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Would someone review the Cyclopentenone prostaglandins article for the purpose of reclassifying it? The article has recently been greatly expanded. Although it is categorized as a Pharmacy and Pharmacology article, it is better categorized in the Molecular and Cellular biology section. All of the prostaglandins are so categorized (e.g. see prostaglandin). Also, the article as currently formatted is correctly redirected from 15-deoxy-Δ12,14-prostaglandin J2 (15-d-Δ12,14-PGJ2), a principal cycloentenone prostaglandin. Is it possible to similarly redirect it from other cyclopenentone prostaglandins viz., Δ12-PGJ2, PGJ2, PGA2, and PGA1, discussed in the article (but not given separate Wikipedia pages elsewhere) and, if so, how do I do that? Thanks, ( User talk:joflaher). 6 December 2016 (UTC)
Illumina sequencing is a very important method to know nowadays, as least for anyone working in molecular biotechnology. The figure for the creation of clusters is correct, but could use someone who puts in some love. It was obviously drawn quickly and I think the article deserves more.
/info/en/?search=Illumina_dye_sequencing
There are many nice resources to find inspirations, such as the Youtube channel of illumina.
Following the discussion above, interested parties should also chime in at WikiProject Microbiology and WikiProject Fungi. -- Nessie ( talk) 15:10, 12 April 2019 (UTC)
It's at Wikipedia_talk:WikiProject_Equine#Gene_names. Iamnotabunny ( talk) 04:54, 2 May 2019 (UTC)
I was looking up phase separation and found biomolecular condensate which has a rather confusing link to Spinodal decomposition - having had only a just an overview after reading a couple of reviews, it looks like these articles need more work considering that there is currently a lot of talk (hype?) on the topic. I hope someone with specialist knowledge on this can improve coverage on this cluster. Shyamal ( talk) 15:57, 6 May 2019 (UTC)
References
Moot
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The current
This is a HGNC search page for entries associated with the parameter input to Example: Q3, methyltransferase coenzyme Q3, methyltransferase contains results for "coenzyme" only; the "Q3, methyltransferase" is omitted because the spaces aren't url-encoded [via replacement with "%20"]). The correct url for that search is https://www.genenames.org/tools/search/#!/genes?query=coenzyme%20Q3,%20methyltransferase.
Since this is a better link target for inputted HGNC ID numbers, would anyone object to me recoding this template using this markup? I can't imagine that this would break any existing links that aren't already broken due to the use of a phrase/string as an input value. Seppi333 ( Insert 2¢) 19:11, 23 November 2019 (UTC) |
Never mind. A number of template calls use the gene symbol in the first parameter, so recoding it as described would break those links.
I’ll just create Template:HGNC for with the url above for HGNC IDs when I’m back on my laptop. Seppi333 ( Insert 2¢) 00:39, 24 November 2019 (UTC)
Can someone take care of this page merge on both WP and wikidata? C19orf44 (gene) has a lot of content; C19orf44 has almost nothing. Found them searching for pages/redirects containing "C#orf#" and "(gene)" in the title. I've taken care of another page that simply needed to be moved from "C#orf# (gene)" to "C#orf#".
There's undoubtedly more duplicate gene articles out there, but I'll look for them later. Going to work on programming a solution to fix the dablinks and mistargeted links to non-gene-related pages in my tables first. Seppi333 ( Insert 2¢) 00:34, 20 November 2019 (UTC)
moot
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Context: for training a speech to text AI. Seppi333 ( Insert 2¢) 20:43, 2 October 2019 (UTC)
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I'm ready to tackle this now. Anyone know of any source (i.e., a single webpage or data file [any format, structured or unstructured]) with a list (preferably expert-reviewed) of just the 20,000-ish HGNC-approved gene symbols? I imagine I could probably find this if I looked hard enough in genomics info/data-bases. With exception for KEGG, I only have familiarity/experience with proteomic and metabolomic DBs; I don't really know what expert-reviewed/annotated genomics DBs are available, so I'm not sure where the best place to start looking for this data would be.
FWIW, it probably wouldn't be a bad idea for this project to have a subpage containing wikilinks to all those symbols for maintenance and bot-related purposes. Seppi333 ( Insert 2¢) 05:42, 29 October 2019 (UTC)
'protein-coding_gene.txt'
file from HGNC, put the .txt file and the python file containing the code below in the same working directory, and then just run the python code; it then creates the 'Human protein-coding genes wikitext.txt'
files, which contain wikitext markup for those wikitables, in the same directory.I was surprised to find that there isn't an article on these topics. The more general article on metagenomics has far too broad a scope to be suitable piped linking since it pertains to aggregation of genomes in an arbitrary environment (e.g., a pond, a person's body, soil, etc.). That said, there are two level 3 sections in that article that pertain to human metagenomics: Metagenomics#Gut Microbe Characterization and Metagenomics#Infectious disease diagnosis. I'm also kind of puzzled as to how there's no article on microbiomics given how much content is contained in the article on the more niche topic of pharmacomicrobiomics. In any event, I'm just posting these here in the event anyone knows of a suitable article for redirecting or wants to create a stub. There obviously a rather large amount of topical overlap between [human] metagenomics and [human] microbiomics (i.e., metagenomic sequencing is used to characterize all of the genomes within an arbitrary microbiome), so I suppose human metagenome could redirect to human microbiome provided that it's covered there. Similarly, microbiomics could probably be covered in a section of metagenomics.
Boghog I wrote a new section in
Amphetamine#Pharmacomicrobiomics which covers material pertaining to these topics (it's censored in the source) but your citation tool is down and I'm too lazy to manually look up the parameter inputs and write the markup for 4 citations. Would you be able to fix it, please?
Seppi333 (
Insert 2¢)
18:17, 10 July 2019 (UTC)
sci-hub.tw/10.1002/jcb.28396
) mentioned the enzyme was tyramine oxidase and linked to ExPASy (
corresponing enzyme entry), but they didn't specify a metabolite. Based upon the reaction listed in the link, wouldn't the product when amphetamine is used as a substrate be
this (alpha-methylphenylacetaldehyde)?
Seppi333 (
Insert 2¢)
16:39, 11 July 2019 (UTC) You are invited to join the discussion at
Draft talk:Horizontal transfer of mitochondria#Opinions of subject matter experts sought.
Worldbruce (
talk)
14:47, 24 June 2019 (UTC)
IMO, well sourced article about a geneticist. But you can help improve it. 7&6=thirteen ( ☎) 15:52, 4 July 2019 (UTC)
Hi all,
I would appreciate your input in this strange case: Wikipedia_talk:Copyright_problems#Wikipedia_page_"later"_published_in_scientific_paper:_copyvio?.
-- Steven Fruitsmaak ( Reply) 20:00, 20 July 2019 (UTC)
Hi WikiProject Molecular Biology members,
I have made numerous small edits to the ATAC-seq page, a page that is within the purview of your project, to improve its quality. I've also rewritten the whole page to remove promotional and overly-technical content and to add citations and crosslinks. But I have a conflict of interest, so I cannot make the changes myself. I copied my rewrite into the talk page. Could a project member please review my rewrite and use it to replace the content that is there?
