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We could instead link to the NCBI taxonomy pages, which give a short summary of the organism. This includes a link to the genome list & a link directly to the reference genome. This is technically not a link to a genome dataset anymore, but I believe this is the closest behavior to how our links
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Things like base counts would be accurate/stable as long as the genome is sequenced with complete coverage and high confidence. I'm more familiar with bacterial genomes where that kind of thing is more common, so I'm not sure how realistic that tends to be for eukaryotic reference genomes. Surely,
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But there's another problem that just as important. Any article on an individual genes is certainly going to bring up the definition of a gene and important issues such as regulation, evolution, and alternative splicing. It is proving to be very difficult to get individual editors to stick to the
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A typical genome infobox contains a link to NCBI and at least three bits of information: ploidy, genome size, and number of chromosomes. I think that ploidy and the number of chromosomes are bits of information that should be in the main body of the article. The size of the genome is not a fixed
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If the citation is no longer reliable, then the article needs to be updated, which could be as minor as the removal/replacement of the citation with a reliable one, to rewriting an entire section that was based on flawed premises. If the citation to a retracted paper was intentional, like in the
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definitions and descriptions of these features that have been thrashed out in the articles specific to those topics. This leads to a lot of confusion and conflict so we should be very cautious about creating any new molecular biology articles unless they are absolutely necessary.
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worked before the NCBI change - and it does still provide easy access to the genome data (including a download button that directly links to the reference genome). We'd change the genome ID on all pages with the taxonomy ID (like option #2) and change the URL in the template to
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Knowledge (XXG) is a popular encyclopedia intended for a diverse audience. There are 25,000 genes in the human genome and something close to one million different different genes in the biosphere. We do not need to have a separate
Knowledge (XXG) article for each
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ID (and this is what articles have been using for this field). This is at the crux of the problem, as these genome IDs appear to no longer be used. When infobox links still work, it's because the NCBI silently redirects the link to one using the organism's
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I think using an
Infobox to pull out (or duplicate) common measures of genetic material from the body text is generally helpful and is especially useful for hosting external links to databases. I support keeping the infobox
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Structural biology lacks any type of wikiproject, at least from what I can find. The core articles surrounding structural biology are scattered, and need a lot of coordinated work done to them. Any thoughts on this?
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I can think of three ways to fix the problem; all would require updating each article using the
Infobox with new IDs, so I wanted to talk about which solution is best before jumping in and making all those changes.
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If we think it's valuable to link users to a list of all the available genomes rather than just the reference, we could instead replace the genome IDs on all pages with the taxonomy IDs (for Bonobo, we'd remove
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I suggest a 4th solution, delete all genome infoboxes. Alternatively, someone could replace all the NCBI links with
Ensembl links then review and update the genome sizes of all infoboxes every few months.
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as it emphasizes one function among many, but mostly b/c the article currently doesn't list any other function so I am not sure if it should be removed. Typical problem with well-studied proteins, really.
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Also I am bringing this up to see what y’all think about there being an article on this gene. When researching the evolution of sexes and mating types I noticed a lot of sources keep mentioning this gene.
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I put the list of articles within the scope of WP:MCB in collapsed sections. Any help you can give with those are greatly appreciated. Feel free to remove/strike through those you've dealt with.
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1786:, a cellular structure found mainly on protists and some fungi. I am not a member of this WikiProject so I thought I would notify it here so that the proper importance assessment can be made. —
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I noticed that the example protein articles referenced in the protein article style guide do not follow the recommended sections layout. Should there be a task to standardize these articles?
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cutting off those numbers at two significant figures would make the estimates close enough for general purposes and pretty stable over time. Same for coding vs. non-coding genes. ―
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that would need to be updated to the new IDs no matter what option is picked; not an insurmountable number but not so few that changing them all would be quick & trivial. —
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Is it a good idea to insert all the latest speculations about the function of a given gene before they are confirmed by additional experiments in other labs? I don't think so.
