Wikipedia talk:WikiProject Microbiology

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WikiProject Microbiology (Rated Project-class)
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Draft:Autodisplay[edit]

Dear microbiology experts: I found some references for this draft article, but I don't really understand the subject. Is this draft about a notable subject, and are the references appropriate?—Anne Delong (talk) 01:03, 13 February 2016 (UTC)

Took a look and left a note on the talk page! Ajpolino (talk) 04:52, 15 February 2016 (UTC)
With the improvements made by Ajpolino, I have accepted the draft. Thanks!—Anne Delong (talk) 23:08, 15 February 2016 (UTC)

Discussion about external links[edit]

See close below. Cunard (talk) 22:27, 3 July 2016 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

[1] pertaining to bacteria articles Doc James (talk · contribs · email) 06:08, 18 May 2016 (UTC)

Hi there, I am one of two editors inserting external links into bacterial species articles to the according type strain in the database http://bacdive.dsmz.de/. We are researchers, working for the german non-commercial research institute DSMZ. We started this as a project to provide additional information for bacterial type strains (which are ~10,000), since many of these strains are poorly described. We are not able to improve thousands of wikipages, also the data of our database are complex and diverse and can not be incorporated into wikipedia. Though our links provide useful scientific data regarding various aspects e.g. taxonomy, morphology, physiology, growth conditions, media recipes, isolation source, molecular biology and so on. Before starting this, we looked up the guidelines and found for Wikipedia:External links "Some acceptable links include those that contain further research that is accurate and on-topic, information that could not be added to the article for reasons such as copyright or amount of detail, or other meaningful, relevant content that is not suitable for inclusion in an article for reasons unrelated to its accuracy." So, our content is absolutely accurate and on-topic and the amount of detail is too high to incorporate. That's why we thought, this would be the right way to do it. By inserting those links we stumbled over a lot of links to other databases, (as for example to Encyclopedia of Life or to http://www.bacterio.net/) which also provide additional information as we do. So we felt confirmed in our doing. I really would appreciate if you rethink about the roll back, since we really offer high quality research data as additional information to the wikipedia users and we do not have any commercial interest or advantage. I am open for questions. L.C.Reimer (talk) 06:59, 18 May 2016 (UTC)
Here is a link to our most recent publication PMID 26424852 free fulltext--L.C.Reimer (talk) 07:13, 18 May 2016 (UTC)
This seems to me to be an appropriate link per our external link guideline. Plantdrew (talk) 17:09, 18 May 2016 (UTC)
Hm. The information in the database looks useful. In certain cases I think the links are appropriate. However, in cases like this at Salmonella enterica or here at Leuconostoc mesenteroides where you turn the external links section into a block of BacDive links, I don't think that is appropriate. The basic issue was raised on the WP:MED discussion that the database focuses on strains and we rarely have separate articles for strains. If you have a type strain which represents the species, that link is (in my opinion) fine. But I would be against adding a pile of links to every relevant strain in your database. Ajpolino (talk) 00:59, 19 May 2016 (UTC)
I admit that in some few cases, when there were only a handful of subspecies, we added several links to the respective subspecies type strains as these subspecies were also mentioned in the infobox. I thought this would be useful for the user, as long as this does not exceed 3-5 strains (there are a lot of cases, where we haven't linked the subspecies, since there are too many of them). But usually we only linked the according type strain. If there is a consensus, that we have to limit to one link per species page, we would be perfectly fine with it.--L.C.Reimer (talk) 05:15, 19 May 2016 (UTC)
IMO this is database information that belongs in Wikidata. Doc James (talk · contribs · email) 05:40, 19 May 2016 (UTC)
User:Doc James can you say more about how that would work? Two levels - the WikiData level the Wikipedia level. On the WikiData level, do you mean that fields would be set up in WIkiData to receive and store data directly mapped from the Bacdive database, or do you mean one field in WikiData would be set up to have a link to an entry in BacDive? Then on the article level, do you mean that fields would be set up in Template:Taxobox to be updated from the Bacdive-filled fields in WIkiData, or just a single new field in the Taxobox that would receive the link to BacDive from Wikidata? complicated... (to me at least) Jytdog (talk) 06:04, 19 May 2016 (UTC)
I would think the fields could be put in wikidata to accept. And then the discussion could occur regarding putting that data in the infobox on the associated infobox page. Doc James (talk · contribs · email) 06:06, 19 May 2016 (UTC)
What kind of data do you think to integrate into wikidata? Since we offer about 140 different data fields with different kind of data formats per strain, this seems to be not feasible. Also the data fields are not filled for all strains. Additionally we regularly update our database, which would mean the data in wikidata has also to be updated, which would be impossible.The only way we see that would work would be using our web services http://bacdive.dsmz.de/api/. So independent from that, we think the easiest way to provide the user with comprehensive, up-to-date information about type strain is the external link. AnnaVetci (talk) 07:02, 19 May 2016 (UTC) — Preceding unsigned comment added by AnnaVetci (talkcontribs) 06:59, 19 May 2016 (UTC)
The earlier discussion at WT:MED suggested a copyright issue, but I don't see why. The data is not a creative expression, just a structured list of facts, links, or identifiers. As such it should not be eligible for copyright in the first place. The only way there could be a concern is if there were embedded images or free text fields. If so, these should not be incorporated to WP without further consideration. LeadSongDog come howl! 21:52, 19 May 2016 (UTC)
So, how is this going to continue? Several voices confirmed that our links are guideline conform. Although we probably should have asked/discuss before. We see no straight forward way to integrate BacDive data into wikidata, but we are still open in this regard. In the meantime I want kindly ask to undo the deletion of our links. I see the links independant from wikidata as the best way for the user to get comprehensive, up-to-date information about the species associated type strain (for those who are not familiar with type strain, in bacteria this is the strain a species is defined on / first described.)I would be happy to get some response. --L.C.Reimer (talk) 06:20, 23 May 2016 (UTC)
Good question. I'd say there appeared to be consensus that adding BacDive links to bacteria articles is fine (and indeed beneficial!). As for undoing the mass rollback, that falls above my pay grade. Perhaps @Doc James: or @CatPath: would be able to help with that. The Wikidata bit is an interesting discussion, but it doesn't look like anyone is willing to take that on and I'm not sure there was any kind of consensus over whether that could be done.
As an added note (for which there was certainly no consensus, so we could talk more elsewhere or maybe someone else would like to comment) I would like to reiterate my concern about several links being added to a single article. I think it it atypical for articles to carry multiple external links to the same database. My general feeling is that if we have an article on a species (for example, Salmonella enterica) and your database only has information for the various subspecies, then perhaps you should just wait until the article for the subspecies is created (or better yet, if you feel the subspecies is well-described in the literature, create the article yourself or convince someone else to do it!!). Alternatively, if there is some "type subspecies" (e.g. maybe Salmonella enterica subspecies enterica?) then perhaps you could just link to that entry in BacDive as a representative of Salmonella enterica. I'd be interested to hear the thoughts of others on this. Thank you for your patience! Ajpolino (talk) 01:40, 24 May 2016 (UTC)

