals that fall under this subject, and the Portals WikiProject is currently undertaking a major drive to automate portals that may affect them.
Portals are being redesigned.
The new design features are being applied to existing portals.
At present, we are gearing up for a maintenance pass of portals in which the introduction section will be upgraded to no longer need a subpage. In place of static copied and pasted excerpts will be self-updating excerpts displayed through selective transclusion, using the template {{ Transclude lead excerpt}}.
The discussion about this can be found here.
Maintainers of specific portals are encouraged to sign up as project members here, noting the portals they maintain, so that those portals are skipped by the maintenance pass. Currently, we are interested in upgrading neglected and abandoned portals. There will be opportunity for maintained portals to opt-in later, or the portal maintainers can handle upgrading (the portals they maintain) personally at any time.
On April 8th, 2018, an RfC ("Request for comment") proposal was made to eliminate all portals and the portal namespace. On April 17th, the Portals WikiProject was rebooted to handle the revitalization of the portal system. On May 12th, the RfC was closed with the result to keep portals, by a margin of about 2 to 1 in favor of keeping portals.
Since the reboot, the Portals WikiProject has been busy building tools and components to upgrade portals.
So far, 84 editors have joined.
If you would like to keep abreast of what is happening with portals, see the newsletter archive.
If you have any questions about what is happening with portals or the Portals WikiProject, please post them on the WikiProject's talk page.
Thank you. — The Transhumanist 10:59, 31 May 2018 (UTC)
Is this worth salvaging? (Delete vs. move to mainspace vs. something else?) Calliopejen1 ( talk) 02:22, 4 June 2018 (UTC)
A large paste of text from WikiJournal of Science/Lysine: biosynthesis, catabolism and roles has been dropped into the article on Lysine. In addition to a number of references breaking in the process, there are issues of overly technical content and copy-paste, even if copyright issues do not apply. I'm too busy to dig into the issues more deeply for at least a few days, so I'm going to punt it over here for now. Sorry and thanks, BiologicalMe ( talk) 03:39, 10 June 2018 (UTC)
Note from OTRS ticket 2018062010005412 - the following pages appear to duplicate the same subject
Ronhjones (Talk) 22:27, 24 June 2018 (UTC)
We have separate articles on Galactoside O-acetyltransferase and Beta-galactoside transacetylase, but are they really different enzymes? The first two sources used at Beta-galactoside transacetylase seem to classify them as synonymous: galactoside acetyltransferase (thiogalactoside transacetylase) (thiogalactoside transacetylase, LacA, GAT). Vaselineeeeeeee ★★★ 22:31, 22 June 2018 (UTC)
[1] [2] Adrian J. Hunter( talk• contribs) 12:40, 25 June 2018 (UTC)
Issue 13 – 29 May 2018
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MediaWiki message delivery ( talk) 18:19, 29 June 2018 (UTC) |
See Wikipedia_talk:WikiProject_Pharmacology#Readability_of_medical_physiology_articles. -- Tom (LT) ( talk) 18:27, 3 July 2018 (UTC)
Readability of medical physiology articles
There is a discussion concerning readability of {{ Infobox gene}} at the above link that is well within the scope this project. In fact, the discussion probably been started here, rather than there. In any case, your input is welcome. Boghog ( talk) 20:06, 5 July 2018 (UTC)
There is a notability/ COI discussion over at Talk:Cellosaurus. Both this discussion and the article itself would benefit from input from WP:MCB members. -- Daniel Mietchen ( talk) 15:49, 10 July 2018 (UTC)
See Wikipedia:Featured article review/Antioxidant/archive1. Seppi333 ( Insert 2¢) 22:34, 10 July 2018 (UTC)
Issue 14 – 21 July 2018
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MediaWiki message delivery ( talk) 06:10, 21 July 2018 (UTC) |
I can see a great deal of effort has gone to producing infobox gene and it clearly has some amazing wikidata integration. I think it could be improved in a number of ways and propose some specific suggestions here for discussion. My aim is to make the infobox shorter, easier to read, and increase the prominence of basic information. (I would normally make a sandbox of my proposed edits but am unable to because the infobox is written in lua.) For my inspiration, I am viewing BRCA1 and MLH1.