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While I think option 3 provides a more informative wrapping around links to genomes per taxon, option 1 actually would link to a genome as you would expect for the field
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number, it changes from year to year as more of a genome is sequenced and annotated. I would argue that putting this number in an infobox gives it too much credence.
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This is great. Thank you. I've always wondered how we deal with retracted articles and now you've presented at least some alerting automation. --User:Ceyockey (
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Just asking to make sure it doesn’t go by a different name or something. I’m also wondering if genes here on
Knowledge (XXG) have a certain style or policies.
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to the correct genome list), but many are. I imagine there's a risk all the links could stop working if/when NCBI completely deprecates the Genome resource.
1458:, it appears a recent NCBI change has broken the links produced by the Infobox genome template. My talk page comment goes into more detail, but in summary:
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or similar. I also see no reason not to exclude linking to
Ensembl or any other database as long as the statistics in the box are of the linked genome.
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Right now, on pages where it's still working properly, the
Infobox links to a list of all the genomes NCBI has available. E.g.: for Bonobo, the
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now incorrectly links to a genome listing for
Impatiophila pipa). Not all pages are affected (e.g., NCBI automatically redirects the link on
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I would also argue that the best link to sequenced genomes is the
Ensembl site and not NCBI. For example, here's the Ensembl link to the
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41:. Please post any comments, suggestions or questions. Also feel free to introduce yourself if you plan on becoming an active editor!
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Link to the NCBI Taxonomy page instead of directly linking to genome data; replace genome IDs on all articles with taxonomy IDs.
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1413:. I removed some obvious vandalism and a partial reference, but this article needs the attention of a subject matter expert.
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linking ETS2 with a wide range of inflammatory diseases. Please amend, or even remove, this if what I've written is wrong. —
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Change the infobox to link to the reference genome only; replace genome IDs on all articles with reference genome IDs.
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ETS2 is a fairly important transcription factor, and these often have multiple functions. I think this addition is
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1755:. We would really appreciate your input; I do not think any CFD regulars are experts in molecular biology. Best,
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https://en.wikipedia.org/Wikipedia:WikiProject_Molecular_Biology/Style_guide_(gene_and_protein_articles)#Sections
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Keep the infobox behavior of linking to genome lists; replace genome IDs on all articles with taxonomy IDs.
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on every organism's page by replacing the genome ID with the reference genome ID (for Bonobo, changing to
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Just a quick question is there any articles about a gene in particular? I’m talking about a gene called
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Do we really need to have separate
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Knowledge (XXG):Categories for discussion/Log/2024 September 12#Category:Pentose phosphate pathway
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Any thoughts on which option is best, or other options I haven't thought of? Of note, there are
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article and wondered if it should be structured consistently with the other protein articles.
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argument; the template now links to incorrect genome lists on some pages (e.g.: the box on
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from the Signpost last month. Things have evolved a bit and now Retraction bot handles
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context of a controversy noting that a paper was later retracted, you can replace
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NCBI genome page lists 8 genomes, with the reference genome at the top
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Thanks for bringing this up, I've taken a moment to smooth it out. ―
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Category:Articles citing publications with expressions of concern
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Talk:3α-Hydroxysteroid dehydrogenase#Requested_move_9_April_2024
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Talk:3α-Hydroxysteroid dehydrogenase#Requested_move_9_April_2024
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https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon={{{taxId}}}
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for closed discussion with outcome of 'Move'. --User:Ceyockey (
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Knowledge (XXG) talk:WikiProject Molecular and Cellular Biology
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The outcome of this request was "Not moved". --User:Ceyockey (
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There does seem to be a lot of sources about this gene from:
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Pentose phosphate pathway, chemokines, myokines categories
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https://www.ncbi.nlm.nih.gov/datasets/taxonomy/{{{taxId}}}
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In 2019 an editor made some fairly substantial changes to
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https://www.ncbi.nlm.nih.gov/datasets/genome/{{{taxId}}}
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that may be of interest to members of this WikiProject.
