Talk:Metagenomics

I think the subject also need some comments the study of organisms acting as a community. An example being the flow of a metabolite through the different metabolisms. Any thoughts? Or Perhaps that comes under systems biology instead?

It does include an aspect of studying an entire community at a genetic level.

I'd say yes and no to this. Following a metabolite through different metabolisms would fall under something like systems biology and might not require any genomic information at all so metagenomics might not be the right label. Such studies are also not the sole concern of metagenomics. Diversity and evolution are also concerns in the field.

On the other hand, such a study is one of the really useful things that metagenomics can do and do well and probably what a lot of people in the field are doing, so it definitely deserves a prominent mention if not is own section. It's just not what I'm doing in metagenomics, so I didn't think to put it in.

Also, just because I started the page page, doesn't mean you can't add what you'd like to it. If you have some knowledge or interest in this area, please contribute. Jmeppley 21:05, 25 Jan 2005 (UTC)

This should probably go into the microbiome article instead. Estevezj (talk) 06:24, 20 December 2011 (UTC)

Diversa Corporation

Obviously someone closely with Diversa Corporation has edited this piece. Metagenomics is obviously not only Diversa Corporation !!! I removed Press releases and all mentions to Diversa Corporation in the references. More editing is neeeded.

--Daniel Vaulot 13:10, 20 January 2007 (UTC)

Wow., the page is just silly with Diversa plugs. I'll have a go at it.

I'll also try to trim the references. It's not really Wikipedia's role to be a warehouse of citations. The references should be largely limited to work directly used in the crafting of the article. If there is strong support for having such a list of metagenomic citations, it should be in a separate page.

Jmeppley 14:50, 11 September 2007 (UTC)

Update: I took out most of the Deiversa plugs and re-worked the first half of the article some. It still needs lots of work. I started using numbered references. This should also be extended to the rest of the article. References should be pulled from the "addtl refs" section once they are used as a citation. Eventually there should be nothing there or just a few important articles. Jmeppley 18:31, 11 September 2007 (UTC)

chip-based pyrosequencing

It's the first time I've seen the term "chip-based pyrosequencing" being used; the reason it's not used so much is that it could cause confusion with oligo-chips based resequencing, which is a totally different technology which is not used at all in metagenomics. The term is otherwise essentially used in one (solid) paper ("Bacterial flora-typing with targeted, chip-based Pyrosequencing" BMC Microbiology). How would others feel about changing the term "chip-based pyrosequencing" to "massively parallel pyrosequencing"? --Pascal.hingamp (talk) 11:30, 16 April 2008 (UTC)

Software

Since CARMA3 has shown to outperform MEGAN and SOrt-ITEMS it should probably also be mentioned, reference here: http://dx.doi.org/10.1093/nar/gkr225 93.130.46.13 (talk) 19:47, 26 June 2011 (UTC)

Reorganization, F'11

I saw that this article has been tagged for a while so I went ahead and cleared out the further reading list. I'm going to work through those and use them to build on the framework that exists. This is my first major edit, so corrections, suggestions are welcome. Estevezj (talk) 05:09, 7 December 2011 (UTC)

Hey there - I've fixed a broken link and also reorganised the External links section - now all the tools are together. Sarahburge (talk) 15:59, 8 December 2011 (UTC)

I'm just going ahead with these edits. You can see what I have planned on my metagenomics sandbox. I also don't think the long list of binning software is necessary; these can be broken out into a separate page, with one or two examples of an algorithm or approach. Estevezj (talk) 06:24, 20 December 2011 (UTC)

Converting footnotes to list-defined (LDR) format

Any objection to converting footnotes to list-defined (LDR) format? This many inline citations are getting awkward. Estevezj (talk) 11:07, 28 December 2011 (UTC)

Done. Estevezj (talk) 23:46, 19 January 2012 (UTC)

Tools vs methods vs. "why"

I'm wondering what the consensus is regarding what the focus of the bioinformatics section should be. I've been operating under the supposition that the focus should be on the rationales and methods behind commonly used tools rather than a list of those tools (cf. how things used to be). I've taken the Koonin (2008) and Wooley (2010) review articles as my models in reorganizing and expanding this section, and the way they handle the balance between discussing approaches versus software would be my suggestion as to how we should proceed. Estevezj (talk) 05:38, 5 January 2012 (UTC)

