Wikipedia talk:WikiProject Microbiology/Archive 6

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Microbes and bots

Following the previous post, I realised there is a nice potential for improvement in a automated way combining some resources which are consistent:

• NCBI has a nice list of genome projects [1], with info such as size, environmental details, protein number, CG etc.
• The List of Prokaryotic names with Standing in Nomenclature has official names, discovery ref and etymology [2]
• Biocyc could yeld some summary statistics [3].
• Arb living tree has a giant cladogram [4] and I have written a Perl script to convert chunks of Newick trees to Wikipedia's template:cladogram.

Would that be a good idea? Is there a better resource (non-copyrighted and consistent in formatting. e.g. tables not text)? I can write in Perl well so can do it (busy though), but I am not that well versed in the http methods post/get and I have no idea about bots and permission (and I am not admin). --Squidonius (talk) 22:44, 12 December 2010 (UTC)

I have made a set of pages with a lists of bacterial genera with all the bits to add, which I am going through, modding and adding, but I am completely and utterly sick of it. Here are the list of genera (I have partially got through deleting the already present ones from the list and some may have some formatting errors):

1. AC: has been split into:
   1. AC good to go
   2. AC ones issues
2. DL User:Squidonius/userpage/microbes2
3. MR User:Squidonius/userpage/microbes3
4. SZ User:Squidonius/userpage/microbes4

Basically, If anyone wants to help please please do (just opne in a new tab the redlink and press edit on the list entry and cut between the nowiki tags) or if someone wants a group done please ask. --Squidonius (talk) 05:48, 28 May 2011 (UTC)

AAAS and Wikipedian biologists

Fellow Wikipedians, I've recently been speaking with a (responsible) New York based journalist who is working on a story on the people and motivations behind the biological content on Wikipedia. She is attending the upcoming American Association for the Advancement of Science meeting and was wondering whether any Wikipedians were going. If you are, she would like to meet with you. Leave me a message or email me and I can put you in touch with her. Her request is as follows:

“I’m a journalist with The Scientist magazine and I’m writing an article about the creators of Wikipedia pages on basic biology. I’m planning on attending the AAAS meeting in Washington DC in February 17-21st [5], and am looking to meet up with Wikipedia writers and editors. I’d like to get a group together and get a better sense of the culture of contributors that write and polish these entries. Alternately, if you know of a different upcoming meeting of life science-Wiki-writers/editors on the east coast, let me know.”

Rockpocket 10:28, 14 January 2011 (UTC)

Actinobacteria

For something that's one of the most common forms of life on Earth, the page sure is short and overly technical. Actinobacteria could use some loving, I'd do it myself but most of what I know about the subject I've learned from that page. --Calibas (talk) 02:38, 4 February 2011 (UTC)

Taxobox color RfC

There's an RfC at Template talk:Taxobox colour#In light of the luminosity increase. Please share your thoughts there. Bob the WikipediaN ^{(talk • contribs)} 15:53, 7 February 2011 (UTC)

Which name to use?

I'm drafting an article on a species of Streptomyces but am unsure what the right name for it is at the moment. It was renamed scabiei in '97 but a publication in '07 recommended it be moved back to scabies. How do I work out which is the accepted one now? (Both have been used by papers published since '07). Thanks SmartSE (talk) 13:44, 23 February 2011 (UTC)

I might choose scabiei to differentiate it from scabies (the mite). The fact that both are used ought to be explained, of course. WhatamIdoing (talk) 17:01, 23 February 2011 (UTC)

Sorry maybe I should have made it clearer - the choice is between Streptomyces scabiei and Streptomyces scabies - there is no risk of getting it mixed up with scabies. I'm inclined to use S. scabies per WP:COMMONNAME as there are far more papers using this (even after it was officially changed to S. scabiei. I just wondered if there is a site where it is possible to find out which one is technically correct. SmartSE (talk) 17:45, 23 February 2011 (UTC)

A quick look over the >1000 results in the Web of Knowledge shows that S. scabies is used more frequently (at least in recent years, haven't checked back that far), so I don't think you can go wrong with that. If it's in error, you'll be able to use your new adminly powers to move over the redirect, so no worries regardless :) Sasata (talk) 17:53, 23 February 2011 (UTC)

The official nomenclature [6] (LPSN) lists Streptomyces scabiei as the correct version due to "The original spelling of the specific epithet, scabies (sic), has been corrected by Trüper and De' Clari 1997", which translates to "Thaxter in 1891 got his latin wrong" (by using the nominative case instead of the genitive of a 4th declension noun, translated in English it should be "Strepto of the rash" and not "Strepto, the rash"?!), while the 07 recommendation seems to not have any impact on the official nomenclature (I am pretty sure TOBA will be the same), what is the reference? However, bacterial taxonomy is a joke, which few pay attention to (as it is so unnecessarily frustratingly complicated, outdated and often written in French) so it does not matter too much. --Squidonius (talk) 20:20, 23 February 2011 (UTC)

Citation templates now support more identifiers

Recent changes were made to citations templates (such as {{citation}}, {{cite journal}}, {{cite web}}...). In addition to what was previously supported (bibcode, doi, jstor, isbn, ...), templates now support arXiv, ASIN, JFM, LCCN, MR, OL, OSTI, RFC, SSRN and Zbl. Before, you needed to place |id={{arxiv|0123.4567}} (or worse |url=http://arxiv.org/abs/0123.4567), now you can simply use |arxiv=0123.4567, likewise for |id={{JSTOR|0123456789}} and |url=http://www.jstor.org/stable/0123456789 → |jstor=0123456789.