I'm starting this part of the discussion back here (rather than WT:PHARM), as boghog points out, this being a more appropriate venue. Ping to editors that have participated: Boghog, Seppi333, Jytdog, Looie496, Ajpolino, Tryptofish. Apologies if I've left anyone out. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
We're moving in that direction globally on WP. The list of 'external IDs' in the infobox could easily be moved to an authority control template for articles. This would also help shorten the infobox, reduce the length of its code, and more importantly, simplify the infobox, which is my goal here.-- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
I refer here to the full chromosome panel, not the horizontal individual chromosome with the gene's location boxed. These pictures take up a lot of space, add to loading times, and don't contribute anything factual. They are also duplicated in text (twice) in the infobox.-- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
The section takes up a large amount of vertical space and is limited to links. I propose collapsing it by default. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
There is a title that is called 'available structures' but it seems to be just some links. I don't know what it does or how it relates to genes, and therefore presume most lay readers won't either. I propose renaming it to something that explains what it does, or merging it to identifiers section if it is related. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
{{
Infobox protein}}
could be merged in?
T.Shafee(Evo&Evo)
talk
11:53, 16 July 2018 (UTC)
A 'basic information' section should be created and placed beneath the picture of the protein ribbon and include basic information about the gene written in a human-readable format. Fields can be discussed once we have some support for this section. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
{{
short description}}
field for every article in WP.) Now a second field of "summary information" is being proposed.. and this is just crazy to me. But I guess people will volunteer doing what they want.I often use WP as revision and for my work as I'm sure many people do. I find many of our articles (e.g. Beta-2 adrenergic receptor, which I'm looking at now) very difficult to read and lacking key information which (I feel at least) could be included in the infobox - e.g. where is that thing, what does that thing do, what makes that thing).. The problem they point out is that articles don't have basic information, and their solution was "infobox". This is the wrong solution in my view. But again people will put time in where they want. This just seems to be a diversion of our most valuable resource to me.
Property | Description |
---|---|
Molecular mechanism | damaged DNA binding |
Biological function | DNA repair |
Subcellular location | plasma membrane, cytoplasm, cell nucleus |
The orthologs part of this section is in fact just the titles 'human' and 'mouse'. The rest are just external links. The proposed change makes the purpose of this section much clearer to readers and reflects what it actually does.
Merging these two parts together reduces the amount of headings in the infobox (which are many) and hopefully also simplifies its display. The section can include a subheading for human and mouse. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
It seems like we're on the way to doing this based on WT:PHARM, but I will propose it here as a plan B. The 'gene ontology' section is not useful as is. It contains 20 - 30 text entries describing processes. None of these reflect the article's lead description of the gene, nor the commonly understood function of a gene, e.g. when it is described as encoding an enzyme, membrane receptor, tumour suppressor gene etc. I propose that this section, if it can't be made easier to read and have a more narrow focus, be removed and we just handwrite everything ourselves. Yes that takes time but as an encyclopedia we are never finished and we should be aiming for the best - and spaghetti lists are not helpful to anyone. These lists are not useful at the moment - experts will already know these facts, and lay readers will not be able to make head nor tail of it, nor know how to extract the important items in the list from the chaff. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
Renaming ontology to function makes the purpose of the section much clearer to end readers, which should be our goal here. I am not sure that readers will even look at the content of the section because they won't know what the section title means. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
Gene location is provided in three sections: gene location (human), and (mouse), and also as a field in orthologs. I propose there that the field 'Location (UCSC)' present in orthologs be moved to the appropriate gene location (human) and (mouse) sections, thus centralising this information and also reducing some duplication. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
Rather than making a large number of changes to the infobox all at once, I think a more limited number of changes could make the infobox much more readable for a general audience without sacrificing the usefulness for specialists. Hence I propose that we implement the following subset of what has been proposed above:
Property | Description |
---|---|
Molecular mechanism | G-protein coupled receptor activity, epinephrine binding, norepinephrine binding |
Biological function | regulation of smooth muscle contraction |
Subcellular location | membrane |
Of course to implement any of this, we must first get buy-in from the those that maintain the infobox and associated wikidata. For example, we have to make sure that changes to the rank of data do not get overwritten by bots. Boghog ( talk) 10:20, 15 July 2018 (UTC)
|most expressed in=
field that auto-filled with text of either the top few hits or all cell types that had expression over some mark (the graphs currently show 3x the median, so perhaps that's a mark of interest?). Bonus points if we could make those top hits wikilink to the relevant wikipedia articles. Of course, the section would also have an external link to the microarray dataset this comes from. As an example, I'm looking at the
BRCA1 infobox which shows
this file and another. Thoughts?