Thank you,
cglife.bmarcus ( talk) 1:17, 5 September 2019 (UTC)
Just found a link on Angelika Amon to the redirect CLB2 which is an airport code. Is CLB2 also an abbreviation for Cyclin B2? CambridgeBayWeather, Uqaqtuq (talk), Sunasuttuq 05:50, 30 September 2019 (UTC)
I need some help interpreting the implications of the TNXB entry in this spreadsheet: [4] (Suspect variants.xlsx). The spreadsheet indicates my brother's TNXB gene is compound heterozygous due to distinct frameshift mutations on each allele, reflecting the autosomal recessive form of "TNXB deficiency". From my understanding, frameshift mutations tend to result in the translation of proteins that are completely functionally borked. So... his genotype predicts a clinical phenotype of "classic-like EDS" (clEDS), which is rather severe. I've repeatedly read a number of times in about 20 or so papers on TNXB this past week that "TNXB haploinsufficiency" (associated with having 1 wild type and 1 mutant allele, autosomal dominant inheritance) causes "hypermobility-type EDS" (hEDS), a milder clinical phenotype than clEDS in which hypermobility can manifest with muscle issues, skin issues, and/or vascular issues. His actual clinical phenotype is User:Seppi333#John, which notably lacks any skin involvement or easy bruising, both of which always occur in TNXB deficient individuals and are required for a clinical diagnosis of clEDS. He meets the straightforward clinical diagnosis for hEDS listed here. In comparison, I am wild-type; I fail to meet both criterion 1 (Beighton Score: 2/9) and criterion 2 (2A: 1/12 total, 2B: obviously applies, 2C: 0/3) in that list and so criterion 3 is N/A. Edit: I have no clue about my genotype since I've never gotten or needed any form of genome sequencing. I'm a bit confused as to how to explain this; the only explanation I can think of is that one or both of his compound heterozygous alleles is creating a functional frameshift-mutated tenascin-X protein. Since he doesn't have skin or vascular symptoms and since the loss of a single TNXB allele is sufficient for – and a common cause of – hEDS, it seems like the combined protein function across both alleles can't be significantly worse than having 1 wild-type allele and 1 allele from which a protein isn't translated. Is that rather unusual or are frameshift mutations simply not as pathogenic as I've been lead to believe? Seppi333 ( Insert 2¢) 23:51, 5 October 2019 (UTC)
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Extended content
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There's two issues I should address before I even consider moving those tables to the article space. The bigger problem is pages where an article for the gene symbol does not exist and the target article of the wikilink is about something completely unrelated. Suppose, for example,
rage was not a disambiguation page, but an article about the emotion and that
RAGE redirected to that article. Then
RAGE would appear as a blue link in the wikitable and not be a link to a disambiguation page. In that case, the
Dablinks tool wouldn't tell me that I should be linking
RAGE to
RAGE (gene) via a piped link ( @ Boghog, Evolution and evolvability, Mark viking, or anyone else for that matter: would you happen to know of a way I might be able to detect problematic wikilinks like that? Seppi333 ( Insert 2¢) 19:53, 4 November 2019 (UTC)
Sorry, late to the discussion. Another option is Wikidata. "protein-coding gene in the species Homo sapiens". Wikidata. These data items provide links to the corresponding Wikipedia article if one exists. Boghog ( talk) 07:49, 5 November 2019 (UTC)
Sigh. The Dablinks tool did not give me all the dablinks in these tables. I'm guessing it only parses a few thousand links before stopping. Working backwards and checking the last 1000 entries in the 2nd table, I found WIZ, WLS, WRN, XDH, XG, XK, XPC, ZYX. I'll need to program a solution to take care of that as well. Seppi333 ( Insert 2¢) 19:52, 6 November 2019 (UTC)
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I'm running my mistargeted link detection script right now. I expect it will take around two hours to finish based upon sample tests. Assuming nothing goes wrong, I'll post the complete list of links here, since I will need help locating the correct link targets if they exist. Seppi333 ( Insert 2¢) 02:49, 26 November 2019 (UTC)
Boghog There's tons of script output spamming my output window right now, but I was curious when I saw a RFNG redirect to Radical Fringe gene( [5] [6]). It doesn't have a gene infobox; could you fix the pair of wikidata items for that? I'm not sure what to do with the one that radical fringe gene is currently linked to. Edit: attempted to just go ahead and move the link to the right data item, but it says the other needs to be deleted. >.> Seppi333 ( Insert 2¢) 04:38, 26 November 2019 (UTC)
Pretty sure this is the very last dablink in the wikitables at the moment.
COQ3 (gene) redirects to COQ3, which includes a list of 2 enzymes. The wikidata item for COQ3 in Homo sapiens isn't linked to a WP article: [9].
From a cursory glance, it looks like 3-demethylubiquinone-9_3-O-methyltransferase is the correct article of those 2. Should the WD item be linked to that and a gene infobox be included in the article? Seppi333 ( Insert 2¢) 19:10, 23 November 2019 (UTC)
It makes sense to merge enzyme EC and gene Wiki articles if and only if there is a one-to-one correspondence between EC number and HUGO gene symbol.That's useful to know. Thanks for resolving the disambiguation issue. Seppi333 ( Insert 2¢) 10:10, 24 November 2019 (UTC)
After I fix the few dozen mistargeted links I mentioned, these tables will contain links to almost all pages in the GeneWiki along with a list of 1 or more UniProt IDs for each gene.
Given that these tables contain all the article links and id numbers I'd need, I could program an algorithm to move all the pages to which the the gene symbols are linked to their official UniProt names a la
MOS:MCB#Article name provided there is only 1 UniProt link associated with the gene symbol; it obviously makes no sense to move a page that corresponds to multiple UniProt IDs. I could also set an upper limit on the length of the string-formatted UniProt name to avoid moving pages to long page titles per this: If the protein name is verbose, either a widely used protein acronym or the official HUGO gene symbol, followed by "(gene)" if necessary to disambiguate.
Should I work on a script to move gene pages that are located at gene symbols to the pagename of their official UniProt name, or are there circumstances where doing that would be problematic?
Seppi333 (
Insert 2¢)
21:30, 25 November 2019 (UTC)
Lines 6–11289 in
User:Seppi333/GeneListNLP#Output show that the vast majority of pages about human protein-coding genes use the gene symbol as the page name. Using ctrl-F to count them, 8600 pages are located at the gene symbol and 2683 are located on pages with a different title (NB: these numbers include the 226 unrelated pages, so they're not exact counts for each). Also, the fact that only 11283 links were processed suggests that Wikipedia is missing around 8000 articles on human protein-coding genes. On a tangential note, I thought I moved almost all of the pages in the
solute carrier family from the gene symbol to the official UniProt name, but that output indicates that I missed a few.
