Opabinia regalis (talk | contribs) →-ome/-omics articles: new section |
Flyer22 Frozen (talk | contribs) →The term "beta cullularis": new section |
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A recent AfD for [[channelomics]] ended in a decision to merge with [[channelome]], but nobody has strong opinions on which way the merge should go. Thoughts at [[Talk:Channelomics#Merge_discussion]]? We have a number of similar pairs of articles - [[glycome]]/[[glycomics]], [[lipidome]]/[[lipidomics]], etc. - for which this might be relevant. [[User:Opabinia regalis|Opabinia regalis]] ([[User talk:Opabinia regalis|talk]]) 04:45, 30 August 2015 (UTC) |
A recent AfD for [[channelomics]] ended in a decision to merge with [[channelome]], but nobody has strong opinions on which way the merge should go. Thoughts at [[Talk:Channelomics#Merge_discussion]]? We have a number of similar pairs of articles - [[glycome]]/[[glycomics]], [[lipidome]]/[[lipidomics]], etc. - for which this might be relevant. [[User:Opabinia regalis|Opabinia regalis]] ([[User talk:Opabinia regalis|talk]]) 04:45, 30 August 2015 (UTC) |
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== The term "beta cullularis" == |
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Per [https://en.wikipedia.org/w/index.php?title=User_talk:Flyer22&diff=679529232&oldid=679522705#Dubious_edit_by_anon_on_humoral_immunity this section] on my talk page, there is concern that the term ''beta cullularis'', which [https://en.wikipedia.org/w/index.php?title=Humoral_immunity&diff=prev&oldid=624707821 was added] to the [[Humoral immunity]] article, is not an actual term. [[User:Flyer22|Flyer22]] ([[User talk:Flyer22|talk]]) 04:15, 5 September 2015 (UTC) |
Revision as of 04:15, 5 September 2015
WikiProject Molecular and Cell Biology
A community for editors of — molecular biology · cell biology · developmental biology · microbiology · biochemistry
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WT:MCB
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A thorough review of the gene article
- Transcluded from Talk:Gene/Review
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)
- It appears the main reason gene was delisted as a GA was sourcing (see Talk:Gene/GA1). The following free textbook is probably sufficient to document most basic facts about genes:
- a second one is even more relevant, but unfortunately not freely accessed:
- I will start working on this as I find time. Boghog (talk) 17:58, 31 March 2015 (UTC)
- Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to give it some attention. Opabinia regalis (talk) 19:19, 31 March 2015 (UTC)
Glossary
Snooping 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)
- Including a glossary could be useful, but I think it should be concise and tailored specifically for this article. Currently {{Genetics glossary}} contains 22 entries and some of the definitions are quite lengthy. A shorter glossary, closer to the size of {{Transcription factor glossary}} or {{Restriction enzyme glossary}}, IMHO would be more effective. Another option is to transclude the {{Genetics sidebar}} which in turn links to {{Genetics glossary}}. Boghog (talk) 06:38, 2 April 2015 (UTC)
- ...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence. Seppi333 (Insert 2¢ | Maintained) 07:25, 2 April 2015 (UTC)
- Collapsed or not collapsed, {{Genetics glossary}} is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article. IMHO, a long glossary defeats its purpose. Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse. Boghog (talk) 08:30, 2 April 2015 (UTC)
- Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article genetics glossary. (I'm not really sure we need both.) I agree that the template is way too long, and as constructed is hard to ctrl-F for a term.