GA Review

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

Reviewer: Allens (talk · contribs) 17:31, 27 January 2012 (UTC)

• I am not taking a position on whether it's a good article or not (I do not regard myself as sufficiently experienced to do so); I will simply note the peer review I did at Wikipedia:Peer_review/Metagenomics/archive1 - I have carried out one of the recommendations (linking genomics) myself, and two of the questions can probably be left for later (regarding searches using HMMs and proportional abundance checking), but the rest do need examining. Allens (talk) 17:31, 27 January 2012 (UTC)

Thanks again for your suggestions and edits. As I understand it, the criteria (see WP:GA?) and process (WP:RGA) for selecting good articles are a bit more flexible than featured articles, and any editor can carry out the review. To address the previous peer review:

• I went through and tagged 3 of the 4 articles tagged as registration warnings by checklinks with the subscription required template. I also checked the redirects, and they are all open (although the national academies requires registration), and include a link to PLoS via the DOI resolver. I figured that was ok, but I can replace the url with a direct link if necessary.
• I've tried to bracket some sections (like bioinformatics) that were largely based upon one or two review articles with citations at the beginning and end of paragraphs as suggested. Again, I'm new here, so if its necessary to increase the citation density it'd be no undue burden to do so. If you could point to a passage or two so that I know what you mean, it'd be a help.
• I expanded the end of the biofuel section a bit to specifically mention the leafcutter ant fungus garden metagenome, with links out to the larger system and its mutualism.

I hope I didn't overlook any. I probably should have explicitly replied on the PR, sorry if that was poor form. Estevezj (talk) 22:10, 27 January 2012 (UTC)

• I'm sorry that I didn't spot these changes. Might I suggest not using the "minor edit" flag for such changes? Most people, including me, don't see "minor edit" revisions in their watchlists, so I didn't spot that any significant changes had taken place and didn't look (I should have, I admit). Upon looking over it now:

GA review (see here for what the criteria are, and here for what they are not)

1. It is reasonably well written.

   a (prose): b (MoS for lead, layout, word choice, fiction, and lists):

   Quite readable; follows MoS as far as I can tell

2. It is factually accurate and verifiable.

   a (references): b (citations to reliable sources): c (OR):

   Well-referenced; plagiarism check vs most-referenced article indicates no problems (material duplicated is either references or very short phrases).

3. It is broad in its coverage.

   a (major aspects): b (focused):

   Actually answers more than I had thought when I read over it for the peer review. Pyrosequencing's advantages and disadvantages in comparison to shotgun sequencing would be nice but not necessary if not findable in a secondary source.

4. It follows the neutral point of view policy.

   Fair representation without bias:

   No problems on NPOV notable.

5. It is stable.

   No edit wars, etc.:

   History indicates stability except for changes to get to GA status.

6. It is illustrated by images, where possible and appropriate.

   a (images are tagged and non-free images have fair use rationales): b (appropriate use with suitable captions):

   Images all check out, and generally have as much data as is suitable in captions (although I did add a link from the IMG/M mention to the appropriate article, for people who read the lead then image captions); further data is available upon clicking.

7. Overall:

   Pass/Fail:

   Good job!

I believe it passes! Next thing to do is to figure out how to list it...

Umm... I may not have been supposed to list it, given that (as part of the peer review process and the above) I did do some editing. I am checking on this now. Allens (talk) 23:36, 28 January 2012 (UTC)

OK, no problem; the criterion is "no substantial editing", which it wasn't. Allens (talk) 00:04, 29 January 2012 (UTC)

Great news. Thanks for your thoughtful reviews and suggestions during both reviews!Estevezj (talk) 10:02, 29 January 2012 (UTC)

Sampling?

This article lacks the discussion on sampling techniques, which I believe is quite particular for environmental analysis. I'm thinking to add a section about it and put it together with the sequencing and bioinformatics sections into a "method" section or something similar. --sentausa (talk) 08:40, 27 February 2015 (UTC)

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Anything salvageable from parallel draft?

I just came across a page from 2013 called Metagenomics: An Alternative Approach to Genomics. Is there anything salvagable from it to merge in here? Otherwise it can be deleted. T.Shafee(Evo&Evo)^talk 10:44, 8 January 2020 (UTC)

  Y Merger complete. Klbrain (talk) 14:17, 23 February 2021 (UTC)