Ajpolino (
talk)
14:45, 15 July 2018 (UTC)I am a new Wikipedia Fellow in the midst of training. I entered " regulatory RNA" and RNAi came up. Of course that's the best worked out regulatory RNA system today, but there are other regulatory RNAs that should be accessed by the general term, such as Xist and others involved in X inactivation and enhancer RNAs, both of which are treated elsewhere on Wikipedia. Does this seem like a problem to others? Is it worth my while to work on putting together a more general treatment of regulatory RNA while I'm in this course? Thank you for considering this. LLMHoopes ( talk) 17:34, 30 July 2018 (UTC)
Hi everyone.
An editor asked me to reproduce File:Estradiol metabolism.png as a wikitext-annotated image. Would anyone here be willing to upload an svg image file with just the 11 compounds in that figure (without any image text except for the letters for the functional groups on the compounds, e.g., the OH for the hydroxyl group) under the file name File:Estradiol metabolitsm.svg? I can't really draw chemical structure diagrams but I can easily draw the pathways, so I intend to edit the uploaded image and add the lines and compound/enzyme annotations + adjust their placement as needed when annotating the image with a template.
@ Boghog: I'm pinging you in the event you're interested in helping with this again and aren't terribly busy. Seppi333 ( Insert 2¢) 22:10, 2 July 2018 (UTC)
@ Boghog: The last thing I need before beginning to annotate and uniformly align the objects in this diagram is an svg image of estrone glucuronide's structure diagram. Could you email me that or add it to File:Estradiol metabolism structures.svg? If you'd prefer the former method, my email is in the source immediately following this sentence. Seppi333 ( Insert 2¢) 11:40, 7 August 2018 (UTC)
Metabolic pathways of
estradiol in humans
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References
I think I'm more-or-less done. Anyone have any feedback/suggestions? Seppi333 ( Insert 2¢) 22:06, 10 August 2018 (UTC)
This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 5 | ← | Archive 7 | Archive 8 | Archive 9 | Archive 10 | Archive 11 |
I recently removed all of the image text from File:ISSN HMB statement Fig 1.jpg and replaced it with wikitext. The background image file is likely going to be changed to an svg format soon. Consequently, I'm open to restructuring the background image and repositioning/resizing the annotations based upon feedback from this project.
The original image file that this diagram is based upon was uploaded from a CC-BY-SA 2.0-copyrighted journal article about β-hydroxy β-methylbutyric acid (HMB), hence why there's a lot of emphasis on HMB in this image (note that there are a few minor differences between this image and the original). Unfortunately, the enzymes that catalyze the reactions HMB ↔ HMB-CoA and HMB-CoA ↔ HMG-CoA aren't currently known. Also, some very minor metabolites of leucine aren't shown in this image (L-Leucine → β-Leucine via leucine aminomutase, and β-Leucine → β-ketoisocaproic acid → β-Ketoisocaproyl-CoA → acetyl-CoA via a sequence of uncharacterized enzymes). This textbook diagram illustrates that tertiary pathway. Seppi333 ( Insert 2¢) 19:01, 2 December 2017 (UTC)
Given that the HMB article has been renominated at FAC for the 4th time after a 12 month wait, further feedback on changes to this diagram for the svg version would be very much appreciated. If you think some part of this diagram should be drawn, depicted, or annotated in a different manner, please say so. I'm looking for both general/non-specific feedback as well as specific feedback on one technical and one cosmetic point:
For additional context/information on the pathway being depicted in this diagram, it would probably help to read the article text in Leucine#Metabolism in humans. Seppi333 ( Insert 2¢) 08:22, 21 January 2018 (UTC)
@ Boghog: I'm creating the SVG diagram right now, but I just noticed something. Since MC-CoA→HMB-CoA requires H2O as an input and both HMB-CoA→HMG-CoA and MC-CoA→MG-CoA require CO2 as an input, wouldn't the MG-CoA→HMG-CoA reaction catalyzed by MG-CoA hydratase also require H2O as an input? If so, I should illustrate that in the diagram. Seppi333 ( Insert 2¢) 10:40, 28 January 2018 (UTC)
@ Boghog: The current version of the annotated SVG diagram is transcluded from the template talk page into the collapse tab below. I've finished re-annotating most of it, but the annotations with an orange background need to be repositioned. Logging off for now. Let me know if you have any feedback. Seppi333 ( Insert 2¢) 13:00, 28 January 2018 (UTC)
@
Boghog: I've finished annotating the new svg diagram below. Unless you have any suggestions for further revision, I'm going to replace the current {{
Leucine metabolism in humans}}
template with this one. I can work on splitting this diagram into two tomorrow if
Galobtter thinks it would be best to move the biosynthesis section out of the
beta-Hydroxy beta-methylbutyric acid#Pharmacology section.