- I suggest just linking to the MBC glossary as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers. Opabinia regalis (talk) 21:47, 2 April 2015 (UTC)
References
I'm planning on adding some more Molecular Biology of the Cell references to the article using {{rp}}
to specify chapter sections. I went to the MBOC 4th ed. online page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for Biochemistry 5th ed. online? Alternatively, maybe there's a more easily refernced online textbook for general citations. T.Shafee(Evo﹠Evo)talk 11:30, 20 April 2015 (UTC)
- I had the same train of thought here on the regular talk page. How about something like this? Uses {{sfn}} to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'. Opabinia regalis (talk) 06:09, 21 April 2015 (UTC)
- You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful. T.Shafee(Evo﹠Evo)talk 08:06, 21 April 2015 (UTC)
- I am not a big fan of {{sfn}} templates. They are more complicated and harder to maintain. Plus they don't directly address the problem of searching Molecular Biology of the Cell. What seems to work is to search for the chapter or subchapter titles in quotes. For example search for "DNA and Chromosomes" provides a link to the introduction of chapter 4. Then one can reference the chapter or subchapter number with {{rp}}. I am busy this week but should have more time this weekend to work on this. Boghog (talk) 12:21, 21 April 2015 (UTC)
- I mis-described my own suggestion; it's actually {{efn}} (not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use {{rp}} like this, but I think the links police won't like that. Opabinia regalis (talk) 18:03, 21 April 2015 (UTC)
- OK, I now see what you mean. The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
- Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. Chapter 4: DNA and Chromosomes; Chapter 7: Control of Gene Expression; Chapter 7.1: An Overview of Gene Control; Chapter 7.2: DNA-Binding Motifs in Gene Regulatory Proteins; Chapter 7.3: How Genetic Switches Work
- or have separate citations for each chapter where only the
|chapter=
and|chapterurl=
parameters differ:- Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Chapter 7: Control of Gene Expression". Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.
{{cite book}}
: External link in
(help); Unknown parameter|chapterurl=
|chapterurl=
ignored (|chapter-url=
suggested) (help)
- Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Chapter 7: Control of Gene Expression". Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.
- Boghog (talk) 18:47, 21 April 2015 (UTC)
- OK, I now see what you mean. The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
- My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a bit silly. I think I like that idea in combination with {{rp}} chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting. Opabinia regalis (talk) 20:49, 21 April 2015 (UTC)
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)
- You're the one currently doing the work, so I think that means you get to decide :) Opabinia regalis (talk) 19:01, 22 April 2015 (UTC)
MBOC references
Article
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)
- I've finished adding MBOC references up to section 3 (gene expression). Also, whoever originally wrote the gene expression section of the article really liked semicolons! T.Shafee(Evo﹠Evo)talk 10:51, 27 April 2015 (UTC)
- Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in WP:ACCESSIBILITY so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue. Opabinia regalis (talk) 07:50, 28 April 2015 (UTC)
- @Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS." I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view. I tried setting the template parameter
expand=true
so the box is expanded by default but that made no difference. Maybe better to change to a bulleted or indented list? Adrian J. Hunter(talk•contribs) 10:50, 30 June 2015 (UTC)- @Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in
{{Hidden begin}}
+{{Hidden end}}
, which renders properly on phones (default expanded). T.Shafee(Evo﹠Evo)talk 12:31, 30 June 2015 (UTC)- Yep, that works – thanks! Adrian J. Hunter(talk•contribs) 13:23, 30 June 2015 (UTC)
- @Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in
- @Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS." I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view. I tried setting the template parameter
Warnowiaceae
I'm not sure how this fits into this class or species, but shouldn't this article include information on the ocelloid bearing dinoflagellates (warnowiids?) - quite unique in being a very complex single-cell organism which simulates a relatively complex 'eye' called an ocelloid that has structures in it similar to parts of mammalian eyes?
The photosensitive ocelloid probably forms from a chloroplast and might be used to hunt or evade. The ocelloid can also be directed within the cell. The erythropsidinium ocelloid dinoflagellates are also apparently unique in that they have a piston-like structure which they can use to move. --24.88.64.22 (talk) 05:28, 4 July 2015 (UTC)
- I completely missed this when it was posted, but someone prodded me about it - there was a widely reported Nature paper a couple of weeks ago on these guys. Warnowiaceae and ocelloid exist now if anyone has more to add! Opabinia regalis (talk) 06:17, 24 July 2015 (UTC)
WP:Lead sentence at the Estrogen article
Opinions are needed on the following matter: Talk:Estrogen#WP:Lead sentence. A WP:Permalink for that discussion is here. Flyer22 (talk) 13:25, 25 July 2015 (UTC)
Creating an infobox template for cell lines
Reading several articles about different cell lines, I noticed that they are mostly very different in regard to style and scope. I was thinking that an infobox that summarises facts that are relevant to all cells lines could be useful in giving them a common appearance and in making key facts more accessible. For example, it could comprise facts such as the tissue and species of origin (epithelial / lymphoid..., human / mouse...), growth type (adherent / suspension) and maybe shortcut links to databases such as ATCC, ECACC or DSMZ using the respective identifiers. Do you think such an infobox could be useful?