For consensus for adding a few thousand links we should have a RfC. Can put one together if people want. Doc James (talk · contribs · email) 01:56, 24 May 2016 (UTC)

That would be great! Thanks for taking the time! Ajpolino (talk) 01:57, 24 May 2016 (UTC)
With respect to adding these if consensus is for it. We could add the url to Wikidata by bot for each of the items that matches some identifier. Than as it would be a property within Wikidata it could be added to all infoboxes through one line in Template:Taxobox if people want. Doc James (talk · contribs · email) 08:54, 24 May 2016 (UTC)
Doc James, sounds like a good solution. As identifier only the species name is available, but this will work. If the other people agree, I would provide the according list.--L.C.Reimer (talk) 09:42, 24 May 2016 (UTC)
  • I started a property proposal here: d:Wikidata:Property_proposal/Natural_science#BacDive_ID. Mapping BacDive IDs to Wikidata is a good idea. Are there any ideas for any other data we should gather and source from BacDive. I have also written a mail to the database owners to make the licensing information more prominent. --Tobias1984 (talk) 19:40, 11 June 2016 (UTC)

RfC regarding EL[edit]

There is a clear consensus to include a few thousand of the external links to the website http://bacdive.dsmz.de/ to the corresponding articles. Cunard (talk) 22:27, 3 July 2016 (UTC)

The following discussion is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Should we add a few thousand of these external links to the corresponding articles? The link is to the website http://bacdive.dsmz.de/

And example of one of the links is here which was on the article Leptospira broomii. Doc James (talk · contribs · email) 08:03, 26 May 2016 (UTC)

Support[edit]

  • Support - Seems relevant and helpful. Sizeofint (talk) 21:31, 26 May 2016 (UTC)
  • Support - Short of a few thousand links per page, I can't see it causing any harm, especially with the links at the bottom of the page. Anyone reading those pages either will want the links or know enough to ignore them. If we have the tools or the contributors to manage them they could be a valuable service. JonRichfield (talk) 05:22, 29 May 2016 (UTC)
  • Support – I support linking to this resource, it appears useful and serious. One question though, could it be done via Wikidata? i.e. define a new Wikidata property pointing to the ID on this website, then use a template to pull that ID from Wikidata and form the URL based on that? I think that is a more elegant solution, even though it is more work to setup. If we had a specific infobox template for microbes (i.e. not just Taxobox) then the template could automatically do this without anything extra required on the pages using that infobox. SJK (talk) 10:34, 1 June 2016 (UTC)
Yes definitely possible through Wikidata. Doc James (talk · contribs · email) 06:40, 2 June 2016 (UTC)
  • Support. Particularly as Bacdive leads to further sources of relevant information. Maproom (talk) 07:02, 10 June 2016 (UTC)
  • Support. It looks like a useful tool. BlackcurrantTea (talk) 07:44, 18 June 2016 (UTC)
  • Support; suck links bring valuable information to the table. Best, FoCuS contribs; talk to me! 14:22, 18 June 2016 (UTC)
  • Strong Support; I edit a lot of bacteria articles and this would be an amazing resource. Also, I am all for changing the infobox for microbiology so that linking to this site is a bit easier. I like that better than making this site an external link. Great find Doc James! Best Regards,
  Bfpage |leave a message  17:29, 18 June 2016 (UTC)
I'm strongly opposed to placing a link in the infoboxes. This is a relatively new database. There are older databases that have the same information. We shouldn't be relying on a single source for taxonomic information. CatPath (talk) 18:24, 20 June 2016 (UTC)
We could make a box of external links and place it in that at the end of the article. I too am not a big fan of putting it in the lead. Doc James (talk · contribs · email) 06:19, 1 July 2016 (UTC)

Oppose[edit]