Seppi333 (
Insert 2¢)
12:36, 29 January 2018 (UTC)
Annotated SVG version of the diagram
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Reflist for
{{
Leucine metabolism in humans}} |
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Beta-Hydroxy beta-methylbutyric acid recently became a good article, so I renominated it FAC for the 4th time: Wikipedia:Featured article candidates/Beta-Hydroxy beta-methylbutyric acid/archive4.
I really need more editors to comment at this nomination and review it against the WP:Featured article criteria. For those who haven't reviewed an article at FAC before, this is the "FAQ" page for reviewing articles at FAC. Seppi333 ( Insert 2¢) 03:46, 2 February 2018 (UTC)
Figured that folks may be interested in this discussion. Jo-Jo Eumerus ( talk, contributions) 14:29, 4 February 2018 (UTC)
There is a discussion at the above link. Your input is most welcome. Boghog ( talk) 17:39, 11 February 2018 (UTC)
Hello there! I just came across this article ( Cooperative antigen transfer) and I was wondering if an expert could take a look at it? I know little about the topic. -- TheSandDoctor ( talk) 20:20, 12 February 2018 (UTC)
Please see the latest discussion at Talk:Sex, which proposes to restrict the scope of the article. -- EncycloPetey ( talk) 16:52, 18 February 2018 (UTC)
Please share your views here: Talk:Umami#This really should be called savory
Anna Frodesiak ( talk) 01:06, 24 February 2018 (UTC)
Facto Post – Issue 10 – 12 March 2018
Milestone for mix'n'matchAround the time in February when Wikidata clicked past item Q50000000, another milestone was reached: the mix'n'match tool uploaded its 1000th dataset. Concisely defined by its author, Magnus Manske, it works "to match entries in external catalogs to Wikidata". The total number of entries is now well into eight figures, and more are constantly being added: a couple of new catalogs each day is normal. Since the end of 2013, mix'n'match has gradually come to play a significant part in adding statements to Wikidata. Particularly in areas with the flavour of digital humanities, but datasets can of course be about practically anything. There is a catalog on skyscrapers, and two on spiders. These days mix'n'match can be used in numerous modes, from the relaxed gamified click through a catalog looking for matches, with prompts, to the fantastically useful and often demanding search across all catalogs. I'll type that again: you can search 1000+ datasets from the simple box at the top right. The drop-down menu top left offers "creation candidates", Magnus's personal favourite. m:Mix'n'match/Manual for more. For the Wikidatan, a key point is that these matches, however carried out, add statements to Wikidata if, and naturally only if, there is a Wikidata property associated with the catalog. For everyone, however, the hands-on experience of deciding of what is a good match is an education, in a scholarly area, biographical catalogs being particularly fraught. Underpinning recent rapid progress is an open infrastructure for scraping and uploading. Congratulations to Magnus, our data Stakhanovite! Links
Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from
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MediaWiki message delivery ( talk) 12:26, 12 March 2018 (UTC)
Hi. I have been thinking over an issue and would appreciate a second opinion.
We have an article about cobalamin, which is another name for vitamin B12. The problem is, as such things sometimes are with vitamins (see vitamin B3 complex/ niacin), that it is a group name for a number of compounds that have a certain structure in common, but depending on the ligand attached they have different names, and slightly different properties, as well as some differences in biological functions. And I was wondering maybe it should be a disambig page?
On the one hand, something indeed can be said about cobalamin as a group, on the other hand it rapidly boils down to "if ligand is this, then it is such and such name with such and such properties". So basically, it has a disambig function.
What do you think, what could be put in that article, if it should remain an article? PubChem has a lot of them for reference (as well as vitamin B12) -- Helixitta ( t.) 14:04, 10 March 2018 (UTC)
Adenosine triphosphate, an article that you or your project may be interested in, has been nominated for an individual good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. AIRcorn (talk) 22:42, 26 March 2018 (UTC)
Article review
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To WP:MCB, WP:GEN, WP:BIOL and WP:EB The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo) talk 09:49, 31 March 2015 (UTC)
GlossarySnooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. -- Squidonius ( talk) 21:47, 1 April 2015 (UTC)
ReferencesI'm planning on adding some more Molecular Biology of the Cell references to the article using
I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat.
