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Talk:Genome-wide association study/GA1

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GA Review

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GA toolbox
Reviewing

Article (edit | visual edit | history) · Article talk (edit | history) · Watch

Reviewer: Estevezj (talk · contribs) 02:48, 9 January 2013 (UTC)[reply]

I've started my first read-through and will update this review as I proceed. — James Estevez (talk) 02:48, 9 January 2013 (UTC)[reply]

Criteria

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Good Article Status - Review Criteria
Further information: WP:WIAGA

A good article is—

  1. Well-written:
    2. (a) the prose is clear, concise, and understandable to an appropriately broad audience; spelling and grammar are correct; and
    (b) it complies with the Manual of Style guidelines for lead sections, layout, words to watch, fiction, and list incorporation.[1]
  2. Verifiable with no original research:
    3. (a) it contains a list of all references (sources of information), presented in accordance with the layout style guideline;
    (b) reliable sources are cited inline. All content that could reasonably be challenged, except for plot summaries and that which summarizes cited content elsewhere in the article, must be cited no later than the end of the paragraph (or line if the content is not in prose);[2] and
    (c) it contains no original research.
  3. Broad in its coverage:
    4. (a) it addresses the main aspects of the topic;[3] and
    (b) 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. [4]
  6. Illustrated, if possible, by media such as images, video, or audio:
    7. [5]
    (a) media are tagged with their copyright statuses, and valid non-free use rationales are provided for non-free content; and
    (b) media are relevant to the topic, and have suitable captions.[6]

Review

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  1. Well-written:
    2. Criteria Notes Result
    (a) (prose)
    1. Background... OK
      1. OK: "In addition to the conceptual framework...": Fine as is, but might be helpful to rephrase to clarify whether you mean other factors besides the conceptual framework or other factors when combined with a conceptual framework.
    2. Methods... OK
    3. Results... OK
      1. OK: "Wellcome Trust Case Control Consortium... was the to date[when?] largest GWA study": Please clarify: largest as of 2007, or to the present day?
    4. Clinical applications... OK
    5. Limitations... OK
      1. OK: "In addition to these preventable issues...": I attempted to rephrase this, but further clarification as to the nature of the criticism would be helpful. Is the criticism of GWAS of the fundamental approach of looking at SNPs, or its hypothesis-free (sort of) approach, or lack of power?
      2. OK: "It can be discussed if...": My personal preference would be to drop this sentence, but its nevertheless acceptable under the GAC.
    		 Pass Pass
    (b) (MoS) The article complies with the five WP:MOS sections required by the GAC. Pass Pass
  2. Verifiable with no original research:
    3. Criteria Notes Result
    (a) (references) The References section contains a properly formatted list of references used in the article.[7] Pass Pass
    (b) (citations to reliable sources)
    1. Background... OK
    2. Methods... OK
      1. Hold: [citation needed] in 1st paragraph.
    3. Results... OK
      1. OK: [citation needed] at beginning of third paragraph.
    4. Clinical applications... OK
    5. Limitations...
      1. OK: Reference 42 is acceptable under WP:BLOGS.[8]
      2. OK: [citation needed] in 2nd paragraph.
    6. See also... OK
    7. References... OK
    		 Pass Pass
    (c) (original research) Besides the tagged exceptions, statments in the article are supported by the sources and contain no original research. Pass Pass
  3. Broad in its coverage:
    4. Criteria Notes Result
    (a) (major aspects) The article offers a good overview of the main aspects of GWAS. Pass Pass
    (b) (focused) The article is concise and adheres to summary style. Pass Pass
  4. Neutral: it represents viewpoints fairly and without editorial bias, giving due weight to each.
    5. Notes Result
    The article fairly represents different significant viewpoints on the topic. Pass Pass
  5. Stable: it does not change significantly from day to day because of an ongoing edit war or content dispute.
    6. Notes Result
    Stable. Article had fewer than 20 edits in the last six months of 2012. Pass Pass
  6. Illustrated, if possible, by media such as images, video, or audio:
    7. Criteria Notes Result
    (a) (images are tagged and non-free images have fair use rationales) Images are available under free licenses and are appropriately cited where necessary. Pass Pass
    (b) (appropriate use with suitable captions) The images are appropriate for the article and the captions are accurate and informative.[9] Pass Pass

Result

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Result Notes
Pass Pass Fine work on this article. There are minor ambiguities in the prose (please see 1a) and missing references (see 2b), that prevent an immediate pass. Thank you for your contributions both to this article in particular and to Wikipedia in general.

Discussion

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Again, fine work on the article. In the course of the review I've made some minor changes to the article to correct for usage, style, and to add a handful of references. I've tagged several statements that require in-line citations under the Good Article criteria.

Moving forward, as work on the article continues I would like to bring to your attention the article available at PLoS Computational Biology.[10] This article is available under the Wikipedia compatible CC-BY license, meaning that figures and text from it can be incorporated in this article. This resource may prove valuable should editors decide to work towards FA status.