Seppi333 (
Insert 2¢)
09:20, 26 November 2019 (UTC)
Specific things I'd like feedback on:
Seppi333 ( Insert 2¢) 05:16, 24 November 2019 (UTC)
There's a discussion going on over at Wikipedia_talk:WikiProject_Biology about whether it is worth consolidating some of the disparate biology wikiprojects. One possibility could be a merger or semi-merger of WP:GEN + WP:MCB + WP:COMBIO + WP:BIOP, since their scopes are well-aligned. Ideas and opinions welcome! T.Shafee(Evo&Evo) talk 01:14, 25 May 2019 (UTC)
Hello, based on the consensus at the
WP:Biol discussion, this is confirmation of my suggestion to merge:
WP:GEN +
WP:MCB +
WP:BIOP +
WP:CELLSIG (possibly +
WP:COMBIO) -> into
Wikipedia:WikiProject Molecular Biology (name to be confirmed)
The new main page should be able combine all of the information of each project (much of which overlaps) and the talkpage should also also centralise discussion to make it more lively and easier for newcomers! Separate
tracking tables of article qualities can still be kept by making them 'taskfores' if people think that'll be useful. If people don't object I'll go about redirecting the WP and WT pages to that centralised location next week per
this process.
T.Shafee(Evo&Evo)
talk
13:09, 10 June 2019 (UTC)
Merger complete! See the new unified talkpage. All talkpage archives should be clearly visible and searchable and the new unified WikiProject page is almost complete. T.Shafee(Evo&Evo) talk 12:25, 16 June 2019 (UTC)
There's a discussion about a possible User Group for STEM over at Meta:Talk:STEM_Wiki_User_Group. The idea would be to help coordinate, collaborate and network cross-subject, cross-wiki and cross-language to share experience and resources that may be valuable to the relevant wikiprojects. Current discussion includes preferred scope and structure. T.Shafee(Evo&Evo) talk 03:04, 26 May 2019 (UTC)
Hello everyone, i am the author of the DNA replication image give or take i made this image arround 2007, i have been asked to modify it to incorporate all the comments and corrections made on the discussion page plus someone left the following request on the Graphics lab on commons:
Now I am an illustrator and by no means expert in this subject so i would really appreciate if someone with the appropriate knowledge could have a look on this
Sketch. it isnt yet on its final form but the elements are in the relative position i am hoping them to have (all marked with ? would need some reassuring). also there is like a ton of questions i would really want to have answer if that is ok:
if you would be so kind to answer my questions i could at least have some degree of confidence in remaking the image in a better more accurate state. 大诺史 was kind to offer this article as reference [10]. I look forward to your feedback. and thank you for your time - LadyofHats ( talk) 18:58, 5 June 2019 (UTC)
The articles pre-replication complex, minichromosome maintenance, and origin recognition complex can use some better images for the protein structures in light of the not-so-recent publications of EM structures. My computer and my brain are currently too messed up to sort out the PyMol or whatever rendering thing, so would anyone please render some views (two will do: front and top) for PDB ID 5v8f (pre-RC OCCM), 3JA8 (MCM; 5UDB will do too), and 4XGC (ORC; 5UDB will do too)? -- Artoria 2e5 🌉 23:48, 23 June 2019 (UTC)
So, below is what my algorithm found.
If the mistargeted gene symbol isn't a redirect, it's listed as en:PAGENAME on that line.
If the term is a redirect, the format below is en:REDIRECT → en:PAGENAME. Seppi333 ( Insert 2¢) 05:15, 26 November 2019 (UTC)
I'm not sure how to address this. For each gene symbol below that no relevant article exists, should we just create a DAB pages with redlinks to SYMBOL (gene) listed on it? A lot of the symbols below should clearly link to disambiguation page. Seppi333 ( Insert 2¢)
It makes sense to merge enzyme EC and gene Wiki articles if and only if there is a one-to-one correspondence between EC number and HUGO gene symbol.
After thinking about how to algorithmically deal with the problem of locating existing articles for the symbols above that do not redirect to enzyme pages – and all the redlinked gene symbols in the wikitables for that matter – I realized that I could do the following in sequence for every gene symbol:
I apologize to everyone in this WikiProject for practically spamming the page with issues related to the wikitables I'm working on; I imagine it might be annoying to some people. I'm done with the tables now. I'm going to write the algorithm I described above, but I'm going to ignore anything I can't quickly address by myself. Seppi333 ( Insert 2¢) 11:43, 27 November 2019 (UTC) |
New RFBA since I now have the data that I was going to program this algorithm to obtain – Wikipedia:Bots/Requests for approval/Seppi333Bot 2. Haven't processed the query results yet, but I expect it'll permit creation of about ~2000 gene symbol redirects. Seppi333 ( Insert 2¢) 01:29, 20 December 2019 (UTC)
Prime editing has hit the mainstream press, with lots of hyperbole about its potential, in spite of it still being at the laboratory proof of concept stage. I've created a stub article for it; can knowledgable people please help improve the article? -- The Anome ( talk) 09:33, 22 October 2019 (UTC)
Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.
We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma ( talk) 04:24, 27 October 2019 (UTC)
The following discussion may be of interest to this project: Wikipedia_talk:WikiProject_Medicine#MEDRS_sourcing_required_for_non-biomedical_information. -- Signimu ( talk) 17:50, 1 November 2019 (UTC)
I wrote the bot script yesterday morning and it's been operating since then. Pending approval of my bot and validating the links as mentioned in the section below, I'll move those tables to the mainspace. Seppi333 ( Insert 2¢) 18:16, 6 November 2019 (UTC)
Identified in
User:Certes/Gene links#Miscellaneous; I've PRODed these per
HGNC:3523. If you agree, you may want to add a {{
Prod2}}
template.
Seppi333 (
Insert 2¢)
01:44, 30 November 2019 (UTC)
On the one hand, this bot had some problematic bugs prior to being blocked; I've personally had to merge/regarget dozens of erroneous pages it created. As far as I am aware, it correctly wrote page content, but sometimes got the page name wrong, created a duplicate entry, and/or created a redirect to the wrong pagename.
On the other hand, subsequent to identifying the 215 mistargeted links in list of human protein-coding genes pages, I've only created 4 new gene/protein stubs [1] while attempting to unbork the articles, redirects, and set index articles identified by my algorithm as well as creating entries for redlinks on DAB pages like (e.g., ALLC (disambiguation)) that WT:WPDAB is helping to create. A few dozen gene articles need to be created to fully address those issues. I currently need to create the 2 redlinked entries listed in User:Certes/Gene links#Redirects, but I would rather repeatedly bang my head against a wall than create another due to how tedious it is to create new gene articles with all the minutia involved. [2]
This led me to an idea that I hope is a viable solution to the problems PBB and I have, assuming that everyone is on board. Consider the following:
A relatively simple solution to keeping my brain intact, my wall stain-free, and PBB's bugs in check is to modify the bot code so that it writes gene articles to the corresponding pagename in the draft namespace upon user activation at
biogps
@
Fram: would you be open to unblocking the bot if it wrote gene articles to the draft namespace so that they can be moved pending validation?
@
Andrew Su and
Julialturner: if either of you are still around and biogps can still trigger PBB to create a gene page, would you be willing to recode the bot so that it writes the corresponding gene entry to
Draft:Pagename instead of
Pagename?
Seppi333 (
Insert 2¢)
04:11, 2 December 2019 (UTC)
For a much less self-centric motivation: WP has ~11500 bluelinked protein-coding gene symbols and ~8500 redlinked ones. PBB created ~9400 articles (non-redirect, still live pages) since it was created. Given its original purpose, I suspect that the majority of the 9400 pages PBB created are the articles or targets of the redirects located at those 11500 symbols. So, in spite of its bugs, Wikipedia needs algorithms like PBB if we’re ever going to finish creating the entries for the other half of the exome. Seppi333 ( Insert 2¢) 04:12, 2 December 2019 (UTC)
There are many of genes whose function has not yet determined and have not been mentioned in reliable secondary sources, hence these genes fail WP:NOTABILITY requirementsI’m well aware.