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that may be of interest to members of this WikiProject.
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https://en.wikipedia.org/Gonadotropin-releasing_hormone
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template links to the old Genome resource when given a
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Albumin transport function analysis by EPR spectroscopy
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Transformation/transcription domain-associated protein
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Threads older than 90 days are automatically archived.
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Welcome to the WikiProject Molecular Biology talk page
1778:New article that might be relevant to this project
1241:Category:Articles citing publications with errata
1084:TP53-inducible glycolysis and apoptosis regulator
1617:. The field label should probably be updated to
1462:, replacing it with the Datasets resource; the
563:Category:Articles citing retracted publications
1645:Standardizing The Sections of Protein Articles
413:Talk:Ketone bodies#Requested move 25 May 2024
399:Talk:Ketone bodies#Requested move 25 May 2024
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1542:). We'd change the URL the template uses to
1447:is linking to incorrect genome lists on NCBI
794:H+, Na+-translocating pyrophosphatase family
558:. These populate the following categories:
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1517:) and change the URL the template uses to
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236:(inactive):
1485:field in the template actually expects a
699:Class A basic helix-loop-helix protein 15
411:There is a requested move discussion at
273:There is a requested move discussion at
451:article to reflect the latest paper in
379:" has been abandoned? --User:Ceyockey (
294:Talk:AKR1C4#Requested move 9 April 2024
1054:Steroidogenic acute regulatory protein
375:Does your response suggest that the "
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1782:I have recently made a new article,
1460:NCBI is removing the Genome resource
969:Poly(3-hydroxybutyrate) depolymerase
979:Protein inhibitor of activated STAT
1661:https://en.wikipedia.org/Protein_C
679:Cathelicidin antimicrobial peptide
669:Calcium signaling in cell division
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1708:Task force for Structural Biology
904:Mir-802 microRNA precursor family
889:Mir-133 microRNA precursor family
804:HHV Latency Associated Transcript
154::
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1575:~62 articles using this Infobox
734:Early prostate cancer antigen-2
186::
1810:16:35, 20 September 2024 (UTC)
1772:15:56, 12 September 2024 (UTC)
1732:Please leave your comments in
1509:. We could instead update the
944:Nuclear receptor coactivator 3
939:Nuclear receptor coactivator 2
934:Nuclear receptor coactivator 1
894:Mir-192/215 microRNA precursor
839:List of phylogenetics software
77:WikiProject Molecular Biology
56:Put new text under old text. (
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949:Nuclear receptor coregulators
854:Lymphocyte expansion molecule
784:Genetically modified organism
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824:Inorganic pyrophosphatase
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1456:Infobox genome talk page
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834:Let-7 microRNA precursor
814:Hypoxia-inducible factor
447:I've added a bit to the
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1203:Nodal signaling pathway
1034:Somatostatin receptor 2
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1297:Variants of SARS-CoV-2
1208:Regeneration (biology)
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929:Non-mevalonate pathway
629:Antonio Arnaiz-Villena
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1337:expression of concern
1329:expression of concern
869:Mesenchymal stem cell
543:Expression of concern