T.Shafee(Evo﹠Evo)
talk
12:24, 22 April 2015 (UTC)
MBOC referencesArticle Genes [1]: 2 are numerous [1]: 4 and useful [1]: 4.1 References
So {{ rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{ rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo) talk 01:29, 27 April 2015 (UTC)
Collapsed the transclusion. Seppi333 ( Insert 2¢) 04:48, 27 March 2018 (UTC) |
Any interest in rescuing this abandoned draft? Espresso Addict ( talk) 01:27, 9 April 2018 (UTC)
Facto Post – Issue 11 – 9 April 2018
The 100 Skins of the OnionOpen Citations Month, with its eminently guessable hashtag, is upon us. We should be utterly grateful that in the past 12 months, so much data on which papers cite which other papers has been made open, and that Wikidata is playing its part in hosting it as "cites" statements. At the time of writing, there are 15.3M Wikidata items that can do that. Pulling back to look at open access papers in the large, though, there is is less reason for celebration. Access in theory does not yet equate to practical access. A recent LSE IMPACT blogpost puts that issue down to "heterogeneity". A useful euphemism to save us from thinking that the whole concept doesn't fall into the realm of the oxymoron. Some home truths: aggregation is not content management, if it falls short on reusability. The PDF file format is wedded to how humans read documents, not how machines ingest them. The salami-slicer is our friend in the current downloading of open access papers, but for a better metaphor, think about skinning an onion, laboriously, 100 times with diminishing returns. There are of the order of 100 major publisher sites hosting open access papers, and the predominant offer there is still a PDF. From the discoverability angle, Wikidata's bibliographic resources combined with the SPARQL query are superior in principle, by far, to existing keyword searches run over papers. Open access content should be managed into consistent HTML, something that is currently strenuous. The good news, such as it is, would be that much of it is already in XML. The organisational problem of removing further skins from the onion, with sensible prioritisation, is certainly not insuperable. The CORE group (the bloggers in the LSE posting) has some answers, but actually not all that is needed for the text and data mining purposes they highlight. The long tail, or in other words the onion heart when it has become fiddly beyond patience to skin, does call for a pis aller. But the real knack is to do more between the XML and the heart. Links
Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. If you wish to receive no further issues of Facto Post, please remove your name from
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MediaWiki message delivery ( talk) 16:25, 9 April 2018 (UTC)
Talk:GBA_(disambiguation)#Requested_move_13_April_2018 Jytdog ( talk) 02:59, 15 April 2018 (UTC)
Wikipedia:WikiProject Cell Signaling has been inactive for several years, yet its tag is on the talk pages of 295 pages. Should we remove the Cell signalling banner from those pages and replace it with the MCB banner where appropriate? I figure the purpose of the project tags on article talk pages is (1) to help projects keep track of pages their editors are interested in, and (2) to point readers/editors towards a Project that could help address concerns about a particular article. It seems like having the banner from a defunct WikiProject just serves to confuse. Thoughts? I assume a bot could be found to do this task if folks think it's a good idea. Cheers Ajpolino ( talk) 19:28, 24 April 2018 (UTC)
An article that you have been involved in editing— Vitamin B3—has been proposed for merging with another article. If you are interested, please participate in the merger discussion. Thank you. SusanLesch ( talk) 13:59, 30 April 2018 (UTC)
Hi, I am not a member of your project but do most of my work at Wikiproject Anatomy. At the anatomy project we recently finished classifying our articles and we have just under 1500 articles and redirects related to cells and microanatomy. What I would to know is what is under the scope of your project? Do you include individual cell types such as alveolar cells, osteocytes or melanocytes? If such articles are within your scope please let me know and I will gladly start tagging/adding your project banner to their talk page (in the hope that your project members can find and will work on some of the articles of interest to both wikiprojects). Kind regards JakobSteenberg ( talk) 20:47, 29 April 2018 (UTC)
I just moved Draft:LCHN into mainspace. @ M.Gray97: The infobox_gene template is generating An Error has occurred retrieving Wikidata item for infobox. My template-fu is insufficient to fix this. Could a SME take a look? Thanks. -- RoySmith (talk) 21:17, 6 May 2018 (UTC)
Draft:Comparison_of_DNA_melting_prediction_software I'm a Afc reviewer with cell biology background but still struggling whether this bioinformatics page can be accepted . do give me an opinion. thanks much Quek157 ( talk) 16:22, 8 May 2018 (UTC)
Hey everyone. I'm no wiki expert and there might be internal reasons not to do this, but I thought I'd float it.
