Talk:European Nucleotide Archive

European Nucleotide Archive has been listed as one of the Natural sciences good articles under the good article criteria. If you can improve it further, please do so. If it no longer meets these criteria, you can reassess it.

Article milestones
Date	Process	Result
April 15, 2013	Good article nominee	Listed

Molecular Biology: COMPBIO

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GA Review

This review is transcluded from Talk:European Nucleotide Archive/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Estevezj (talk · contribs) 22:04, 20 March 2013 (UTC)[reply]

Criteria

Good Article Status - Review Criteria

Further information: WP:WIAGA

A good article is—

Well-written:

(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]

Verifiable with no original research:

(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.

Broad in its coverage:

(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).

Neutral: it represents viewpoints fairly and without editorial bias, giving due weight to each.
Stable: it does not change significantly from day to day because of an ongoing edit war or content dispute.

^[4]

Illustrated, if possible, by media such as images, video, or audio:

^[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

Well-written:

Criteria	Notes	Result
(a) (prose)	No copyright issues detected. Corrected one or two mistakes during reading. Concise and well-organized.	Pass
(b) (MoS)	MOS:LEAD: Good summary of article, hitting all major points. Made some minor changes to wikilinks. Notes.^[a]	Pass

Verifiable with no original research:

Criteria	Notes	Result
(a) (references)	Contains an appropriately formatted reference section. Notes^[b]Cite error: A `<ref>` tag is missing the closing `</ref>` (see the help page).	Pass
(b) (citations to reliable sources)	Given statistics are supported by their respective inline citations. Hold: I haven't got access to reference 6 to check the Kennard quotation.^[c] Notes.^[d]	On hold
(c) (original research)	None detected, statements are supported by the cited material. Routine calculations contained within in the figures are permissible.	Pass

Broad in its coverage:

Criteria	Notes	Result
(a) (major aspects)	This article touches upon ENA's main attributes as reflected in the literature, and adds relevant context and historical background. Level of technical detail is appropriate.	Pass
(b) (focused)	The level of detail is consistent with an encyclopedic treatment of the relevant literature.	Pass

Neutral: it represents viewpoints fairly and without editorial bias, giving due weight to each.

Notes	Result
Article is on an uncontroversial topic, and complies with WP:NPOV	Pass

Stable: it does not change significantly from day to day because of an ongoing edit war or content dispute.

Notes	Result
Stable since end of January 2013.	Pass

Illustrated, if possible, by media such as images, video, or audio:

Criteria	Notes	Result
(a) (images are tagged and non-free images have fair use rationales)	OK. All images are properly tagged with their respective copyright status.	Pass
(b) (appropriate use with suitable captions)	OK. Images are relevant and contain succinct and properly formatted captions.^[e]	Pass

Result

Result	Notes
Pass	~~Waiting on source to verify Kennard quote (2 (b))~~.

Discussion

Apologies for the delayed review. I had set this aside in order to submit an interlibrary loan to obtain Ref. #6, but as it already has been too long I thought I should submit the review as is.

All in all, the article is a concise, well-illustrated, and well-referenced overview of the ENA and its history. The article meet or exceeds the criteria for a good article, and as such, it will pass once I get a copy of Kneale and Kennard (1984).^[7] It is a good model for the development of other articles on biological databases to follow.

Additional suggestions below.^[f]^[g]

Many thanks for such a thorough review. I'd noticed the et al.-related hidden category but didn't really understand it; it's now fixed and I've learnt something for next time so thanks (same goes for the val template).

I am keen to expand the article further but am wary of WP:NOTMANUAL and relying too much on their website as a self-published primary source. Still if you have further thoughts on expansion I'd be interested in hearing them. Thanks for the help with image licensing too Jebus989 ^✰ 11:42, 15 April 2013 (UTC)[reply]

It is easy to see how one could quickly run afoul of WP:NOTEVERYTHING-type concerns in an article like this. That said, this is the best article in its category Category:Biological databases (at least as far as I can tell), and to a certain extent it will serve as a model for many others, including defining the parameters of a focused or comprehensive article on the topic. Which is all a rather long-winded way of saying that I think you have substantial discretion in how to proceed. Some ideas:

How is data synchronized between databases? Other back-end questions.
Flat-file format, expand until you have enough for a stub, then split it off.
Doubling time figure. Graphical view
How much does it all cost? What's the ROI?
Brief examples from the literature of the kinds of analyses and meta-analyses that scientists can use it for.

Some of these are dependent on finding secondary sources, others are dependent on the intended audience (undergraduates? Beginning grad students?). One or more may be inane. There should be some additional attention from editors who notice its listing.