@ Andrew Su: Ty for creating that; makes all the work ahead of me seem much more bearable now. Seppi333 ( Insert 2¢) 06:14, 2 December 2019 (UTC)
{{
Infobox gene}}
to work, identify and add the corrsponding gene-chromosome-stub template like {{
gene-1-stub}}
, cite the UniProt-recommended protein name and HGNC-approved gene symbol in the first sentence, figure out something of note to write and cite to pad the page so that I'm not literally creating an article that just says "X is a protein encoded by Y", and then do everything else that any other Wikipedia article normally requires (i.e., sections, formatting, reference template, project tags on talk page, etc.). Then again, I don't like creating articles to begin with.
I have nominated Folding@home for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. GamerPro64 17:18, 9 December 2019 (UTC)
I saw a Science Reference Desk question about this article. I've edited some of the references but have concerns about the content in this article. I've started a discussion at Talk:Non-helical models of DNA structure#Work from X, Y. C. about my concerns. Any and all comments, edits, etc welcome. Thanks, EdChem ( talk) 04:14, 13 December 2019 (UTC)
I figured someone would do this sooner or later. Seppi333 ( Insert 2¢) 13:08, 2 January 2020 (UTC) |
So, this is something I wondered about years ago, but it's time for me to raise it again. What are the thoughts of people about writing articles like List of human Nrf2 targets (i.e lists of genes that are regulated by a given transcription factor)? They might be of interest to readers, but I don't know what kind of issues they might do. Jo-Jo Eumerus ( talk) 19:01, 17 April 2020 (UTC)
First off, I feel like a bit of a dumbass for asking if one of my brother's frameshift mutations could be functional a while back because I didn't know how to read this earlier in the annotated file I had linked:
According to UniProt, the canonical protein isoform of TNXB has a length of 4244 AA. These frameshifts both occur at glycine residue 362, are >90% truncated relative to the wild-type tenascin-X protein, and they lack nearly all functional domains on the wild-type protein ( https://www.uniprot.org/uniprot/P22105#family_and_domains). Complete deficiency in this gene is supposedly highly penetrant for clEDS, but it's somehow only partially penetrant in my brother's case; it's definitely not because one of these proteins is expressed, partially folded, and somehow functional on the sequence preceding the mutation though.
In any event, I'm finding it pretty hard to grasp how this is possible in terms of genetic inheritance unless this involved some abnormal form of inheritance; it just seems unfathomably unlikely that both my parents carry nearly identical frameshift mutations which haven't been previously reported and that both involve an A>G mutation and affect the same protein residue. Sequencing them both would obviously determine if that's the case, but TNXB sequencing is prone to errors due to significant pseudogene interference from TNXA and I don't think it's likely to happen anyway.
Could this arise from
uniparental disomy? Or is there another abnormal mode of inheritance that might give rise to seeing mutations like this? I'm just a bit baffled due to my ignorance in this area.
Facepalm
Seppi333 (
Insert 2¢)
12:40, 20 May 2020 (UTC)
Hello guys and gals,
Can someone get the archiving fixed on Talk:Archaea, please? It is getting long and has posts going back to 2014. Thanks, Galendalia Talk to me CVU Graduate 13:58, 30 May 2020 (UTC)
I have nominated
DNA repair for a
featured article review here. Please join the discussion on whether this article meets
featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are
here.
SandyGeorgia (
Talk)
22:51, 14 June 2020 (UTC)
I've also copied this over to
WT:MOLBIO.
T.Shafee(Evo&Evo)
talk
03:15, 15 June 2020 (UTC)
There have been a lot of small edits from brand new users to this article. Just about every red name in the edit history has made exactly that one edit. I thought they were all one person, but it looks like I was wrong. A lot of them are unsourced with no edit summary and change around the meaning of the article. I don't have the subject knowledge to say if these are vandalism or plausible though, perhaps someone on this WikiProject can take a look through edits such as these? 1 2 3 4 5 For example, I can vaguely say that the first edit I linked is probably incorrect...? But I'm far from certain. (Those 5 are just an example, there are many more in the history, some reverted, some accepted) Leijurv ( talk) 20:48, 8 July 2020 (UTC)
Talk:G4 EA H1N1#Proposal: Redirect to main H1N1 article SandyGeorgia ( Talk) 04:46, 12 July 2020 (UTC)
Cis-regulatory module and Cis-regulatory element seem to overlap largely, and to a non-geneticist they seem extremely similar if not a WP:FORK. It doesn't look as if a simple redirect would do the job, so perhaps someone could look at the matter, and either make the articles clearly distinct or merge them. Editors have noted the issue since, ah, 2011. All the best, Chiswick Chap ( talk) 21:14, 17 July 2020 (UTC)
The articles /info/en/?search=Cell_communication_(biology) and /info/en/?search=Cellular_communication_(biology) should be merged. RIT RAJARSHI ( talk) 09:34, 30 July 2020 (UTC)
It looks like many of the Wikiproject Molecular Cell biology articles lacking details and remaining unimproved for years to decades. Recently I noticed an article whose title does not match with its content ( /info/en/?search=Membrane_topology). Looks like there are scope of lot of improvements in many of the articles, which are not happening. Is there a deficit or reduction of contributors? Also is there a general reduction of wikipedia activities? How can we again increase activity in Wikipedia? With best wishes for Wikipedia. Thanks in advance. RIT RAJARSHI ( talk) 09:38, 30 July 2020 (UTC)
I have nominated Cell nucleus for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. ( t · c) buidhe 22:16, 11 September 2020 (UTC)
In retrospect, it does seem rather inappropriate for me to have posted what DGG deleted in this section, so I wanted to apologize to those here (re this discussion:
User talk:Seppi333#October 2020). My bad. I hope everyone can forgive my lack of forethought and stupidity for committing a faux pas.