  • Oppose. I don't question that this would be a helpful resource for some readers, but why promote this database over other similar ones that are better established and kept up-to-date (at least with the bacteria I'm interested in)? I'm also wondering what happens if the web address changes or if the database loses funding and disappears? We'll be left with a lot of dead links to clean up. CatPath (talk) 18:05, 20 June 2016 (UTC)
CatPath I just gave some information about the background and the sustainability of BacDive below. I would be interested in what you meant by "other similar ones that are better established and kept up-to-date"? BacDive is a relatively new database (first published 2012) though to our knowledge, there is no comparable database at the moment. Please keep this discussion alive. L.C.Reimer (talk) 05:16, 30 June 2016 (UTC)
Two that have been around for a while are the LPSN (which you mention below) and the NCBI Taxonomy Browser. There's also the GCM [2]. CatPath (talk) 00:09, 1 July 2016 (UTC)
Doc James earlier provided an example of a link ([3]) that was added to the article Leptospira broomii. I noticed a few problems when I took a look at the Leptospira pages in the BacDive site. The site provides information on only 14 of the over 20 species of Leptospira. There are at least six species of Leptospira missing, including Leptospira biflexa, a prominent species (at least among those who study spirochetes) that has been known for decades. The LSPN and NCBI sites list the species that are missing from the BacDive site. I also noticed that the wrong minimum culture temperature is listed in all of the Leptospira pages. CatPath (talk) 00:40, 1 July 2016 (UTC)
CatPath, you are comparing apples to oranges. BacDive is not a taxonomy service, it is a database for metadata about bacteria and archaea. We offer a taxonomy service Prokaryotic Nomenclature Up-to-date separately, which provides monthly updated manually curated taxon data and where you will find Leptospira biflexa and the other missing species of Leptospira. In BacDive we have integrated the taxonomy from this service for our 53,978 strains. When it is all about taxonomy we should talk about PNU, not about BacDive. But the idea was to give users a link with additional scientific information about the species, represented by the type strain. The mentioned wrong minimum culture temperature is a nasty error that is known to us and that will be fixed with the next update end of august. L.C.Reimer (talk) 05:21, 1 July 2016 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Discuss[edit]

I little more info about who maintains and publishes this site would satisfy my curiosity. I don't see a home page. Here is how the reference is formatted by my Chrome browser and the Wikipedia ref generator:[1]

  Bfpage |leave a message  17:33, 18 June 2016 (UTC)

References

  • Here some short infos about the background of BacDive and it's long term sustainability: BacDive is hosted at the DSMZ which is the german culture collection for microorganisms and cell cultures. Data in BacDive originate from four main sources, that are internal descriptions of culture collections, expert compiled compendia, the taxon reference list “prokaryotic nomenclature up-to-date” (PNU) and primary scientific literature. By publishing data from internal culture collection descriptions and mobilizing data from expert compiled collections we make unique data collections public accessible. The PNU (also hosted at the DSMZ) provides monthly updated manually curated taxon data. To our knowledge BacDive is unique in terms of provided data and coverage of strains, though there is also LPSN which is restricted to taxonomy data. BacDive is updated at least once a year, though we work on a shorter update cycle. As one of the world’s major culture collections, the Leibniz-Institute DSMZ is an ideal host for BacDive. Due to its function as an infrastructure facility the sustainability and long-term maintenance of the database can be guaranteed. In consequence also our IDs are stable and will be long-term accessible. I hope that we can find a consensus about where BacDive data/link will be placed. L.C.Reimer (talk) 07:55, 27 June 2016 (UTC)

The discussion above is closed. Please do not modify it. Subsequent comments should be made on the appropriate discussion page. No further edits should be made to this discussion.

Auto-assessment of article classes[edit]

Following a recent discussion at WP:VPR, there is consensus for an opt-in bot task that automatically assesses the class of articles based on classes listed for other project templates on the same page. In other words, if WikiProject A has evaluated an article to be C-class and WikiProject B hasn't evaluated the article at all, such a bot task would automatically evaluate the article as C-class for WikiProject B.

If you think auto-assessment might benefit this project, consider discussing it with other members here. For more information or to request an auto-assessment run, please visit User:BU RoBOT/autoassess. This is a one-time message to alert projects with over 1,000 unassessed articles to this possibility. ~ RobTalk 01:16, 4 June 2016 (UTC)

Bacterial morphological plasticity[edit]

Bacterial morphological plasticity is a hefty referenced article that could use some expert attention to assess, edit, and deorphan it. Thanks, ~Hydronium~Hydroxide~(Talk)~ 10:44, 5 June 2016 (UTC)

Orphan no more.
  Bfpage |leave a message  17:36, 18 June 2016 (UTC)

Need another pair of eyes[edit]

Unfortunately, I make a lot of errors when I create microbiological articles and expand content in articles. I know some editors enjoy proofreading as one of their editing activities. First let me thank those who 'clean up' after me with my sloppy editing. I am requesting that an editor take a look at List of human flora, especially the content that I have recently added since I'm pretty sure that I may not have formatted everything correctly. Thank you so much. Best Regards,

Barbara (WVS) (talk) 11:32, 25 June 2016 (UTC)

Merge discussion[edit]

A merge discussion is taking place here to determine whether Gene and Genomic organization should be merged. Seems important. Best Regards,

Barbara (WVS) (talk) 10:58, 30 June 2016 (UTC)

Bacdive ID on Wikidata[edit]

Hi all! Bacdive ID is now a property on Wikidata: d:Property:P2946. I am currently adding 10k identifiers with a bot. Going slow, so I can check on the bot. It will probably be finished within a day. Here is a query of all the IDs currently on Wikidata: d:Property_talk:P2946#Query_of_all_the_IDs. --Tobias1984 (talk) 17:53, 6 July 2016 (UTC)