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172:Computational Biology
49:, be respectful, and
1567:this link for Bonobo
1550:this link for Bonobo
1525:this link for Bonobo
1039:Sphingosine kinase 1
634:Arsenic biochemistry
228:(inactive):
106::
1659:Example articles:
1652:I'm working on the
954:Paracrine signaling
844:Long non-coding RNA
829:Large tumor antigen
719:Netrin receptor DCC
609:Alveolar macrophage
1355:|...|checked=yes}}
714:De novo gene birth
644:Autoimmune disease
619:Antiglucocorticoid
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1292:SNARE protein
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739:Garth Ehrlich
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520:RetractionBot
519:
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477:Jo-Jo Eumerus
473:
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418:Safari Scribe
414:
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1738:Marcocapelle
1731:
1711:
1684:— Preceding
1678:
1658:
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1648:
1631:
1618:
1614:
1572:
1555:
1530:
1502:
1496:
1491:
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1391:
1359:
1307:
724:DNA ligase 3
523:
452:
446:
429:
410:
381:
340:
337:
332:
327:
322:
317:
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298:
272:
255:
220:(inactive):
204:
102:
96:
95:
76:
75:
47:remain civil
38:
37:
28:
1770:• he/they)
1536:taxId=10729
1454:As per the
1415:76.14.122.5
1064:Subtelomere
919:Neurogenins
749:Epigenetics
1784:rhizoplast
1715:Niashervin
1540:taxId=9597
1472:Chimpanzee
1393:talk to me
1321:retraction
1313:retraction
1228:Vitamin K2
1198:Morpholino
1158:DNA repair
769:Galectin-9
584:Adrenaline
526:this story
431:talk to me
383:talk to me
300:talk to me
206:Biophysics
1792:Snoteleks
1049:Stem cell
1024:Slit-Robo
624:Apoptosis
553:Retracted
524:I posted
457:The Anome
184:Gene Wiki
1698:contribs
1686:unsigned
1601:Genome42
1492:taxonomy
1451:Hi all,
1363:Headbomb
1193:MicroRNA
1183:Inositol
959:Pericyte
874:MicroRNA
759:Florigen
504:Genome42
472:WP:UNDUE
363:Genome42
312:MID gene
152:Genetics
79:Archives
1762:Blaster
1751:Now at
1625:around.
1411:PACSIN1
1405:PACSIN1
1353:Erratum
1345:Erratum
1277:MiR-203
1223:TAS2R46
1074:SUPT16H
1029:SMARCC2
994:Reprimo
899:MiR-203
754:FAM162A
614:ANGPTL8
533:Erratum
343:CycoMa1
279:Natg 19
174::
45:Please
1487:genome
1476:Bonobo
1347:|...}}
1331:|...}}
1315:|...}}
1168:HSPA1B
1099:TSG101
1069:SUCNR1
884:Mir-31
789:GPR132
664:C9orf3
548:, and
453:Nature
1758:House
1579:nmael
1511:taxId
1483:taxId
1468:taxId
1349:with
1333:with
1317:with
1153:CXCL9
1079:TIMD4
1009:ROCK1
984:RAP1B
964:PHLPP
864:MED24
859:MED12
849:LOXL2
819:IFI16
809:HYAL1
799:HEPN1
744:EP300
729:DSCAM
684:CEBPB
654:BCAS3
565:(274)
357:gene.
1802:talk
1768:talk
1742:talk
1719:talk
1694:talk
1671:talk
1636:path
1605:talk
1494:ID.
1435:path
1419:talk
1243:(66)
1138:Cln3
1119:(79)
1094:TSC2
1059:STK3
1044:SRA1
1019:SKP2
914:MTDH
694:CHUK
599:AKT2
508:talk
481:talk
461:talk
449:ETS2
443:ETS2
367:talk
347:talk
334:here
329:here
324:here
292:See
283:talk
1632:Syn
1431:Syn
234:RNA
104:MCB
1744:)
1736:.
1721:)
1700:)
1696:•
1673:)
1607:)
1569:).
1552:).
1527:).
1421:)
1397:)
1377:·
1373:·
1369:·
1357:.
1351:{{
1343:{{
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550:{{
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538:,
536:}}
530:{{
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463:)
435:)
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369:)
349:)
304:)
285:)
212:,
198:,
194:,
190:,
178:,
166:,
162:,
158:,
148:11
146:,
144:10
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138:,
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230:1
222:1
214:2
210:1
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192:2
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176:1
168:4
164:3
160:2
156:1
140:9
136:8
132:7
128:6
124:5
120:4
116:3
112:2
108:1
92:3
88:2
84:1
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53:.
20:)
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