Seppi333 (
Insert 2¢)
07:45, 15 October 2020 (UTC)
Yes I could be BOLD and do everything but it is pretty disconcerting that so many of our GPCR articles (case in point, several of our mGluR articles) fail even to discuss the G-proteins / second messenger pathways coupled to the GPCR, which is pretty frustrating as it promotes an inherent tendency among many in the "real world" to fail to consider interactions of second messenger pathways or functional selectivity. Some time ago, our article on the mu opioid receptor failed to even mention that it is canonically Gi-coupled (functional selectivity and downstream effects on dFOSB aside) -- until I fixed it. Such core details are pretty important when evaluating whether a receptor's known effects make physiological sense. Could there be a prioritization of ensuring that all second messenger receptors actually discuss the actual known specific pathways they are coupled to? It is pretty frustrating to have so many articles on GPCRs only to have to hunt for some other article to see which actual G-protein(s) it is coupled to. Yanping Nora Soong ( talk) 23:44, 12 October 2020 (UTC)
References
![]() | This page 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. |
![]() | 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 9 | Archive 10 | Archive 11 |
Would someone review the Cyclopentenone prostaglandins article for the purpose of reclassifying it? The article has recently been greatly expanded. Although it is categorized as a Pharmacy and Pharmacology article, it is better categorized in the Molecular and Cellular biology section. All of the prostaglandins are so categorized (e.g. see prostaglandin). Also, the article as currently formatted is correctly redirected from 15-deoxy-Δ12,14-prostaglandin J2 (15-d-Δ12,14-PGJ2), a principal cycloentenone prostaglandin. Is it possible to similarly redirect it from other cyclopenentone prostaglandins viz., Δ12-PGJ2, PGJ2, PGA2, and PGA1, discussed in the article (but not given separate Wikipedia pages elsewhere) and, if so, how do I do that? Thanks, ( User talk:joflaher). 6 December 2016 (UTC)
Illumina sequencing is a very important method to know nowadays, as least for anyone working in molecular biotechnology. The figure for the creation of clusters is correct, but could use someone who puts in some love. It was obviously drawn quickly and I think the article deserves more.
/info/en/?search=Illumina_dye_sequencing
There are many nice resources to find inspirations, such as the Youtube channel of illumina.
Following the discussion above, interested parties should also chime in at WikiProject Microbiology and WikiProject Fungi. -- Nessie ( talk) 15:10, 12 April 2019 (UTC)
It's at Wikipedia_talk:WikiProject_Equine#Gene_names. Iamnotabunny ( talk) 04:54, 2 May 2019 (UTC)
I was looking up phase separation and found biomolecular condensate which has a rather confusing link to Spinodal decomposition - having had only a just an overview after reading a couple of reviews, it looks like these articles need more work considering that there is currently a lot of talk (hype?) on the topic. I hope someone with specialist knowledge on this can improve coverage on this cluster. Shyamal ( talk) 15:57, 6 May 2019 (UTC)
References
Moot
|
---|
The current
This is a HGNC search page for entries associated with the parameter input to Example: Q3, methyltransferase coenzyme Q3, methyltransferase contains results for "coenzyme" only; the "Q3, methyltransferase" is omitted because the spaces aren't url-encoded [via replacement with "%20"]). The correct url for that search is https://www.genenames.org/tools/search/#!/genes?query=coenzyme%20Q3,%20methyltransferase.
Since this is a better link target for inputted HGNC ID numbers, would anyone object to me recoding this template using this markup? I can't imagine that this would break any existing links that aren't already broken due to the use of a phrase/string as an input value. Seppi333 ( Insert 2¢) 19:11, 23 November 2019 (UTC) |
Never mind. A number of template calls use the gene symbol in the first parameter, so recoding it as described would break those links.
I’ll just create Template:HGNC for with the url above for HGNC IDs when I’m back on my laptop. Seppi333 ( Insert 2¢) 00:39, 24 November 2019 (UTC)
Can someone take care of this page merge on both WP and wikidata? C19orf44 (gene) has a lot of content; C19orf44 has almost nothing. Found them searching for pages/redirects containing "C#orf#" and "(gene)" in the title. I've taken care of another page that simply needed to be moved from "C#orf# (gene)" to "C#orf#".
There's undoubtedly more duplicate gene articles out there, but I'll look for them later. Going to work on programming a solution to fix the dablinks and mistargeted links to non-gene-related pages in my tables first. Seppi333 ( Insert 2¢) 00:34, 20 November 2019 (UTC)
moot
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Context: for training a speech to text AI. Seppi333 ( Insert 2¢) 20:43, 2 October 2019 (UTC)
|
I'm ready to tackle this now. Anyone know of any source (i.e., a single webpage or data file [any format, structured or unstructured]) with a list (preferably expert-reviewed) of just the 20,000-ish HGNC-approved gene symbols? I imagine I could probably find this if I looked hard enough in genomics info/data-bases. With exception for KEGG, I only have familiarity/experience with proteomic and metabolomic DBs; I don't really know what expert-reviewed/annotated genomics DBs are available, so I'm not sure where the best place to start looking for this data would be.
FWIW, it probably wouldn't be a bad idea for this project to have a subpage containing wikilinks to all those symbols for maintenance and bot-related purposes. Seppi333 ( Insert 2¢) 05:42, 29 October 2019 (UTC)
'protein-coding_gene.txt'
file from HGNC, put the .txt file and the python file containing the code below in the same working directory, and then just run the python code; it then creates the 'Human protein-coding genes wikitext.txt'
files, which contain wikitext markup for those wikitables, in the same directory.I was surprised to find that there isn't an article on these topics. The more general article on metagenomics has far too broad a scope to be suitable piped linking since it pertains to aggregation of genomes in an arbitrary environment (e.g., a pond, a person's body, soil, etc.). That said, there are two level 3 sections in that article that pertain to human metagenomics: Metagenomics#Gut Microbe Characterization and Metagenomics#Infectious disease diagnosis. I'm also kind of puzzled as to how there's no article on microbiomics given how much content is contained in the article on the more niche topic of pharmacomicrobiomics. In any event, I'm just posting these here in the event anyone knows of a suitable article for redirecting or wants to create a stub. There obviously a rather large amount of topical overlap between [human] metagenomics and [human] microbiomics (i.e., metagenomic sequencing is used to characterize all of the genomes within an arbitrary microbiome), so I suppose human metagenome could redirect to human microbiome provided that it's covered there. Similarly, microbiomics could probably be covered in a section of metagenomics.
Boghog I wrote a new section in
Amphetamine#Pharmacomicrobiomics which covers material pertaining to these topics (it's censored in the source) but your citation tool is down and I'm too lazy to manually look up the parameter inputs and write the markup for 4 citations. Would you be able to fix it, please?
Seppi333 (
Insert 2¢)
18:17, 10 July 2019 (UTC)
sci-hub.tw/10.1002/jcb.28396
) mentioned the enzyme was tyramine oxidase and linked to ExPASy (
corresponing enzyme entry), but they didn't specify a metabolite. Based upon the reaction listed in the link, wouldn't the product when amphetamine is used as a substrate be
this (alpha-methylphenylacetaldehyde)?
Seppi333 (
Insert 2¢)
16:39, 11 July 2019 (UTC) You are invited to join the discussion at
Draft talk:Horizontal transfer of mitochondria#Opinions of subject matter experts sought.
Worldbruce (
talk)
14:47, 24 June 2019 (UTC)
IMO, well sourced article about a geneticist. But you can help improve it. 7&6=thirteen ( ☎) 15:52, 4 July 2019 (UTC)
Hi all,
I would appreciate your input in this strange case: Wikipedia_talk:Copyright_problems#Wikipedia_page_"later"_published_in_scientific_paper:_copyvio?.
-- Steven Fruitsmaak ( Reply) 20:00, 20 July 2019 (UTC)
Hi WikiProject Molecular Biology members,
I have made numerous small edits to the ATAC-seq page, a page that is within the purview of your project, to improve its quality. I've also rewritten the whole page to remove promotional and overly-technical content and to add citations and crosslinks. But I have a conflict of interest, so I cannot make the changes myself. I copied my rewrite into the talk page. Could a project member please review my rewrite and use it to replace the content that is there?