Well, if that's the case, rather than adding Bacdive as a stand alone external link as was discussed above, may I suggest including it through {{Taxonbar}}? Taxonbar links to external biodiversity databases that have identifiers in Wikidata. Support for Bacdive would need to be added to Taxonbar. Plantdrew (talk) 18:35, 6 July 2016 (UTC)
@Plantdrew, at the moment the idea is to place the BacDive links in a box of external links. Although it is a good idea to place a BacDive-ID/link in the Taxonbar, I suspect that the BacDive link is reduced to its taxonomy data, as the label says 'Taxon Identifiers'. So I would favor doing both, placing the BacDive ID within the Taxonbar and in an additional box for external links, which gives the opportunity to declare, what the user can find behind the link. L.C.Reimer (talk) 08:05, 29 July 2016 (UTC)

Bromocresol purple[edit]

I'd appreciate if someone could check (and improve on, if desired) my recent edit to Bromocresol purple. I created the article a decade ago, but I am neither a chemist nor a microbiologist so I'm not confident in how accurately I'm reading these journal articles. Thanks, Pi.1415926535 (talk) 20:39, 8 July 2016 (UTC)

Thanks for the message! I'm no chemist so I won't be able to do much for any chemistry-flavored parts, but I'll take a look at the uses section and the papers used there! Ajpolino (talk) 05:40, 9 July 2016 (UTC)
Thanks for your help! Pi.1415926535 (talk) 16:50, 9 July 2016 (UTC)

DYK[edit]

Congratulations to Project Microbiology! The article Uterine microbiome was featured as a DYK today! Barbara (WVS) (talk) 02:24, 9 July 2016 (UTC)

Unassessed articles < 100 words[edit]

I see that there are ~2000 unassessed articles in WP:MICRO. 929 of these have < 100 words, going by AWB's word count. I can mass-assign |class=Stub to these (or to some other numerical cutoff), if there's support from project members.   ~ Tom.Reding (talkdgaf)  04:13, 13 July 2016 (UTC)

  • Support - that'd be great! I assume everything with <100 words fits that bill. Thanks! Ajpolino (talk) 02:51, 6 September 2016 (UTC)

Place to integrate scientific database links in species articles of bacteria[edit]

After the discussion about external links and the according RFC found there is a consensus “to include few thousand of the external links to the website http://bacdive.dsmz.de/ to the corresponding articles” , we now have to discuss how and especially where those links should be integrated. Thanks to the great work of Tobias we have now have 9675 BacDive IDs on Wikidata: BacDive ID. At the moment 3065 of the entries are matching bacteria articles in the english wikipedia (you can check that here wikidata query). The discussion where to place these links started already within the previous discussion. The idea was to place it in infoboxes like in Taxobox. Though there were concerns to “promote this database over other similar ones”. In my opinion it makes sense to place links to scientific databases on a prominent place as the taxobox, as this is common for other infoboxes as well. For example for enzymes Infobox enzymes. Of course there is no reason to “promote” BacDive over other databases and the others should be integrated as well. However, I am not sure how to do this without a matching in wikidata. As we have this data for BacDive now, I suggest we can start with this database and the others will follow. I am hoping for a fruitful discussion. L.C.Reimer (talk) 06:05, 2 September 2016 (UTC)

@L.C.Reimer: I think that we are currently migrating away from Identifiers in Infoboxes. Identifiers are usually appreciated by experts in their respective fields, while the common reader wants a good summary of the subject. See for example how the disease infobox has transformed in the past years (d:Wikidata:Infobox_Tutorial#Best_practices). A much better place is shown in e.g. Steven Pinker. The authority control template is close to the bottom, where experts usually end up pretty quickly eager to find more information. I propose therefore to add the identifier to the taxon identifiers to {{Taxonbar}} --Tobias1984 (talk) 17:14, 2 September 2016 (UTC)
I agree that Taxonbar is a more appropriate place to include the BacDive ID than the Taxobox. Plantdrew (talk) 20:24, 2 September 2016 (UTC)
@L.C.Reimer: The now added the links, but there is some weird stuff happening in that Template code. Maybe it would be more foolproof to make a Lua module for the template. The template is also not used on all the pages about Bacteria, so we could add that using Pywikibot. But I would need to get approval form the en-wiki community first to add it to so many pages. --Tobias1984 (talk) 17:37, 4 September 2016 (UTC)
@L.C.Reimer: The now added the links, but there is some weird stuff happening in that Template code. Maybe it would be more foolproof to make a Lua module for the template. The template is also not used on all the pages about Bacteria, so we could add that using Pywikibot. But I would need to get approval form the en-wiki community first to add it to so many pages. --Tobias1984 (talk) 17:37, 4 September 2016 (UTC)
I appreciate the integration of the BacDive ID into the Taxonbar, though I am still irritated to find those important identifiers at the bottom of a page. I admit that I got used to find the most important data in the top right corner of wikipedia articles like chemicals or enzymes. Moreover I am concerned that BacDive is reduced to its taxonomy data, as the label says 'Taxon Identifiers'. As mentioned before I would like to have an additional link, which gives the opportunity to declare, what the user can find behind the link. This probably means to place it in the 'external links' section. Would it be possible to do this automatically? Anyway the Taxonbar is a good idea and it would be great if Tobias could place the Taxonbar automatically in the species articles of the bacteria.L.C.Reimer (talk) 07:57, 5 September 2016 (UTC)
@L.C.Reimer: Bacdive is already listed at Escherichia_coli#General_databases_with_E._coli-related_information and I think a better description would also help potential readers navigate to the page. - About the identifiers in the infobox: Wikipedia tries to compromise between a very diverse readership. As a rough guideline the first few paragraphs or mobile screen should be completely understandable and inviting to a person with a high school degree. I am not sure I remember correctly, but there might have been some data suggesting that actually almost nobody clicks on the identifiers (e.g. the ICD-9) codes in the infoboxes. Hopefully experts have already learned that they find very detailed information at the bottom of a page and it might be only a matter of time unitl chembox and infobox-enzyme switch to the bottom-template approach. - As a pragmatic note I would also like to say that it is much easier to get your information into Wikipedia by starting out at the bottom. When more people then get used to it and find it useful it might very well wander upwards slowly. - As for the smaller articles (e.g. Escherichia vulneris), there is actually a lot of room for your ideas. The article only has one bottom template and a specialised bacteria template could be proposed, if we have something to put into it. The infobox is also not overly wrong, and some kind of information (sourced to bacdive in this case) could be put there. For example the es:Erithacus rubecula has the conservation status sourced to IUCN. So a similar useful piece of information could also always be sourced to Bacdive. - But in the case of the infoboxes you should probably prepare yoruself for a lot of discussions. --Tobias1984 (talk) 17:47, 5 September 2016 (UTC)
As discussed earlier, the most of the data provided by BacDive are not suitable to be deposited in a small infobox. Anyway I would really like to follow that approach and see if there are data that can be provided in this way (e.g. culture collection numbers) and see if the community is interested in. Furthermore the Taxonbar is a useful tool and I support the approach to integrate this into the bacterial species articles, which will help the users to orientate themselves in the jungle of prokaryotic taxonomy (even though I have to adapt to looking at the bottom for this information). As only the External links section provides the opportunity to declare the content of a link to a scientific database, we will continue to integrate BacDive type strain links into bacterial species articles as it has been confirmed to be a useful tool and providing valuable data. I would like to kindly ask @CatPath: and @Doc James: to undo the mass rollback of the already integrated links, so that we can continue to work.L.C.Reimer (talk) 10:27, 6 September 2016 (UTC)
Links were removed one by one, not by mass rollback. The links are now in Wikidata. We know just need to get consensus on how the community wishes to add them to articles. Doc James (talk · contribs · email) 10:33, 6 September 2016 (UTC)
I stumbled over another infobox called TaxonIds. Compared to Taxonbar the TaxonIds-Infobox offers the advantage of a short description of the identifier. I hope we get some comments on this topic so that we can find out, what the community wants. Is it appropriate to do a RFC? L.C.Reimer (talk) 08:23, 9 September 2016 (UTC)
TaxonIds needs to have the identifiers added manually, and doesn't support as many databases as Taxonbar. It's been around quite a bit longer than Taxonbar, and is currently used on more pages, it's not really being actively added to pages. Taxonbar is being actively added and is likely to surpass TaxonIds in usage in a few months. Plantdrew (talk) 16:21, 9 September 2016 (UTC)
Ok, it seems as TaxonIds has several issues and therefore is not used anymore, as can be found on the talk page of TaxonIds. So Taxonbar is at the moment the favourite way to integrate Taxon IDs? Any comments? L.C.Reimer (talk) 04:53, 12 September 2016 (UTC)

