Talk:Transcriptomics technologies/GA1

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GA Review

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Reviewer: Stigmatella aurantiaca (talk · contribs) 10:49, 24 August 2017 (UTC)

I will begin the review on the weekend. Stigmatella aurantiaca (talk) 10:49, 24 August 2017 (UTC)

Rate Attribute Review Comment
1. Well written:
1a. the prose is clear and concise, and the spelling and grammar are correct. I anticipate that most of my forthcoming detailed comments will concern this topic. There is a significant amount of jargon that, although familiar to workers in the field, may require the addition of explanatory footnotes before this article will be suitable reading for, say, college sophomore/junior students in life sciences who have finished a year long course in cell biology, a semester course in biotechnology, but not much else. For the purposes of this review, I'm brushing up with Alberts, Molecular Biology of the Cell, 6th edition (2014) and Clark, Biotechnology, Second Edition (2015).
1b. it complies with the manual of style guidelines for lead sections, layout, words to watch, fiction, and list incorporation.
2. Verifiable with no original research:
2a. it contains a list of all references (sources of information), presented in accordance with the layout style guideline.
2b. all in-line citations are from reliable sources, including those for direct quotations, statistics, published opinion, counter-intuitive or controversial statements that are challenged or likely to be challenged, and contentious material relating to living persons—science-based articles should follow the scientific citation guidelines.
2c. it contains no original research. Although principal editor is involved in this work, he has done an excellent job placing his own contributions in proper perspective. I have no issues with possible COI.
2d. it contains no copyright violations nor plagiarism. Large parts are derived from Lowe R, ShirleyN, Bleackley M, Dolan S, Shafee T (2017) Transcriptomics technologies. PLoS Comput Biol 13(5) e1005457 which is published under Creative Commons Attribution License. Likewise also matches against abstract on PubMed.
3. Broad in its coverage:
3a. it addresses the main aspects of the topic. This article focuses on transcriptomics technologies rather than on transcriptomics. The articles on Transcriptome and Expressomics provide rather inadequate introduction to concepts that this article takes for granted. No fault of this article, of course.
3b. it stays focused on the topic without going into unnecessary detail (see summary style).
4. Neutral: it represents viewpoints fairly and without editorial bias, giving due weight to each.
5. Stable: it does not change significantly from day to day because of an ongoing edit war or content dispute.
6. Illustrated, if possible, by media such as images, video, or audio:
6a. media are tagged with their copyright statuses, and valid fair use rationales are provided for non-free content.
6b. media are relevant to the topic, and have suitable captions. See questions below
7. Overall assessment.
  • Questions on table Comparison of contemporary methods
  • Throughput: What does "High" and "Higher" mean in quantitative terms?
  • Sensitivity: What units are 10-6 and 10-3? Micrograms? Nanograms? Tons? Miles?
  • Questions on table RNA-Seq de novo assembly software
  • What is "Resource load"?
  • "Repetitive sequences, hybrid data input, wide range of sequence platforms accepted." Unclear. Do you mean that the software is baffled by repetitive sequences (a weakness), or that it handles repetitive sequences well? What do you mean by "hybrid data input"? That it can accept heterogeneously formatted input from a "wide range of sequence platforms"?
  • Is homo-polymer error handling a strength or a weakness? In other words, is the system baffled by a long stretch of, say, poly-A, or does it handle such situations well?
  • Is CLC unique in offering a GUI?
Stigmatella aurantiaca (talk) 23:41, 31 August 2017 (UTC)
  • Questions on table RNA-Seq differential gene expression software
  • No questions. Only jargon word (isoform) should be within working vocabulary of my assumed target audience of sophomore/junior life sciences students.
  • Questions on table Transcriptomic databases
  • No questions. Descriptions in this table are much fuller and more complete than the often overly terse descriptions in the other tables. It would be nice if the other tables could be brought up to the standard of this table.
Stigmatella aurantiaca (talk) 18:50, 1 September 2017 (UTC)