I am currently building an experimental template on my userpage, you can access it at User:Shinryuu/Template:Infobox cell line. In my sandbox I created a test infobox based on the widely used HEK 293 cells to test the template. However, it is the first template I ever built, and it is still fairly rudimentary. If you think this could be a useful contribution, any advice or contribution would be very welcome. Shinryuu (talk) 18:33, 3 August 2015 (UTC)
- These articles truly need more love, including templates and sourcing. I approve of this idea. I'll also stick some of these articles on my create/expand to-do list. Jo-Jo Eumerus (talk, contributions) 18:37, 3 August 2015 (UTC)
- If the idea is generally approved, I would say the template is almost good to go. I'm not sure if I've included all major cell line databases though. Currently, the template has shortcuts to the ATCC, DSMZ and ECACC as well as the Italian CLDB (Cell Line Data Base), but are those four really all there are? Most other databases and culture collections I know or found, such as ICMP, BCCM/LMG, NCPPB and CDBP (Collection Française de Bactéries associées aux Plantes), have bacteria or other organisms, but no cell lines as far as I know. Is that correct? Shinryuu (talk) 20:12, 5 August 2015 (UTC)
"Radical"
The naming of Radical (chemistry) is under discussion, see Talk:Radical (chemistry) -- 67.70.32.190 (talk) 04:58, 6 August 2015 (UTC)
New article
Pangenom was recently created. I suspect it may be about the same subject as the article pan-genome, but in any case it needs attention from members of this WikiProject. Everymorning (talk) 18:56, 13 August 2015 (UTC)
- My suggestion is: not merge but to delete Pangenom. The name is misspelled (the single quoted reference calls it pangenome) and the WP article is terribly written. After a look at Google Scholar, my impression is that the article currently presented here as "Pangenom" is a concept proposed 10 years ago that took no apparent hold in the field of molecular biology and therefore made no impact, so it lacks notoriety for Wikipedia. All the sources in the literature I saw, use the term pangenome (or pan-genome) in the context of the sum of all the genes in a given species, in a clade or even in a Kingdom. BatteryIncluded (talk) 21:33, 28 August 2015 (UTC)
Proposed major overhaul of Cell (biology)
I am planning a major overhaul of Cell (biology) in the next couple of months. Please see my full proposal at Talk:Cell (biology)#Proposed major overhaul and leave any suggestions or comments you have for me there; I would like to keep the discussion all in one place if it's at all possible. Thank you. AmericanLemming (talk) 00:13, 22 August 2015 (UTC)
- Good plan. I'll help out where I can. Luckily there are already some good images about the place by user:LadyofHats and user:Kelvinsong. It might also be worthwhile having a look at the Gene article for a possible way to reference MBOC. T.Shafee(Evo﹠Evo)talk 01:22, 22 August 2015 (UTC)
Juvenile hormone epoxide hydrolase
I created a new article by this name about a a week ato, submitted for checking. How long until it apprears> Graybeard biochemist.
- User:GraybeardBiochemist/sandbox? That needs a bit of structure and wikifying. Also, there is a huge block of italicized text in the middle. Jo-Jo Eumerus (talk, contributions) 09:51, 28 August 2015 (UTC)
- @GraybeardBiochemist: You didn't actually submit the article for submission. There is a button at the top of your sandbox which needs to be pressed before in order to submit it. In any case, I have wikified it and moved it into mainspace (see Juvenile hormone epoxide hydrolase). Boghog (talk) 11:03, 29 August 2015 (UTC)
-ome/-omics articles
A recent AfD for channelomics ended in a decision to merge with channelome, but nobody has strong opinions on which way the merge should go. Thoughts at Talk:Channelomics#Merge_discussion? We have a number of similar pairs of articles - glycome/glycomics, lipidome/lipidomics, etc. - for which this might be relevant. Opabinia regalis (talk) 04:45, 30 August 2015 (UTC)
The term "beta cullularis"
Per this section on my talk page, there is concern that the term beta cullularis, which was added to the Humoral immunity article, is not an actual term. Flyer22 (talk) 04:15, 5 September 2015 (UTC)