BioRxiv support in citations[edit]

This project's feedback would be appreciated in this discussion, as this could greatly (and positively) affect biological citations! Headbomb {talk / contribs / physics / books} 21:54, 7 September 2016 (UTC)

About genome annotation[edit]

Hi! I prepared a table that includes an updated genome annotation of Brucella abortus. We intended to add this to a separated page in Wikipedia, however it seems to be very big and difficult to verify. A reviewer suggested me to ask about that here... We thought to add this information to Wikipedia because constantly "hypothetical o predicted proteins" functions are being descovered, so it is very difficult to keep an updated annotation if only one group can modify the page. I will highly appreciate any advice. Marsuareze (talk) 23:14, 12 September 2016 (UTC)

The inclusion of raw genome data is a problem, it falls foul of WP:INDISCRIMINATE and it also makes the article excessively long, far in excess of the ~100kB recommended maximum. An External link to the original publication(s) of the organism's genome may be useful instead. Roger (Dodger67) (talk) 17:40, 11 October 2016 (UTC)

Amoebozoan taxoboxes[edit]

Taxoboxes for amoebozoans and other microbial eukaryotes often contain inconsistent, outdated, or simply erroneous entries. To take a typical example, the box at Vexilliferidae ranks Amoebozoa as a kingdom, and Flabellinea as a phylum (in current classifications, the former is usually either a phylum or an unranked supergroup; the latter was erected as a class, and recently reduced to a subclass under Discosea). Readers who follow the links will find themselves at articles that present the hierarchy differently than the template at Vexilliferidae. At best, it's confusing.

These inconsistencies span dozens, if not hundreds, of articles, so harmonizing the entries manually is time-consuming. I have AWB privileges, and can use that tool to introduce a bit of nomenclatural consistency across these articles, but thought I should check here first, to make sure nobody objects.

I'd start by standardizing the rank of Amoebozoa itself. Like other supergroups (Stramenopiles, Archaeplastida, etc) it is sometimes described as a kingdom-level group, and occasionally appears in published sources as "kingdom Amoebozoa." However, these usages are generally casual and idiosyncratic, and whenever the group has been formally proposed as a taxon in a ranked classification scheme (as in Smirnov et al, 2011, and Cavalier-Smith, 2015) it appears as a phylum. In the very influential scheme of Adl et al, 2005 & 2012, it is unranked, like all their taxa. My preference would be to change occurrences of regnum = [[Amoebozoa]] to unranked_phylum = [[Amoebozoa]]. The group will simply appear as: (unranked): Amoebozoa.  Deuterostome  (Talk) 01:24, 27 October 2016 (UTC)