Hi @Stigmatella aurantiaca:, just wondering what the status of this review was - is there still work ongoing or are these the only issues? If so, I (and I assume Evolution and evolvability (talk · contribs)) can work on addressing them. Thanks! Amkilpatrick (talk) 08:12, 18 October 2017 (UTC)

Sorry, I'd been distracted by issues with my parents' health (they are both in their 90s), and completely forgot about this. Thanks for reminding me. I'll get back on track with this review. Stigmatella aurantiaca (talk) 22:39, 18 October 2017 (UTC)
@Stigmatella aurantiaca: Thank you for the review, comments and queries. I'll get onto them over this weekend! T.Shafee(Evo&Evo)talk 11:24, 19 October 2017 (UTC)
@Stigmatella aurantiaca: no worries, just checking in! Thanks for your work on this so far! Amkilpatrick (talk) 13:50, 19 October 2017 (UTC)
@Evolution and evolvability: Crisis is over, for now. Nobody died. I can get back to work. Stigmatella aurantiaca (talk) 00:35, 4 December 2017 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── @Stigmatella aurantiaca and Amkilpatrick: I'm glad to hear that the family crisis resolved well, and apologies for the additional delay at our end. Rohan Lowe and I will have a go at doing some updates over the coming weeks. Rohan has made a start and fixed the jargon used in the tables and main text (eg 'Resource load'). He's also added in table legends to make them easier to interpret and bring them up to the standard of the Transcriptomic databases table. If there's anything we've missed, it would be very useful if you could point to some examples for us to 'calibrate' to. We've tried to make sure that any necessary technical terms are wikilinked so that the link's lead sentence acts as a definition. Rohan has put in some example footnotes, although they sort of double up on some of the links (e.g. hybridisations[note 1]). Let us know any further recommendations and we'll do another round up updates.

  1. ^ In molecular biology, hybridisation is a phenomenon in which single-stranded deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) molecules anneal to complementary DNA or RNA.

Thanks again for all your reviewing work on this, your recommendations are definitely aiding readability. T.Shafee(Evo&Evo)talk 00:08, 20 December 2017 (UTC)

@Evolution and evolvability, Stigmatella aurantiaca, and Amkilpatrick: Hi everyone! What is the status of this review? It looks like no progress has been made in the past month.--Dom497 (talk) 03:19, 21 January 2018 (UTC)

Since this review has been stagnant for so long, I plan to pick it up and complete it. I'll start a separate section below for my comments. Mike Christie (talk - contribs - library) 13:21, 10 March 2018 (UTC)

Secondary review by Mike Christie

I'll copyedit as I go through the article; please revert if I make any mistakes. FYI, as context for my comments, I am reasonably scientifically literate, but have no expertise in this area.