Thank you,
cglife.bmarcus ( talk) 1:17, 5 September 2019 (UTC)
Just found a link on Angelika Amon to the redirect CLB2 which is an airport code. Is CLB2 also an abbreviation for Cyclin B2? CambridgeBayWeather, Uqaqtuq (talk), Sunasuttuq 05:50, 30 September 2019 (UTC)
I need some help interpreting the implications of the TNXB entry in this spreadsheet: [4] (Suspect variants.xlsx). The spreadsheet indicates my brother's TNXB gene is compound heterozygous due to distinct frameshift mutations on each allele, reflecting the autosomal recessive form of "TNXB deficiency". From my understanding, frameshift mutations tend to result in the translation of proteins that are completely functionally borked. So... his genotype predicts a clinical phenotype of "classic-like EDS" (clEDS), which is rather severe. I've repeatedly read a number of times in about 20 or so papers on TNXB this past week that "TNXB haploinsufficiency" (associated with having 1 wild type and 1 mutant allele, autosomal dominant inheritance) causes "hypermobility-type EDS" (hEDS), a milder clinical phenotype than clEDS in which hypermobility can manifest with muscle issues, skin issues, and/or vascular issues. His actual clinical phenotype is User:Seppi333#John, which notably lacks any skin involvement or easy bruising, both of which always occur in TNXB deficient individuals and are required for a clinical diagnosis of clEDS. He meets the straightforward clinical diagnosis for hEDS listed here. In comparison, I am wild-type; I fail to meet both criterion 1 (Beighton Score: 2/9) and criterion 2 (2A: 1/12 total, 2B: obviously applies, 2C: 0/3) in that list and so criterion 3 is N/A. Edit: I have no clue about my genotype since I've never gotten or needed any form of genome sequencing. I'm a bit confused as to how to explain this; the only explanation I can think of is that one or both of his compound heterozygous alleles is creating a functional frameshift-mutated tenascin-X protein. Since he doesn't have skin or vascular symptoms and since the loss of a single TNXB allele is sufficient for – and a common cause of – hEDS, it seems like the combined protein function across both alleles can't be significantly worse than having 1 wild-type allele and 1 allele from which a protein isn't translated. Is that rather unusual or are frameshift mutations simply not as pathogenic as I've been lead to believe? Seppi333 ( Insert 2¢) 23:51, 5 October 2019 (UTC)
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Extended content
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There's two issues I should address before I even consider moving those tables to the article space. The bigger problem is pages where an article for the gene symbol does not exist and the target article of the wikilink is about something completely unrelated. Suppose, for example,
rage was not a disambiguation page, but an article about the emotion and that
RAGE redirected to that article. Then
RAGE would appear as a blue link in the wikitable and not be a link to a disambiguation page. In that case, the
Dablinks tool wouldn't tell me that I should be linking
RAGE to
RAGE (gene) via a piped link ( @ Boghog, Evolution and evolvability, Mark viking, or anyone else for that matter: would you happen to know of a way I might be able to detect problematic wikilinks like that? Seppi333 ( Insert 2¢) 19:53, 4 November 2019 (UTC)
Sorry, late to the discussion. Another option is Wikidata. "protein-coding gene in the species Homo sapiens". Wikidata. These data items provide links to the corresponding Wikipedia article if one exists. Boghog ( talk) 07:49, 5 November 2019 (UTC)
Sigh. The Dablinks tool did not give me all the dablinks in these tables. I'm guessing it only parses a few thousand links before stopping. Working backwards and checking the last 1000 entries in the 2nd table, I found WIZ, WLS, WRN, XDH, XG, XK, XPC, ZYX. I'll need to program a solution to take care of that as well. Seppi333 ( Insert 2¢) 19:52, 6 November 2019 (UTC)
|
I'm running my mistargeted link detection script right now. I expect it will take around two hours to finish based upon sample tests. Assuming nothing goes wrong, I'll post the complete list of links here, since I will need help locating the correct link targets if they exist. Seppi333 ( Insert 2¢) 02:49, 26 November 2019 (UTC)
Boghog There's tons of script output spamming my output window right now, but I was curious when I saw a RFNG redirect to Radical Fringe gene( [5] [6]). It doesn't have a gene infobox; could you fix the pair of wikidata items for that? I'm not sure what to do with the one that radical fringe gene is currently linked to. Edit: attempted to just go ahead and move the link to the right data item, but it says the other needs to be deleted. >.> Seppi333 ( Insert 2¢) 04:38, 26 November 2019 (UTC)
Pretty sure this is the very last dablink in the wikitables at the moment.
COQ3 (gene) redirects to COQ3, which includes a list of 2 enzymes. The wikidata item for COQ3 in Homo sapiens isn't linked to a WP article: [9].
From a cursory glance, it looks like 3-demethylubiquinone-9_3-O-methyltransferase is the correct article of those 2. Should the WD item be linked to that and a gene infobox be included in the article? Seppi333 ( Insert 2¢) 19:10, 23 November 2019 (UTC)
It makes sense to merge enzyme EC and gene Wiki articles if and only if there is a one-to-one correspondence between EC number and HUGO gene symbol.That's useful to know. Thanks for resolving the disambiguation issue. Seppi333 ( Insert 2¢) 10:10, 24 November 2019 (UTC)
After I fix the few dozen mistargeted links I mentioned, these tables will contain links to almost all pages in the GeneWiki along with a list of 1 or more UniProt IDs for each gene.
Given that these tables contain all the article links and id numbers I'd need, I could program an algorithm to move all the pages to which the the gene symbols are linked to their official UniProt names a la
MOS:MCB#Article name provided there is only 1 UniProt link associated with the gene symbol; it obviously makes no sense to move a page that corresponds to multiple UniProt IDs. I could also set an upper limit on the length of the string-formatted UniProt name to avoid moving pages to long page titles per this: If the protein name is verbose, either a widely used protein acronym or the official HUGO gene symbol, followed by "(gene)" if necessary to disambiguate.
Should I work on a script to move gene pages that are located at gene symbols to the pagename of their official UniProt name, or are there circumstances where doing that would be problematic?
Seppi333 (
Insert 2¢)
21:30, 25 November 2019 (UTC)
Lines 6–11289 in
User:Seppi333/GeneListNLP#Output show that the vast majority of pages about human protein-coding genes use the gene symbol as the page name. Using ctrl-F to count them, 8600 pages are located at the gene symbol and 2683 are located on pages with a different title (NB: these numbers include the 226 unrelated pages, so they're not exact counts for each). Also, the fact that only 11283 links were processed suggests that Wikipedia is missing around 8000 articles on human protein-coding genes. On a tangential note, I thought I moved almost all of the pages in the
solute carrier family from the gene symbol to the official UniProt name, but that output indicates that I missed a few.