I'm all consistency and following recent classifications that have a general consensus. I'd say go for it, but with two considerations.
1 In the long run, I think it's probably better to go with {{Automatic taxobox}} than conventional taxoboxes. If there's any possibility of future upheaval in the classification scheme (or current lack of consensus), it's much easier to adjust a single template than making changes in hundreds or thousands of articles. But switching from conventional to automatic taxoboxes is probably getting out of the kind of edits AWB is useful for.
2 I'm not quite sure how {{Taxobox colour}} functions, but it automatically provides a color for Amoebozoa at certain ranks. Color seems to be functional for Amoebozoa at regnum or unranked_phylum. Make sure your edits don't break automatically provided colors and consider using AWB to remove any colors that are hard coded through the taxobox template. Plantdrew (talk) 03:43, 27 October 2016 (UTC)
I agree, it would be easier if all of the taxoboxes were automatic, but converting all those pages would be a mighty task, and probably hard to automate (I did some test edits, and was not encouraged :D ). I did adjust the Amoebozoa taxonomy template, but that doesn't affect many articles.
Good point about colors. After the kingdom --> unranked_phylum conversion, I'll see if all the non-standard hard-coded colors in articles like Amoeba (genus) can be extracted without disruption.  Deuterostome  (Talk) 13:09, 27 October 2016 (UTC)
No major mishaps in the Amoebozoa edits, so I shifted attention to "Kingdom Excavata." Most of these had been cleaned up, already, and there were only a few dozen pages to fix. I had to add some hard-coded taxobox colors, unfortunately, but at least they're now fairly consistent across the excavate articles. A large number of excavate taxoboxes had non-standard colors (mostly color = khaki), and I've switched those to rgb(250,250,100), per Template:Taxobox color.
The next problem is "Kingdom Chromalveolata", which still haunts hundreds of articles. I'll raise that on Wikipedia talk:WikiProject Algae before starting on it.  Deuterostome  (Talk) 18:06, 28 October 2016 (UTC)

Taxobox colour for Bacteria[edit]

The template at Template:Taxobox colour scheme claims that a slightly bluish-grey colour – rgb(220,235,245) – is used for taxoboxes involving bacteria. However, since Bacteria is a domain, and the taxobox code doesn't at present allow domains to determine the colour of a taxobox, {{Taxobox colour}} doesn't work automatically. You have to put color = {{Taxobox colour|Bacteria}} in the taxobox if you want the colour to be supplied by {{Taxobox colour}}.

In practice, many Bacteria taxoboxes seem to have |color=lightgrey set.

So my question is: what colour should Bacteria taxoboxes be? Lightgrey, as seems to be a regular practice, including the FA Bacteria, or the supposedly agreed rgb(220,235,245)?

A separate issue is whether it's possible to get the domain to set the taxobox colour automatically for Bacteria and Archaea; technically this poses some problems but may be doable.

Peter coxhead (talk) 10:57, 31 October 2016 (UTC)

As far as I've seen, setting |domain=bacteria in a taxobox does in fact provide a bluish color; see E. coli for example. I don't see how that is happening in the code for Taxobox colour, but presumably there's a subsidiary template out there that treats domain as equivalent to regnum. Plantdrew (talk) 16:18, 31 October 2016 (UTC)
@Plantdrew: yes, you're right. I was partly misled by Bacteria: when I removed |color=lightgrey, the error colour appeared. But this is because it had |domain='''Bacteria''', when it should have had |domain=[[Bacteria]], relying on the Wikimedia software to bold self-links. Now I've fixed that, removing |color=lightgrey produces the 'correct' colour. But since this article is an FA, and there are quite a few other bacteria articles with the colour set to light grey, I don't want to change to the 'correct' colour without some input from other editors.
I've now realized that if you look at the top of Template:Taxobox, |domain=Bacteria is treated as a special case, which is why it works. I'll do the same for Archaea, then it will work too. However, note that this means the colour is set top down if a lower taxon would have produced a different colour. I've revised my earlier posts. Thanks!! Peter coxhead (talk) 17:37, 31 October 2016 (UTC)
And now Archaea works properly, with no need to set the taxobox colour. We're getting there, slowly! But my question remains: what colour should bacterial taxoboxes be? Peter coxhead (talk) 17:59, 31 October 2016 (UTC)
I would think any colour will do as long as it's consistent? I can't imagine there being a practical advantage to turning them all light grey over light blue. Does anyone know if there's some reason some taxoboxes started getting manually flipped to lightgrey? Ajpolino (talk) 03:16, 1 November 2016 (UTC)

Go with rgb(220,235,245). Lightgrey was chosen (or at least reaffirmed) in a 2007 discussion. rgb(220,235,245) was selected in a 2015 discussion, and while I don't quite understand the accessibility issues driving that discussion, it seems that a great deal of thought was put into the color choices at that time. The 2007 colors seem to be chosen pretty arbitrarily. I think the reason lightgrey is so prevalent is two-fold. 1) Bacteria don't get edited very much, so hard-coded colors from the early days of Wikipedia were never stripped out. 2) A very large number of bacteria articles are the work of one editor, who consistently hard codes lightgrey (probably following the example of existing articles at the time he started editing). I'd ping him, but he never participates in talk page discussions. He's created more than 1500 articles in the last year alone (out of 7671 with the microbiology project banner) and is responsible for at least 95% of new articles on bacteria in the 2-3 years I've been paying attention to newly created articles. Plantdrew (talk) 18:04, 1 November 2016 (UTC)

Ok, well no-one seems to be objecting to these being restored/changed to the colour in {{Taxobox colour}}, but there are a lot of them at lightgrey, so ideally it needs a bot to fix them. Peter coxhead (talk) 10:10, 3 November 2016 (UTC)

Taxobox incertae sedis colour[edit]

Short history

When the taxobox system was set up, the idea was that the colour of the taxobox would be determined by the kingdom/regnum to which the taxon belonged. It was assumed that organisms would belong to one kingdom/regnum, which would determine the colour of the taxobox (there are comments in the template code explicitly saying this); then any organisms with no clear kingdom/regnum were treated as incertae sedis.