There is an excellent+beautiful+open source molecular graphics thing called NGL. It is being developed at UCSD as part of the protein data bank, and I know the person doing it. Some examples: Ribosome https://www.rcsb.org/3d-view/4V4J RNA pseudoknot http://www.rcsb.org/3d-view/2LC8 Dorothy Hodgkin's Insulin https://www.rcsb.org/3d-view/4INS
You can see a (super cool+interactive) presentation on it here http://nglviewer.org/talks/ngl-3dsig/
Adopting ngl would be great for wiki because: -Everything would look super beautiful and make the molecular biology pages more readable -It would allow you to have images of any molecule for which we have a model (= any molecule for which you would want to see an "image") on any page, because you wouldn't need to find a public domain picture. In principle you could just have some markup like <ngl window: "pdbID:4ins"> or whatever and suddenly your webpage has an excellent up-to-date structure
NGL is very cross platform and works well on smartphones. However, it is obviously dependent on webGL.
Using NGL would take more bandwidth. For each structure you'd need to download a pdb file, plus the ngl javascript (which you'd have to do for every page?). That said, I'd like to point out that a 500KB pdb file is smaller than a 1MB animated gif of the same molecule performing a rotation, so a small number of pages would be compressed by this adoption.
NGL is better than the visualizer that proteopedia use http://proteopedia.org/wiki/index.php/Main_Page as you can verify for yourself. — Preceding unsigned comment added by Hamishtodd1 ( talk • contribs) 12:06, 10 May 2018 (UTC)
You are invited to join the discussion at Wikipedia talk:WikiProject Medicine#MicroDNA. – Finnusertop ( talk ⋅ contribs) 22:53, 10 May 2018 (UTC)
Facto Post – Issue 12 – 28 May 2018
ScienceSource fundedThe Wikimedia Foundation announced full funding of the ScienceSource grant proposal from ContentMine on May 18. See the ScienceSource Twitter announcement and 60 second video.
The proposal includes downloading 30,000 open access papers, aiming (roughly speaking) to create a baseline for medical referencing on Wikipedia. It leaves open the question of how these are to be chosen. The basic criteria of WP:MEDRS include a concentration on secondary literature. Attention has to be given to the long tail of diseases that receive less current research. The MEDRS guideline supposes that edge cases will have to be handled, and the premature exclusion of publications that would be in those marginal positions would reduce the value of the collection. Prophylaxis misses the point that gate-keeping will be done by an algorithm. Two well-known but rather different areas where such considerations apply are tropical diseases and alternative medicine. There are also a number of potential downloading troubles, and these were mentioned in Issue 11. There is likely to be a gap, even with the guideline, between conditions taken to be necessary but not sufficient, and conditions sufficient but not necessary, for candidate papers to be included. With around 10,000 recognised medical conditions in standard lists, being comprehensive is demanding. With all of these aspects of the task, ScienceSource will seek community help. Links
Editor Charles Matthews, for ContentMine. Please leave feedback for him. Back numbers are here. Reminder: WikiFactMine pages on Wikidata are at WD:WFM. ScienceSource pages will be announced there, and in this mass message. If you wish to receive no further issues of Facto Post, please remove your name from
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MediaWiki message delivery ( talk) 10:16, 28 May 2018 (UTC)
The reason I am contacting you is because there are one or more portals that fall under this subject, and the Portals WikiProject is currently undertaking a major drive to automate portals that may affect them.
Portals are being redesigned.
The new design features are being applied to existing portals.
At present, we are gearing up for a maintenance pass of portals in which the introduction section will be upgraded to no longer need a subpage. In place of static copied and pasted excerpts will be self-updating excerpts displayed through selective transclusion, using the template {{ Transclude lead excerpt}}.
The discussion about this can be found here.
Maintainers of specific portals are encouraged to sign up as project members here, noting the portals they maintain, so that those portals are skipped by the maintenance pass. Currently, we are interested in upgrading neglected and abandoned portals. There will be opportunity for maintained portals to opt-in later, or the portal maintainers can handle upgrading (the portals they maintain) personally at any time.
On April 8th, 2018, an RfC ("Request for comment") proposal was made to eliminate all portals and the portal namespace. On April 17th, the Portals WikiProject was rebooted to handle the revitalization of the portal system. On May 12th, the RfC was closed with the result to keep portals, by a margin of about 2 to 1 in favor of keeping portals.
Since the reboot, the Portals WikiProject has been busy building tools and components to upgrade portals.
So far, 84 editors have joined.
If you would like to keep abreast of what is happening with portals, see the newsletter archive.
If you have any questions about what is happening with portals or the Portals WikiProject, please post them on the WikiProject's talk page.