Seppi333 (
Insert 2¢)
09:20, 26 November 2019 (UTC)
Specific things I'd like feedback on:
Seppi333 ( Insert 2¢) 05:16, 24 November 2019 (UTC)
There's a discussion going on over at Wikipedia_talk:WikiProject_Biology about whether it is worth consolidating some of the disparate biology wikiprojects. One possibility could be a merger or semi-merger of WP:GEN + WP:MCB + WP:COMBIO + WP:BIOP, since their scopes are well-aligned. Ideas and opinions welcome! T.Shafee(Evo&Evo) talk 01:14, 25 May 2019 (UTC)
Hello, based on the consensus at the
WP:Biol discussion, this is confirmation of my suggestion to merge:
WP:GEN +
WP:MCB +
WP:BIOP +
WP:CELLSIG (possibly +
WP:COMBIO) -> into
Wikipedia:WikiProject Molecular Biology (name to be confirmed)
The new main page should be able combine all of the information of each project (much of which overlaps) and the talkpage should also also centralise discussion to make it more lively and easier for newcomers! Separate
tracking tables of article qualities can still be kept by making them 'taskfores' if people think that'll be useful. If people don't object I'll go about redirecting the WP and WT pages to that centralised location next week per
this process.
T.Shafee(Evo&Evo)
talk
13:09, 10 June 2019 (UTC)
Merger complete! See the new unified talkpage. All talkpage archives should be clearly visible and searchable and the new unified WikiProject page is almost complete. T.Shafee(Evo&Evo) talk 12:25, 16 June 2019 (UTC)
There's a discussion about a possible User Group for STEM over at Meta:Talk:STEM_Wiki_User_Group. The idea would be to help coordinate, collaborate and network cross-subject, cross-wiki and cross-language to share experience and resources that may be valuable to the relevant wikiprojects. Current discussion includes preferred scope and structure. T.Shafee(Evo&Evo) talk 03:04, 26 May 2019 (UTC)
Hello everyone, i am the author of the DNA replication image give or take i made this image arround 2007, i have been asked to modify it to incorporate all the comments and corrections made on the discussion page plus someone left the following request on the Graphics lab on commons:
Now I am an illustrator and by no means expert in this subject so i would really appreciate if someone with the appropriate knowledge could have a look on this
Sketch. it isnt yet on its final form but the elements are in the relative position i am hoping them to have (all marked with ? would need some reassuring). also there is like a ton of questions i would really want to have answer if that is ok:
if you would be so kind to answer my questions i could at least have some degree of confidence in remaking the image in a better more accurate state. 大诺史 was kind to offer this article as reference [10]. I look forward to your feedback. and thank you for your time - LadyofHats ( talk) 18:58, 5 June 2019 (UTC)
The articles pre-replication complex, minichromosome maintenance, and origin recognition complex can use some better images for the protein structures in light of the not-so-recent publications of EM structures. My computer and my brain are currently too messed up to sort out the PyMol or whatever rendering thing, so would anyone please render some views (two will do: front and top) for PDB ID 5v8f (pre-RC OCCM), 3JA8 (MCM; 5UDB will do too), and 4XGC (ORC; 5UDB will do too)? -- Artoria 2e5 🌉 23:48, 23 June 2019 (UTC)
So, below is what my algorithm found.
If the mistargeted gene symbol isn't a redirect, it's listed as en:PAGENAME on that line.
If the term is a redirect, the format below is en:REDIRECT → en:PAGENAME. Seppi333 ( Insert 2¢) 05:15, 26 November 2019 (UTC)
I'm not sure how to address this. For each gene symbol below that no relevant article exists, should we just create a DAB pages with redlinks to SYMBOL (gene) listed on it? A lot of the symbols below should clearly link to disambiguation page. Seppi333 ( Insert 2¢)
It makes sense to merge enzyme EC and gene Wiki articles if and only if there is a one-to-one correspondence between EC number and HUGO gene symbol.
After thinking about how to algorithmically deal with the problem of locating existing articles for the symbols above that do not redirect to enzyme pages – and all the redlinked gene symbols in the wikitables for that matter – I realized that I could do the following in sequence for every gene symbol:
I apologize to everyone in this WikiProject for practically spamming the page with issues related to the wikitables I'm working on; I imagine it might be annoying to some people. I'm done with the tables now. I'm going to write the algorithm I described above, but I'm going to ignore anything I can't quickly address by myself. Seppi333 ( Insert 2¢) 11:43, 27 November 2019 (UTC) |
New RFBA since I now have the data that I was going to program this algorithm to obtain – Wikipedia:Bots/Requests for approval/Seppi333Bot 2. Haven't processed the query results yet, but I expect it'll permit creation of about ~2000 gene symbol redirects. Seppi333 ( Insert 2¢) 01:29, 20 December 2019 (UTC)
Prime editing has hit the mainstream press, with lots of hyperbole about its potential, in spite of it still being at the laboratory proof of concept stage. I've created a stub article for it; can knowledgable people please help improve the article? -- The Anome ( talk) 09:33, 22 October 2019 (UTC)
Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.
We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma ( talk) 04:24, 27 October 2019 (UTC)
The following discussion may be of interest to this project: Wikipedia_talk:WikiProject_Medicine#MEDRS_sourcing_required_for_non-biomedical_information. -- Signimu ( talk) 17:50, 1 November 2019 (UTC)
I wrote the bot script yesterday morning and it's been operating since then. Pending approval of my bot and validating the links as mentioned in the section below, I'll move those tables to the mainspace. Seppi333 ( Insert 2¢) 18:16, 6 November 2019 (UTC)
Identified in
User:Certes/Gene links#Miscellaneous; I've PRODed these per
HGNC:3523. If you agree, you may want to add a {{
Prod2}}
template.
Seppi333 (
Insert 2¢)
01:44, 30 November 2019 (UTC)
On the one hand, this bot had some problematic bugs prior to being blocked; I've personally had to merge/regarget dozens of erroneous pages it created. As far as I am aware, it correctly wrote page content, but sometimes got the page name wrong, created a duplicate entry, and/or created a redirect to the wrong pagename.
On the other hand, subsequent to identifying the 215 mistargeted links in list of human protein-coding genes pages, I've only created 4 new gene/protein stubs [1] while attempting to unbork the articles, redirects, and set index articles identified by my algorithm as well as creating entries for redlinks on DAB pages like (e.g., ALLC (disambiguation)) that WT:WPDAB is helping to create. A few dozen gene articles need to be created to fully address those issues. I currently need to create the 2 redlinked entries listed in User:Certes/Gene links#Redirects, but I would rather repeatedly bang my head against a wall than create another due to how tedious it is to create new gene articles with all the minutia involved. [2]
This led me to an idea that I hope is a viable solution to the problems PBB and I have, assuming that everyone is on board. Consider the following:
A relatively simple solution to keeping my brain intact, my wall stain-free, and PBB's bugs in check is to modify the bot code so that it writes gene articles to the corresponding pagename in the draft namespace upon user activation at
biogps
@
Fram: would you be open to unblocking the bot if it wrote gene articles to the draft namespace so that they can be moved pending validation?
@
Andrew Su and
Julialturner: if either of you are still around and biogps can still trigger PBB to create a gene page, would you be willing to recode the bot so that it writes the corresponding gene entry to
Draft:Pagename instead of
Pagename?