This came not to work as cladistic approaches got going on the higher levels of classification, for two reasons. First, any taxa, like domain, above the rank of kingdom/regnum had no taxobox colour assigned. Second, researchers simply didn't assign traditional ranks, like kingdom, to their clades, and large groups, particularly of former "protists", ended up without a kingdom.

So various fixes and kludges were added step by step to the taxobox colour determining system, so that most taxa got a colour. However, it did leave a significant group out: known eukaryotes not falling into one of the groups with a colour. Haptophytes and cryptophytes are a couple of examples, based on their latest classifications.

We can't keep adding colours for all the eukaryote groups currently without a taxobox colour, because we are running out of suitable distinctive colours.

My actions

It seems to me that the taxobox colour for incertae sedis should only be used for organisms like Charnia or trace fossils, where it really is unclear what they are. Eukaryotes that don't fall into one of the major groups for which we have a colour should be treated belonging to Eukaryota (we have colours for the other domains).

So I've created a colour for Eukaryota (see {{Taxobox colour scheme}}). At present it's not assigned automatically, but can be set manually by |color={{Taxobox colour|Eukaryota}} or, better, |color_as=Eukaryota.

I'm using this colour for all entries in Category:Taxoboxes with the incertae sedis color that are actually eukaryotes. Later I want this colour to be set automatically, but the code to do it isn't fully ready yet. Peter coxhead (talk) 10:31, 3 November 2016 (UTC)

Thanks for doing all that work, Peter. I'll revisit the taxoboxes on which I've used the incertae sedis colour (haptophytes and cryptophytes, mostly) and replace with the new Eukaryota colour.  Deuterostome  (Talk) 11:36, 3 November 2016 (UTC)

Taxonbar[edit]

There is a discussion about the usage of {{taxonbar}}, here: Template talk:Taxonbar#Linking to cross project wikiproject --Tobias1984 (talk) 21:15, 17 November 2016 (UTC)

2016 Community Wishlist Survey Proposal to Revive Popular Pages[edit]

Magic Wand Icon 229981 Color Flipped.svg

Greetings WikiProject Microbiology Members!

This is a one-time-only message to inform you about a technical proposal to revive your Popular Pages list in the 2016 Community Wishlist Survey that I think you may be interested in reviewing and perhaps even voting for:

If the above proposal gets in the Top 10 based on the votes, there is a high likelihood of this bot being restored so your project will again see monthly updates of popular pages.

Further, there are over 260 proposals in all to review and vote for, across many aspects of wikis.

Thank you for your consideration. Please note that voting for proposals continues through December 12, 2016.

Best regards, SteviethemanDelivered: 18:04, 7 December 2016 (UTC)

Thanks for putting that out here! Hard to know which proposals to vote for. Icebob99 (talk) 18:17, 7 December 2016 (UTC)

Viewing the source of the project page[edit]

Hi, I can make neither heads nor tails of the templates that form the project page for this WikiProject. Can someone decipher for me how the page loads all its content when it doesn't seem to have any templates that do so? Thanks, Icebob99 (talk) 00:55, 18 December 2016 (UTC)

I'm not entirely sure how it all works or why it was set up this way (perhaps someone more knowledgeable could chime in), but if you'd like to edit a panel, just scroll to the bottom of it and click "edit this panel" in the bottom-right. It's not very intuitive, but hopefully that helps. Ajpolino (talk) 01:48, 18 December 2016 (UTC)

Active members[edit]

Hi, anyone opposed to me going to Wikipedia:WikiProject Microbiology/Participants and adding a column saying whether a user has edited a page in the project in the last two weeks? Maybe a bot can do this for us; I think I've seen WikiProject member lists which bots update. Icebob99 (talk) 01:32, 18 December 2016 (UTC)

You may be interested in this page which is updated by User:Reports bot. It shows all users (and IPs) who have made more than 5 edits to WP Micro-tagged pages in the last 30 days. I'm not sure how adding a column to the participants page would add extra value beyond this, and may be challenging to maintain (not sure how we would request a bot do this), so hopefully you find the page linked above sufficiently helpful! Ajpolino (talk) 01:56, 18 December 2016 (UTC)
Thanks! Just when I had made an updated list in my sandbox-- oh well! Icebob99 (talk) 03:11, 18 December 2016 (UTC)
How about that list replaces the existing member list? Seems more logical. Icebob99 (talk) 03:13, 18 December 2016 (UTC)
@Harej: is responsible for that report and is involved in improving WikiProjects on a meta-level. He probably knows how to best incorporate the report results as a member list for the project page (where, per the thread above, it is not very obvious how the content is generated). Plantdrew (talk) 03:50, 18 December 2016 (UTC)

Articles with milestones[edit]

How about we make something like Wikipedia:WikiProject Energy/Recognized content and put it on the project page? Good articles and featured article counts are low enough that we can do it manually, and we can find the DYK articles through this search. I can do it myself if everyone is in agreement. Icebob99 (talk) 02:19, 21 December 2016 (UTC)

All articles assessed![edit]

Hi all, I assessed all the remaining articles unassessed for quality and importance! I'm removing it from the "things to do" list. Icebob99 (talk) 20:34, 21 December 2016 (UTC)

New article[edit]

Hi all, I'm not a member of this WikiProject but I wanted to make you aware that I've started a new article on Legionella clemsonensis. Please feel free to contribute to it as you desire. I've already categorized it under this WikiProject. This bacterium was newly named this year. N. Jain talk to me 14:29, 1 January 2017 (UTC)

Any responses to me should be addressed at my talk page. N. Jain talk to me 14:29, 1 January 2017 (UTC)

WikiJournal of Medicine promotion[edit]

WJM Poster (hyperlinked).pdf
WikiJournal of Medicine logo.svg

The WikiJournal of Medicine is a free, peer reviewed academic journal which aims to provide a new mechanism for ensuring the accuracy of Wikipedia's biomedical content. We started it as a way of bridging the Wikipedia-academic gap.[1] It is also part of a WikiJournal User Group with other WikiJournals under development.[2] The journal is still starting out and not yet well known, so we are advertising ourselves to WikiProjects that might be interested.