Thank you. — The Transhumanist 10:59, 31 May 2018 (UTC)
Is this worth salvaging? (Delete vs. move to mainspace vs. something else?) Calliopejen1 ( talk) 02:22, 4 June 2018 (UTC)
A large paste of text from WikiJournal of Science/Lysine: biosynthesis, catabolism and roles has been dropped into the article on Lysine. In addition to a number of references breaking in the process, there are issues of overly technical content and copy-paste, even if copyright issues do not apply. I'm too busy to dig into the issues more deeply for at least a few days, so I'm going to punt it over here for now. Sorry and thanks, BiologicalMe ( talk) 03:39, 10 June 2018 (UTC)
Note from OTRS ticket 2018062010005412 - the following pages appear to duplicate the same subject
Ronhjones (Talk) 22:27, 24 June 2018 (UTC)
We have separate articles on Galactoside O-acetyltransferase and Beta-galactoside transacetylase, but are they really different enzymes? The first two sources used at Beta-galactoside transacetylase seem to classify them as synonymous: galactoside acetyltransferase (thiogalactoside transacetylase) (thiogalactoside transacetylase, LacA, GAT). Vaselineeeeeeee ★★★ 22:31, 22 June 2018 (UTC)
[1] [2] Adrian J. Hunter( talk• contribs) 12:40, 25 June 2018 (UTC)
Issue 13 – 29 May 2018
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MediaWiki message delivery ( talk) 18:19, 29 June 2018 (UTC) |
See Wikipedia_talk:WikiProject_Pharmacology#Readability_of_medical_physiology_articles. -- Tom (LT) ( talk) 18:27, 3 July 2018 (UTC)
Readability of medical physiology articles
There is a discussion concerning readability of {{ Infobox gene}} at the above link that is well within the scope this project. In fact, the discussion probably been started here, rather than there. In any case, your input is welcome. Boghog ( talk) 20:06, 5 July 2018 (UTC)
There is a notability/ COI discussion over at Talk:Cellosaurus. Both this discussion and the article itself would benefit from input from WP:MCB members. -- Daniel Mietchen ( talk) 15:49, 10 July 2018 (UTC)
See Wikipedia:Featured article review/Antioxidant/archive1. Seppi333 ( Insert 2¢) 22:34, 10 July 2018 (UTC)
Issue 14 – 21 July 2018
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MediaWiki message delivery ( talk) 06:10, 21 July 2018 (UTC) |
I can see a great deal of effort has gone to producing infobox gene and it clearly has some amazing wikidata integration. I think it could be improved in a number of ways and propose some specific suggestions here for discussion. My aim is to make the infobox shorter, easier to read, and increase the prominence of basic information. (I would normally make a sandbox of my proposed edits but am unable to because the infobox is written in lua.) For my inspiration, I am viewing BRCA1 and MLH1.
I'm starting this part of the discussion back here (rather than WT:PHARM), as boghog points out, this being a more appropriate venue. Ping to editors that have participated: Boghog, Seppi333, Jytdog, Looie496, Ajpolino, Tryptofish. Apologies if I've left anyone out. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
We're moving in that direction globally on WP. The list of 'external IDs' in the infobox could easily be moved to an authority control template for articles. This would also help shorten the infobox, reduce the length of its code, and more importantly, simplify the infobox, which is my goal here.-- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
I refer here to the full chromosome panel, not the horizontal individual chromosome with the gene's location boxed. These pictures take up a lot of space, add to loading times, and don't contribute anything factual. They are also duplicated in text (twice) in the infobox.-- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
The section takes up a large amount of vertical space and is limited to links. I propose collapsing it by default. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
There is a title that is called 'available structures' but it seems to be just some links. I don't know what it does or how it relates to genes, and therefore presume most lay readers won't either. I propose renaming it to something that explains what it does, or merging it to identifiers section if it is related. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
{{
Infobox protein}}
could be merged in?
T.Shafee(Evo&Evo)
talk
11:53, 16 July 2018 (UTC)
A 'basic information' section should be created and placed beneath the picture of the protein ribbon and include basic information about the gene written in a human-readable format. Fields can be discussed once we have some support for this section. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
{{
short description}}
field for every article in WP.) Now a second field of "summary information" is being proposed.. and this is just crazy to me. But I guess people will volunteer doing what they want.I often use WP as revision and for my work as I'm sure many people do. I find many of our articles (e.g. Beta-2 adrenergic receptor, which I'm looking at now) very difficult to read and lacking key information which (I feel at least) could be included in the infobox - e.g. where is that thing, what does that thing do, what makes that thing).. The problem they point out is that articles don't have basic information, and their solution was "infobox". This is the wrong solution in my view. But again people will put time in where they want. This just seems to be a diversion of our most valuable resource to me.