  • The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline. Transcriptomics has been defined by repeated technological innovations that transform the field: there's some overlap between the second sentence and the end of the previous sentence. How about "The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have repeatedly transformed the field, and have now made transcriptomics a widespread discipline"?
 Done. I've changed the sentences to something similar to suggested. T.Shafee(Evo&Evo)talk 09:57, 14 March 2018 (UTC)
  • The lead seems a little short for the length of the article.
    I have added some more text to better reflect the content of the article, adding some text about data analysis. It is currently 309 words, which is fairly average for the Featured Articles I looked at in the category biology. Seven of the eight featured leads I looked at were between 252 and 425 words.--Rohan Lowe (talk) 11:18, 19 March 2018 (UTC)
    I think that's a definite improvement. Mike Christie (talk - contribs - library) 22:11, 19 March 2018 (UTC)
  • in different tissues, conditions, or time points gives information on: suggest "in different tissues or conditions, or at different times, gives information on"
 Done. T.Shafee(Evo&Evo)talk 10:23, 14 March 2018 (UTC)
  • Can we get an explanation of "GeneChip", either inline or as a footnote? I was going to suggest linking it, but it redirects to Affymetrix which doesn't explain the term. Is it just another term for a microarray? Ah, I see it's mentioned later; we should give some sort of explanation on first use.
 Done. We don't need to use the term "genechip" here, I have changed genechip to the more general term "microarray". There is only one other use of Genechip in the article, and I think that is suitably explained in the text and also contains a link to the Affymetrix wiki page. I have modified the link to include the word genechip.--Rohan Lowe (talk) 01:41, 19 March 2018 (UTC)
  • The "Expressed sequence tags" section repeats some information about the Sanger method already covered in the "Early attempts" section; I don't think we need it again.
     Question: I have reviewed the paragraphs "History- Early Attempts" and "Data gathering - Expressed sequence tags", however I am struggling to find any substantial duplication of text on the Sanger method, or other context within these paragraphs. Could you have another look and quote some sentences with duplicated information? or perhaps you were thinking of another section? --Rohan Lowe (talk) 02:06, 19 March 2018 (UTC)
    Sorry, it was the "Before transcriptomics" section. The repeated sentence is The Sanger method of sequencing was predominant until the advent of high-throughput methods such as sequencing by synthesis (Solexa/Illumina). Mike Christie (talk - contribs - library) 22:11, 19 March 2018 (UTC)
 Done. I found the duplication and removed the second instance in the expressed sequence tags section.--Rohan Lowe (talk) 22:59, 25 March 2018 (UTC)

  • There are quite a few uncited sentences. Can you confirm that these are covered by WP:SCICITE; that is, a reader could verify each of them by a general reference cited earlier in that section?
     Done. I've gone though to make sure that there's at lease one citation per paragraph. Occasionally a single ref supports several sentences, but I've placed it so that it should be clear which refs support which statements. I've also updated a few references and added new ones. T.Shafee(Evo&Evo)talk 03:17, 26 March 2018 (UTC)
  • What's the difference between single-channel and dual-channel detection of fluorescent tags?
    Good point, it's apiece of technical jargon - essentially how many colours are being looked at at a time. Interestingly, it doesn't have a page (the closest is probably channel (digital image) or optical filter, though neither are exactly how its used in microscopy). I'll work out a better wording to avoid/define the term. T.Shafee(Evo&Evo)talk 10:36, 14 March 2018 (UTC)
    I have changed the sentence to avoid referring to single- or dual-channel. I think it can be considered jargon and is not required here. I replaced it by referring to the fluorescent tags used, and also managed to correct a slight error where we mentioned fluorescently tagged probes - I believe the transcripts are tagged, not the probes. --Rohan Lowe (talk) 06:57, 19 March 2018 (UTC)
    I've unstruck this point temporarily; there's still one instance of "single channel detection" in the article, in the "Microarrays" section; I assume we'd want to rephrase this too? Mike Christie (talk - contribs - library) 22:11, 19 March 2018 (UTC)
 Done. I have rephrased that second sentence - I changed it to refer to fluorescent labels instead of channels, which I think is a good improvement.--Rohan Lowe (talk) 23:05, 25 March 2018 (UTC)
  • typically lack the transcript resolution: I'm not clear what's meant by resolution here.
 Done. Good point, I have revised the text from "The probes are longer than those of high-density arrays and typically lack the transcript resolution of high-density arrays" to "The probes are longer than those of high-density arrays and can not identify alternative splicing events" including a link to explain alternative splicing --Rohan Lowe (talk) 02:06, 19 March 2018 (UTC)
  • The typical dynamic range of 5 orders of magnitude for RNA-Seq is a key advantage over microarray transcriptomes: what does "dynamic range" mean here?
 Done. I've defined dynamic range as part of the sentence. T.Shafee(Evo&Evo)talk 11:45, 15 March 2018 (UTC)
  • background signal is very low for 100 bp reads in non-repetitive regions: the background signal is effectively noise in the desired signal, if I understand this correctly; the word "signal" is a bit misleading for the non-expert reader.
 Done. T.Shafee(Evo&Evo)talk 10:54, 14 March 2018 (UTC)
  • the use of chain-terminating nucleotides during reverse transcription or utilise simultaneous fragmentation and tagging of cDNA by transposase enzymes: something wrong here; looks like "utilise" should be "the use of"?
 Done. I've also split the sentence in two. T.Shafee(Evo&Evo)talk 11:16, 15 March 2018 (UTC)
  • Spike-in controls can be used to provide quality control assessment of library preparation and sequencing: what is a spike-in control?
 Done. I've updated the sentence to add a definition wikilink, as well as organise it to make it a bit clearer what is being spiked in. T.Shafee(Evo&Evo)talk 11:20, 14 March 2018 (UTC)
  • Direct sequencing of RNA using nanopore sequencing represents a current state-of-the-art RNA-Seq technique in its infancy (in pre-release beta testing as of 2016). Can this be updated?
 Done.I have replaced the citation to a pre-print bioarchive website to the newly peer-reviewed resultant journal article in Nature Methods. I deleted the reference to beta-testing as nanopore direct RNA sequencing is now commercially available.--Rohan Lowe (talk) 06:57, 19 March 2018 (UTC)