Engaging Wikipedians

  • Original articles on topics that don't yet have a Wikipedia page, or only a stub/start
  • Wikipedia articles that you are willing to see through external peer review (either solo or as in a group, process analagous to GA / FA review)
  • Image articles, based around an important medical image or summary diagram

Engaging non-Wikipedians

We hope that an academic journal format may also encourage non-Wikipedians to contribute who would otherwise not. Therefore, please consider:

  • Printing off the advertisement poster an distribute in tearooms & noticeboards at your place of work
  • Emailing around the pdf through contact networks or mailing lists (suggested wording)

If you want to know more, we recently published an editorial describing how the journal developed.[3] Alternatively, check out the journal's About or Discussion pages.

  1. ^ Masukume, G; Kipersztok, L; Das, D; Shafee, T; Laurent, M; Heilman, J (November 2016). "Medical journals and Wikipedia: a global health matter". The Lancet Global Health. 4 (11): e791. doi:10.1016/S2214-109X(16)30254-6. 
  2. ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15. 
  3. ^ Shafee, T; Das, D; Masukume, G; Häggström, M. "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine. 4. doi:10.15347/wjm/2017.001. 
WikiJournal of Science logo.svg

Additionally, the WikiJournal of Science is just starting up under a similar model and looking for contributors. Firstly it is seeking editors to guide submissions through external academic peer review and format accepted articles. It is also encouraging submission of articles in the same format as Wiki.J.Med. If you're interested, please come and discuss the project on the journal's talk page, or the general discussion page for the WikiJournal User group.
T.Shafee(Evo&Evo)talk 10:33, 19 January 2017 (UTC)

www.bacterio.net and www.straininfo.net[edit]

These are two very highly cited websites on Wikipedia according to WP:JCW, but they have no corresponding articles. I'm not saying they are necessarily notable, but some information should be available about this sources, like we have for www.uniprot.org or www.dsmz.de. Headbomb {talk / contribs / physics / books} 00:45, 21 January 2017 (UTC)

Turns out List of Prokaryotic names with Standing in Nomenclature (which is what is hosted at bacterio.net) already has a page. I had never noticed it before. Set up the web address as a redirect and will try to clean up that page. Ajpolino (talk) 23:07, 21 January 2017 (UTC)

WikiJournal of Science promotion[edit]

WikiJournal of Science logo.svg

The WikiJournal of Science is a start-up academic journal which aims to provide a new mechanism for ensuring the accuracy of Wikipedia's scientific content. It is part of a WikiJournal User Group that includes the flagship WikiJournal of Medicine.[1][2]. Like Wiki.J.Med, it intends to bridge the academia-Wikipedia gap by encouraging contributions by non-Wikipedians, and by putting content through peer review before integrating it into Wikipedia.

Since it is just starting out, it is looking for contributors in two main areas:

Editors

  • See submissions through external academic peer review
  • Format accepted articles
  • Promote the journal

Authors

  • Original articles on topics that don't yet have a Wikipedia page, or only a stub/start
  • Wikipedia articles that you are willing to see through external peer review (either solo or as in a group, process analagous to GA / FA review)
  • Image articles, based around an important medical image or summary diagram

If you're interested, please come and discuss the project on the journal's talk page, or the general discussion page for the WikiJournal User group.

  1. ^ Shafee, T; Das, D; Masukume, G; Häggström, M. "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine. 4. doi:10.15347/wjm/2017.001. 
  2. ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15. 

T.Shafee(Evo&Evo)talk 10:39, 24 January 2017 (UTC)

Contributing to the Streptococcus pneumoniae page[edit]

I've got to edit an article about a specific bacteria, in my case S. pneumoniae for my Bio 495 class. Some ideas I have for contributing to the S. pneumoniae wikipedia page are adding some information about the history of S. pneumoniae from a reputable source, as well as information discovered by the researchers in a primary literature article (scholarly article/scientific study peer reviewed and accepted into a scientific journal) I summarized, primarily about the researchers findings on two new transcription factors that cause upregulation and downregulation in four genes that potentially cause the virulent pathogenesis of S. pneumoniae

Sources:

Mahdi L.K., Ebrahimie E., Adelson D.L., Paton J.C., Ogunniyi A.D. (2013) A Transcription Factor Contributes to Pathogenesis and Virulence in Streptococcus pneumoniae. PLoS ONE 8(8): e70862. doi:10.1371/journal.pone.0070862 Review article citation

Watson D.A., Musher D.M., Jacobson J.W, Verhoef J. (1993) A Brief History of the Pneumococcus in Biomedical Research: A Panoply of Scientific Discovery. Clinical Infectious Diseases 17:913-924


When was penicillin first used to combat virulent strains of Streptococcus pneumoniae and by whom? John JohnCCWilliams (talk) 12:11, 31 January 2017 (UTC)

Answer: I found out that in the mid 1940's, Dr. Chester Keefer first tried treating patients with penicillin and achieved remarkable results, it was also the first treatment of a virulent bacteria in the United States via penicillin.

Thanks for your time

JohnJohnCCWilliams (talk) 12:24, 31 January 2017 (UTC)