Property | Description |
---|---|
Molecular mechanism | damaged DNA binding |
Biological function | DNA repair |
Subcellular location | plasma membrane, cytoplasm, cell nucleus |
The orthologs part of this section is in fact just the titles 'human' and 'mouse'. The rest are just external links. The proposed change makes the purpose of this section much clearer to readers and reflects what it actually does.
Merging these two parts together reduces the amount of headings in the infobox (which are many) and hopefully also simplifies its display. The section can include a subheading for human and mouse. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
It seems like we're on the way to doing this based on WT:PHARM, but I will propose it here as a plan B. The 'gene ontology' section is not useful as is. It contains 20 - 30 text entries describing processes. None of these reflect the article's lead description of the gene, nor the commonly understood function of a gene, e.g. when it is described as encoding an enzyme, membrane receptor, tumour suppressor gene etc. I propose that this section, if it can't be made easier to read and have a more narrow focus, be removed and we just handwrite everything ourselves. Yes that takes time but as an encyclopedia we are never finished and we should be aiming for the best - and spaghetti lists are not helpful to anyone. These lists are not useful at the moment - experts will already know these facts, and lay readers will not be able to make head nor tail of it, nor know how to extract the important items in the list from the chaff. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
Renaming ontology to function makes the purpose of the section much clearer to end readers, which should be our goal here. I am not sure that readers will even look at the content of the section because they won't know what the section title means. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
Gene location is provided in three sections: gene location (human), and (mouse), and also as a field in orthologs. I propose there that the field 'Location (UCSC)' present in orthologs be moved to the appropriate gene location (human) and (mouse) sections, thus centralising this information and also reducing some duplication. -- Tom (LT) ( talk) 23:32, 13 July 2018 (UTC)
Rather than making a large number of changes to the infobox all at once, I think a more limited number of changes could make the infobox much more readable for a general audience without sacrificing the usefulness for specialists. Hence I propose that we implement the following subset of what has been proposed above:
Property | Description |
---|---|
Molecular mechanism | G-protein coupled receptor activity, epinephrine binding, norepinephrine binding |
Biological function | regulation of smooth muscle contraction |
Subcellular location | membrane |
Of course to implement any of this, we must first get buy-in from the those that maintain the infobox and associated wikidata. For example, we have to make sure that changes to the rank of data do not get overwritten by bots. Boghog ( talk) 10:20, 15 July 2018 (UTC)
|most expressed in=
field that auto-filled with text of either the top few hits or all cell types that had expression over some mark (the graphs currently show 3x the median, so perhaps that's a mark of interest?). Bonus points if we could make those top hits wikilink to the relevant wikipedia articles. Of course, the section would also have an external link to the microarray dataset this comes from. As an example, I'm looking at the
BRCA1 infobox which shows
this file and another. Thoughts?
Ajpolino (
talk)
14:45, 15 July 2018 (UTC)I am a new Wikipedia Fellow in the midst of training. I entered " regulatory RNA" and RNAi came up. Of course that's the best worked out regulatory RNA system today, but there are other regulatory RNAs that should be accessed by the general term, such as Xist and others involved in X inactivation and enhancer RNAs, both of which are treated elsewhere on Wikipedia. Does this seem like a problem to others? Is it worth my while to work on putting together a more general treatment of regulatory RNA while I'm in this course? Thank you for considering this. LLMHoopes ( talk) 17:34, 30 July 2018 (UTC)
Hi everyone.
An editor asked me to reproduce File:Estradiol metabolism.png as a wikitext-annotated image. Would anyone here be willing to upload an svg image file with just the 11 compounds in that figure (without any image text except for the letters for the functional groups on the compounds, e.g., the OH for the hydroxyl group) under the file name File:Estradiol metabolitsm.svg? I can't really draw chemical structure diagrams but I can easily draw the pathways, so I intend to edit the uploaded image and add the lines and compound/enzyme annotations + adjust their placement as needed when annotating the image with a template.
@ Boghog: I'm pinging you in the event you're interested in helping with this again and aren't terribly busy. Seppi333 ( Insert 2¢) 22:10, 2 July 2018 (UTC)
@ Boghog: The last thing I need before beginning to annotate and uniformly align the objects in this diagram is an svg image of estrone glucuronide's structure diagram. Could you email me that or add it to File:Estradiol metabolism structures.svg? If you'd prefer the former method, my email is in the source immediately following this sentence. Seppi333 ( Insert 2¢) 11:40, 7 August 2018 (UTC)
Metabolic pathways of
estradiol in humans
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References
I think I'm more-or-less done. Anyone have any feedback/suggestions? Seppi333 ( Insert 2¢) 22:06, 10 August 2018 (UTC)