Seppi333 (
Insert 2¢)
04:11, 2 December 2019 (UTC)
For a much less self-centric motivation: WP has ~11500 bluelinked protein-coding gene symbols and ~8500 redlinked ones. PBB created ~9400 articles (non-redirect, still live pages) since it was created. Given its original purpose, I suspect that the majority of the 9400 pages PBB created are the articles or targets of the redirects located at those 11500 symbols. So, in spite of its bugs, Wikipedia needs algorithms like PBB if we’re ever going to finish creating the entries for the other half of the exome. Seppi333 ( Insert 2¢) 04:12, 2 December 2019 (UTC)
There are many of genes whose function has not yet determined and have not been mentioned in reliable secondary sources, hence these genes fail WP:NOTABILITY requirementsI’m well aware.
@ Andrew Su: Ty for creating that; makes all the work ahead of me seem much more bearable now. Seppi333 ( Insert 2¢) 06:14, 2 December 2019 (UTC)
{{
Infobox gene}}
to work, identify and add the corrsponding gene-chromosome-stub template like {{
gene-1-stub}}
, cite the UniProt-recommended protein name and HGNC-approved gene symbol in the first sentence, figure out something of note to write and cite to pad the page so that I'm not literally creating an article that just says "X is a protein encoded by Y", and then do everything else that any other Wikipedia article normally requires (i.e., sections, formatting, reference template, project tags on talk page, etc.). Then again, I don't like creating articles to begin with.
I have nominated Folding@home for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. GamerPro64 17:18, 9 December 2019 (UTC)
I saw a Science Reference Desk question about this article. I've edited some of the references but have concerns about the content in this article. I've started a discussion at Talk:Non-helical models of DNA structure#Work from X, Y. C. about my concerns. Any and all comments, edits, etc welcome. Thanks, EdChem ( talk) 04:14, 13 December 2019 (UTC)
I figured someone would do this sooner or later. Seppi333 ( Insert 2¢) 13:08, 2 January 2020 (UTC) |
So, this is something I wondered about years ago, but it's time for me to raise it again. What are the thoughts of people about writing articles like List of human Nrf2 targets (i.e lists of genes that are regulated by a given transcription factor)? They might be of interest to readers, but I don't know what kind of issues they might do. Jo-Jo Eumerus ( talk) 19:01, 17 April 2020 (UTC)
First off, I feel like a bit of a dumbass for asking if one of my brother's frameshift mutations could be functional a while back because I didn't know how to read this earlier in the annotated file I had linked:
According to UniProt, the canonical protein isoform of TNXB has a length of 4244 AA. These frameshifts both occur at glycine residue 362, are >90% truncated relative to the wild-type tenascin-X protein, and they lack nearly all functional domains on the wild-type protein ( https://www.uniprot.org/uniprot/P22105#family_and_domains). Complete deficiency in this gene is supposedly highly penetrant for clEDS, but it's somehow only partially penetrant in my brother's case; it's definitely not because one of these proteins is expressed, partially folded, and somehow functional on the sequence preceding the mutation though.
In any event, I'm finding it pretty hard to grasp how this is possible in terms of genetic inheritance unless this involved some abnormal form of inheritance; it just seems unfathomably unlikely that both my parents carry nearly identical frameshift mutations which haven't been previously reported and that both involve an A>G mutation and affect the same protein residue. Sequencing them both would obviously determine if that's the case, but TNXB sequencing is prone to errors due to significant pseudogene interference from TNXA and I don't think it's likely to happen anyway.
Could this arise from
uniparental disomy? Or is there another abnormal mode of inheritance that might give rise to seeing mutations like this? I'm just a bit baffled due to my ignorance in this area.
Facepalm
Seppi333 (
Insert 2¢)
12:40, 20 May 2020 (UTC)
Hello guys and gals,
Can someone get the archiving fixed on Talk:Archaea, please? It is getting long and has posts going back to 2014. Thanks, Galendalia Talk to me CVU Graduate 13:58, 30 May 2020 (UTC)
I have nominated
DNA repair for a
featured article review here. Please join the discussion on whether this article meets
featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are
here.
SandyGeorgia (
Talk)
22:51, 14 June 2020 (UTC)
I've also copied this over to
WT:MOLBIO.
T.Shafee(Evo&Evo)
talk
03:15, 15 June 2020 (UTC)
There have been a lot of small edits from brand new users to this article. Just about every red name in the edit history has made exactly that one edit. I thought they were all one person, but it looks like I was wrong. A lot of them are unsourced with no edit summary and change around the meaning of the article. I don't have the subject knowledge to say if these are vandalism or plausible though, perhaps someone on this WikiProject can take a look through edits such as these? 1 2 3 4 5 For example, I can vaguely say that the first edit I linked is probably incorrect...? But I'm far from certain. (Those 5 are just an example, there are many more in the history, some reverted, some accepted) Leijurv ( talk) 20:48, 8 July 2020 (UTC)
Talk:G4 EA H1N1#Proposal: Redirect to main H1N1 article SandyGeorgia ( Talk) 04:46, 12 July 2020 (UTC)
Cis-regulatory module and Cis-regulatory element seem to overlap largely, and to a non-geneticist they seem extremely similar if not a WP:FORK. It doesn't look as if a simple redirect would do the job, so perhaps someone could look at the matter, and either make the articles clearly distinct or merge them. Editors have noted the issue since, ah, 2011. All the best, Chiswick Chap ( talk) 21:14, 17 July 2020 (UTC)
The articles /info/en/?search=Cell_communication_(biology) and /info/en/?search=Cellular_communication_(biology) should be merged. RIT RAJARSHI ( talk) 09:34, 30 July 2020 (UTC)
It looks like many of the Wikiproject Molecular Cell biology articles lacking details and remaining unimproved for years to decades. Recently I noticed an article whose title does not match with its content ( /info/en/?search=Membrane_topology). Looks like there are scope of lot of improvements in many of the articles, which are not happening. Is there a deficit or reduction of contributors? Also is there a general reduction of wikipedia activities? How can we again increase activity in Wikipedia? With best wishes for Wikipedia. Thanks in advance. RIT RAJARSHI ( talk) 09:38, 30 July 2020 (UTC)
I have nominated Cell nucleus for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. ( t · c) buidhe 22:16, 11 September 2020 (UTC)
In retrospect, it does seem rather inappropriate for me to have posted what DGG deleted in this section, so I wanted to apologize to those here (re this discussion:
User talk:Seppi333#October 2020). My bad. I hope everyone can forgive my lack of forethought and stupidity for committing a faux pas.
Seppi333 (
Insert 2¢)
07:45, 15 October 2020 (UTC)
Yes I could be BOLD and do everything but it is pretty disconcerting that so many of our GPCR articles (case in point, several of our mGluR articles) fail even to discuss the G-proteins / second messenger pathways coupled to the GPCR, which is pretty frustrating as it promotes an inherent tendency among many in the "real world" to fail to consider interactions of second messenger pathways or functional selectivity. Some time ago, our article on the mu opioid receptor failed to even mention that it is canonically Gi-coupled (functional selectivity and downstream effects on dFOSB aside) -- until I fixed it. Such core details are pretty important when evaluating whether a receptor's known effects make physiological sense. Could there be a prioritization of ensuring that all second messenger receptors actually discuss the actual known specific pathways they are coupled to? It is pretty frustrating to have so many articles on GPCRs only to have to hunt for some other article to see which actual G-protein(s) it is coupled to. Yanping Nora Soong ( talk) 23:44, 12 October 2020 (UTC)
References
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