Best regards, — James Estevez (talk) 02:26, 18 January 2013 (UTC)[reply]

Working my way slowly through it. Have a bit at work right now, so apologies for the small steps approach - I will be able to make it in the 14 days though. Today I figured the "there have been two general trends" citation need. First I wanted to claim that this was not needed since the previous paragraphs cites a 2005, n=146 study for main disease phenotype (ARM), and the following 4 citations give later studies that are larger or directed towards more narrowly defined phenotypes. But I think I found an ok article for it now (the Ioannidis et al 2009, nature review one). However, particularly the size statement is so self-evident that it's kinda hard to find stated clearly in reviews. I hope "Consortia of investigators are also becoming increasingly popular" should cover it ok. The defined phenotypes is easier, and it's summed up by the "Phenome mapping" mapping section. Also updated the 200 wellcome trust with a slight re-write that should fix the 'when' mark.--LasseFolkersen (talk) 21:08, 20 January 2013 (UTC)[reply]
Same way I reviewed it. Anyhow, that's no problem, just let me know if you get slammed and need a bit more time. From what I understand, things that are self-evident to experts getting tagged with {{fact}} is a fairly common point of frustration for people (Wikipedia:Expert retention), but I think that'll suffice. Include it in your next GWAS article and problem solved.☺ (I also moved the WTCCC section around a bit.) — James Estevez (talk) 22:38, 20 January 2013 (UTC)[reply]
Haha, yeah - I'll try to get a short sentence into the next publication "by the way, GWA studies are larger today than in 2007"  :-) at least it's hard to argue against. But seriously - no worries. I do understand the need for good sources for this. Got one more citation needed now. That Bush et al that you suggested - its section 6.3 covers the basic P-value thresholds pretty well. Will look at the last citation needed and prose tomorrow--LasseFolkersen (talk) 19:58, 21 January 2013 (UTC)[reply]
Ok, I figured out the last citation missing and also re-wrote some of that paragraph to address your prose hold. I also removed those extra reviews as by your note 7 - there's plenty of good reviews in the text already. What about the "external links"? I removed some of them now, leaving only the ones I had heard about as main resources often used. For your point about ref-previously-known-as-42/the MacArthur blog, I'll make a note of looking for articles for it later. I'm not sure that one ever came up in official review afterwards, but I'll change it if I find something. Also I wanted to ask you about note 9 - Do you suggest that I remove the horizontal dashed lines, or that I try to explain them in caption? It can't be much more than "the top dashed lines represents the chosen cutoff for significance at p < 5×10^−8, since that's as much as I could get from the article myself. I have no clue why they put in a line at P=10^-5 (and frankly I think it's quite arbitrary). --LasseFolkersen (talk) 21:04, 21 January 2013 (UTC)[reply]
External links are beyond the scope of the GAC. That said, the guideline (WP:EL) goes into detail, but I see no problem with it as it currently exists. I've reconsidered my note for the lead figure: I think that further detail would probably be better placed in the Manhattan plot (the same image is used to illustrate both articles) caption or in the description. If you choose to add it here I suggest dropping the final sentence of the caption ("This example is...") and then tacking on "the top dashed lines represents the chosen cutoff for significance at p < 5.0×10−8" or some concise variation. In any event, I've passed the article and everything should update once the bot comes through. Thanks again for your work on this. — James Estevez (talk) 22:10, 22 January 2013 (UTC)[reply]

Additional Notes

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  1. ^ Compliance with other aspects of the Manual of Style, or the Manual of Style mainpage or subpages of the guides listed, is not required for good articles.
  2. ^ Either parenthetical references or footnotes can be used for in-line citations, but not both in the same article.
  3. ^ This requirement is significantly weaker than the "comprehensiveness" required of featured articles; it allows shorter articles, articles that do not cover every major fact or detail, and overviews of large topics.
  4. ^ Vandalism reversions, proposals to split or merge content, good faith improvements to the page (such as copy editing), and changes based on reviewers' suggestions do not apply. Nominations for articles that are unstable because of unconstructive editing should be placed on hold.
  5. ^ Other media, such as video and sound clips, are also covered by this criterion.
  6. ^ The presence of images is not, in itself, a requirement. However, if images (or other media) with acceptable copyright status are appropriate and readily available, then some such images should be provided.
  7. ^ NB: The references given in the "Reviews" subsection are acceptable (per WP:GENREF), but are likely to draw opposition during any future WP:FAC.
  8. ^ NB: I would expect this to be an issue at WP:FAC.
  9. ^ NB: I would suggest updating the caption of the lead article to note what the dashed lines represent. These are presumably significance levels, but the original figure caption at PLOS Genetics isn't clear. This issue doesn't merit a hold, but it is something editors may wish to address in the future.
  10. ^ Bush, W. S.; Moore, J. H. (2012). Lewitter, Fran; Kann, Maricel (eds.). "Chapter 11: Genome-Wide Association Studies". PLoS Computational Biology. 8 (12): e1002822. doi:10.1371/journal.pcbi.1002822. PMC 3531285. PMID 23300413.{{cite journal}}: CS1 maint: unflagged free DOI (link)
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