However, as far as this review is concerned, I have received a copy of Kneale and Kennard (1984), confirmed the quotation, and passed the article. Thanks for your work here.— James Estevez (talk) 19:49, 15 April 2013 (UTC)[reply]

Great, thanks a lot for the ideas and for the review Jebus989 ^✰ 21:09, 15 April 2013 (UTC)[reply]

Beyond the scope

^ §Sequence Read Archive, ¶2: over 500,000,000,000: changed IAW MOS:NUM#Large_numbers. As an aside: I find that Template:Val comes in handy when dealing with large numbers. YMMV.
^ This is so far down the list of things to do (at least in my view) that I hesitate to mention it, but seven references (1,5,12,14,17,18,28) are using the implicit et al (see Category:Pages using citations with old-style implicit et al.). As mentioned in the linked page, while citation templates can display any number of authors, I think {{cite doi}} defaults to nine, so make of that what you will. I don't participate in WP:FAC so I don't know whether it'll come up, or if anyone else has ever noticed anything of the kind. Just FYI.
^ Kneale, G.; Kennard, O. (1984). "The EMBL nucleotide sequence data library". Biochemical Society transactions. 12 (6): 1011–1014. PMID 6530028.
^ N.B.: Lead, ¶2: ...the ENA contained complete genomes of 5,682 organisms and sequence data for almost 700,000.: Reference given states: "International Nucleotide Sequence Database Collaboration [...] databases hold complete genomes from 5,682 organisms and sequence from almost 700,000 organisms". INSDC databases are synchronized so that number is correct for ENA, but you may want to clarify this.
^ NB: I would argue that a screenshot of the ENA interface that includes the ENA logo would be free because of the software license. In addition, the logo used at the top of the article itself falls under the LGPL, as it was included as part of a library they've released (European Nucleotide Archive (2013-03-27). "webin-data-streamer-ENA-Client" (Software repository). GitHub.), if I understand the rules correctly.
^ I think that the article could be expanded, especially in the data format and access sections.
^ "See also" section should probably include GenBank and DDBJ.

Additional Notes

^ 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.
^ Either parenthetical references or footnotes can be used for in-line citations, but not both in the same article.
^ 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.
^ 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.
^ Other media, such as video and sound clips, are also covered by this criterion.
^ 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.
^ This is if editors have no objection to my doing so. While I have tried to check every accessible reference, this is not required by the GAC, at least by my reading.

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Syncing

Is the dataset synced with others? I know that NCBI syncs their dataset to japan and europe but I am unsure about the ENA being included here. 2A02:8388:1641:3580:BE5F:F4FF:FECD:7CB2 (talk) 17:54, 16 June 2017 (UTC)[reply]

[7] §Sequence Read Archive, ¶2: over 500,000,000,000: changed IAW MOS:NUM#Large_numbers. As an aside: I find that Template:Val comes in handy when dealing with large numbers. YMMV.

[implicit-8] This is so far down the list of things to do (at least in my view) that I hesitate to mention it, but seven references (1,5,12,14,17,18,28) are using the implicit et al (see Category:Pages using citations with old-style implicit et al.). As mentioned in the linked page, while citation templates can display any number of authors, I think {{cite doi}} defaults to nine, so make of that what you will. I don't participate in WP:FAC so I don't know whether it'll come up, or if anyone else has ever noticed anything of the kind. Just FYI.

[9] Kneale, G.; Kennard, O. (1984). "The EMBL nucleotide sequence data library". Biochemical Society transactions. 12 (6): 1011–1014. PMID 6530028.

[10] N.B.: Lead, ¶2: ...the ENA contained complete genomes of 5,682 organisms and sequence data for almost 700,000.: Reference given states: "International Nucleotide Sequence Database Collaboration [...] databases hold complete genomes from 5,682 organisms and sequence from almost 700,000 organisms". INSDC databases are synchronized so that number is correct for ENA, but you may want to clarify this.

[11] NB: I would argue that a screenshot of the ENA interface that includes the ENA logo would be free because of the software license. In addition, the logo used at the top of the article itself falls under the LGPL, as it was included as part of a library they've released (European Nucleotide Archive (2013-03-27). "webin-data-streamer-ENA-Client" (Software repository). GitHub.), if I understand the rules correctly.

[13] I think that the article could be expanded, especially in the data format and access sections.

[14] "See also" section should probably include GenBank and DDBJ.

[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.

[12] This is if editors have no objection to my doing so. While I have tried to check every accessible reference, this is not required by the GAC, at least by my reading.

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