The full list of supported identifiers is given here (with dummy values):

• {{cite journal |author=John Smith |year=2000 |title=How to Put Things into Other Things |journal=Journal of Foobar |volume=1 |issue=2 |pages=3–4 |arxiv=0123456789 |asin=0123456789 |bibcode=0123456789 |doi=0123456789 |jfm=0123456789 |jstor=0123456789 |lccn=0123456789 |isbn=0123456789 |issn=0123456789 |mr=0123456789 |oclc=0123456789 |ol=0123456789 |osti=0123456789 |rfc=0123456789 |pmc=0123456789 |pmid=0123456789 |ssrn=0123456789 |zbl=0123456789 |id={{para|id|____}} }}

Obviously not all citations needs all parameters, but this streamlines the most popular ones and gives both better metadata and better appearances when printed. Headbomb {talk / contribs / physics / books} 03:06, 8 March 2011 (UTC)

Tuberculosis' FAR

I have nominated Tuberculosis for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Delist" the article's featured status. The instructions for the review process are here. GamerPro64 (talk) 22:59, 6 April 2011 (UTC)

history of microbiology

The article History of microbiology does not exist. But there are many article with variations in focus. To name some:

• Microbiology talks about culturing techniques (falls short of modern methods)
• Bacterial taxonomy talks about the placement/rank of Bacteria and its major subdivisions
• Archaea talks in depth about the 3 domains
• Bacteria has a copypaste version of microbiology

Consequently, would anyone want to amalgamate by copy-paste these and more in a article? (I am overtaxed at present so cannot) --Squidonius (talk) 10:12, 12 May 2011 (UTC)

I have been working on History of viruses and History of virology, which are articles that I started late last year. After a spurt of writing, followed by a disappointing FAC, I haven't had much time lately to concentrate on them. Graham Colm (talk) 18:16, 12 May 2011 (UTC)

I may try my hand at this once I get Metagenomics squared away, but I don't think I could do it alone. Estevezj (talk) 12:18, 30 December 2011 (UTC)

Food web

Food web is currently being rewritten, and will hopefully go to FA. Any relevant contributions from people in this project will be much appreciated. --Epipelagic (talk) 06:38, 15 June 2011 (UTC)

Amoebozoa

...is a mess currently and need to be updated to Cavalier-Smith, 2009, if only for consistency. Various groups currently use different systems. Like Flabellinea being a subphylum instead of the clade Discosea under Lobosa. I tried fixing what I could by replacing them with autotaxoboxes for consistency, but it's too much for me. Microbiology is a very unfamiliar subject for me, heh, so if anyone is interested and have the necessary expertise in the subejct, please update the different taxa affected by Cavalier-Smith's revision.

That is, of course, if you guys adopted it. The text in Amoebozoa seem to indicate that you guys did (previously the taxobox's classification clashed with the information in the text). If I assumed wrongly, please revert.-- Obsidi♠n^Soul 14:57, 23 June 2011 (UTC)

I would expect the text to present different hypotheses, especially if there is uncertainty which is generally par for the course in these matters. The taxobox is a different case, because it has to pick something. According to the text, Lobosa is paraphyletic (not sure whether there are different circumscriptions of Lobosa around), so it might not be the best thing for the taxobox. But my expertise is at least as small as yours, and I didn't research this stuff. Kingdon (talk) 01:18, 24 June 2011 (UTC)

Hm yeah. In addition, Cavalier-Smith's six-kingdom system does affect more than Amoebozoa and is very controversial. Seeing that groups like Chromista doesn't seem to have been adopted, I guess it's best if someone else more knowledgeable can judge which taxonomic system to adopt. I'd be happy to help place autotaxoboxes though once a decision is reached, heh. -- Obsidi♠n^Soul 02:58, 24 June 2011 (UTC)

Health disasters by year categories proposed

I propose to make categories for health disasters by year eg Category 2011 health disasters; an alternative would be Category:Health disasters in 2011. This is the only category of disaster which does not have a “by year” category. An alternative name could be “Health accidents and incidents” but “Health disasters” seems to be accepted as the overall category. To be subcategorised by century eg 21st-century health disasters. Initially to be for 2000 to 2012; there seem to be enough incidents or disasters to populate every year!

The category should include Epidemics, Pandemics, Flu outbreaks, Faulty or contaminated equipment, food or medicines etc. Also animal outbreaks like swine fly, foot and mouth outbreaks and pet food contamination. Also perhaps incidents of toxic metal/chemical poisoning and radiation poisoning. Possibly the categories Category:2000s medical outbreaks and Category:2010s medical outbreaks could be renamed to Category:2000s health disasters etc to be a subcategory by decade? PS: I will put this on several Wikiproject pages, so could you add comments to my talk page please. Hugo999 (talk) 01:34, 25 September 2011 (UTC)

Multiple fission in animals

Unsourced stub by new editor, not my subject area (found while stub-sorting), sounds as if it should be a subject already covered in WP so perhaps needs to be a redirect - could an expert have a look, perhaps? Thanks. PamD 09:08, 1 October 2011 (UTC)

Ok I added descriptions of multiple fission in both Asexual reproduction and Fission (biology). I redirected the above article to the latter. However, I am not an expert. Please check if there have been any errors in my descriptions.-- Obsidi♠n Soul 10:04, 1 October 2011 (UTC)

Mispelling in the SVG file

http://en.wikipedia.org/wiki/File:Toxoplasmosis_life_cycle_en.svg The very far left says, "tachyzoites invide almost...", should be "invade". Also, many of the sentences start with a lower case letter instead of being captialized. Thanks, marasama.

You should be able to find what you need to be bold at Wikipedia:SVG image support, including people who know about editing SVGs if you need help. Kingdon (talk) 02:21, 24 November 2011 (UTC)