* Can we get a link or explanation for "cufflinks software"? "Kallisto" and "tophat" should also be explained; a single note would probably suffice for all three. If the answer is that these are just names for particular pieces of software, that's all we need to say.

  •  Done I have edited the text to make it clear that they are the names of programs. I have also added links to the external github software repositories for Kallisto, Cufflinks, and Tophat software. --Rohan Lowe (talk) 07:34, 19 March 2018 (UTC)
    OK on the text change; I moved the links down to the "External links" section of the article since Wikipedia tries to avoid external links from within the body of articles. Mike Christie (talk - contribs - library) 22:11, 19 March 2018 (UTC)
  • Most read a table of genes: suggest "Most tools read a table of genes".
     Done I have made this change. --Rohan Lowe (talk) 07:34, 19 March 2018 (UTC)

The article is very impressive, and appears to be comprehensive. The prose is very clean; I've made a couple of minor edits. Once the points above are addressed I will promote this to GA. Pinging the nominator, Amkilpatrick, since this is not a new review and won't post a talk page note. Mike Christie (talk - contribs - library) 15:23, 10 March 2018 (UTC)

Mike Christie, you can always place this nomination on hold, which does post to the nominator's talk page; pings don't always go through, unfortunately. BlueMoonset (talk) 05:31, 11 March 2018 (UTC)
Hello, just a note to confirm that I've seen the comments above and have also notified Rohan_Lowe. We'll try to get onto these asap! T.Shafee(Evo&Evo)talk 10:35, 11 March 2018 (UTC)
Thanks for picking this up Mike! I'll try and help with some of these this week. Amkilpatrick (talk) 09:39, 13 March 2018 (UTC)

Evolution and evolvability, Rohan Lowe, Amkilpatrick: just checking in to see what's happening -- this is almost ready to promote, just a couple more things to address. Mike Christie (talk - contribs - library) 15:22, 25 March 2018 (UTC)

The last edits fixed one issue. The only remaining question is the uncited sentences. Per WP:SCICITE, these are OK if the information is covered by a general reference work cited elsewhere in the article; can you just confirm that that's so, and indicate which reference would cover those points? Or if you prefer you can just cite them in the article. Mike Christie (talk - contribs - library) 23:31, 25 March 2018 (UTC)

@Mike Christie: thank you for pinging us again. I've done a full readthough to check that the referencing is no WP:SCICITE-compliant. Let me know if there are any additional aspects you'd like us to address. T.Shafee(Evo&Evo)talk 03:20, 26 March 2018 (UTC)
That looks good. Promoting to GA. Mike Christie (talk - contribs - library) 09:25, 26 March 2018 (UTC)
@Mike Christie: Thank you very much for your helpful review! T.Shafee(Evo&Evo)talk 23:38, 26 March 2018 (UTC)
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