Talk:Pathogenic bacteria

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I support the proposed merge. --Arcadian (talk) 19:00, 21 July 2008 (UTC)

Possible image/ reference for this article[edit]

Phylogenetic distribution of zoonosis, genome size and secretome size for 191 pathogenic bacteria.jpg

This image from an open access journal might be of interest to editors of this article: it's a phylogenetic tree of 191 pathogenic bacteria, indicating which are zoonotic (transmissable between human and animal). From

  • McNally, Luke; Viana, Mafalda; Brown, Sam P. (5 August 2014). "Cooperative secretions facilitate host range expansion in bacteria". Nature Communications 5. doi:10.1038/ncomms5594. 

MartinPoulter (talk) 22:56, 14 November 2014 (UTC)

Copyright tags placed[edit]

The two extensive tables that appear in this Wikipedia article are not [a] compilations from multiple sources, [b] example illustrations from the single source relied (almost entirely) upon, or [c] representative selections from that comprehensive text source. Rather, the two tables appear as a typed-in or cut-and-paste cribbing of nearly the full content of the cited pages from that source, in essence reproducing that copyrighted material in full, here, as free content. Use of a single protected compendium source—reproducing its tables—has to violate fair use, and the sections and article are marked accordingly. Le Prof Leprof 7272 (talk) 14:34, 14 April 2015 (UTC)

It was not a copy-paste, since I only had the printed textbook. Would it be acceptable if another overview of pathogenic bacteria was found, and used to make the table a compilation of multiple sources? I don't see any other way of having an overview table of pathogenic bacteria. It would be unfortunate if Wikipedia can never ever have one by the reason that someone else has done it before in a textbook. Mikael Häggström (talk) 15:03, 14 April 2015 (UTC)
Leprof 7272 Mikael Häggström In my opinion, if any similar compendium were found in a another source, then that would be supporting evidence that this kind of presentation is not a creative presentation which can be copyrighted, but rather a standard sort of factual presentation which is common in the field. The potentially copyrightable part of this is the creative design to use the headings of the columns applied to the names of pathogenic bacteria in the rows. I have doubts that this is actually creative, though, and expect that anyone publishing on this topic would present this same factual information in almost this same way. This information is fundamental to the discussion of this topic and there might not be another way to present it except in a similar table.
If other sources are identified doing something similar were cited as Mikael suggested, then in my opinion that would be supporting evidence that this presentation is not eligible for copyright protection. Even if other sources are not identified then I have doubt that this can be copyrighted just because a struggle to see what here is not a straightforward presentation of facts which must be listed to discuss this topic. Blue Rasberry (talk) 18:40, 14 April 2015 (UTC)
Apologies, but I know in point of fact the Lippincott editors would disagree that whole tables from their medical textbook series can be reproduced, just because the table is "a straightforward presentation of facts which must be listed to discuss this topic." For goodness sake, the whole of the CRC Publishing company's history is producing compendia of tables, copyright protected for years; there are no exceptions of which I am aware, for tabular material. And each medical textbook author, editor, and publisher has to strive to make their material original within the textbook, so that they do not infringe on the content of other copyrighted textbooks. This is a simple legal matter, and not a matter for either of our opinions, Blue. Forward it on to WP legal folks. Our agreement or disagreement is immaterial to the clear claim that it is mass transfer of copyrighted material to WP. That matter is clearcut, the rest is for lawyers, and not us. Le Prof Leprof 7272 (talk) 21:12, 14 April 2015 (UTC)
TIme-limited this moment, Mikael, can only say this: If the content was drawn solely from that one source, whether by typing or cut and paste, the result is the same: We transferred a large body of copyrighted source material, en masse, to WP. Granted, every medical textbook on microbiology is going to have a similar table. But each is unique in its way, and each is copyrighted. If we create an a novel, amalgamated table, picking and choosing from (and citing each of) the sources, we are creating encyclopedic writing. If we choose one, and enter only its material, even if substantial amounts are shared in other sources, we are not creating novel encyclopedic content (and are plagiarising). Surely there are specialists here to rule on "close calls," but in my long work in academic writing, this does not seem close, and this [foregoing argument] is how I have been counseled about fair use and original contribution. Why not create a table mockup on paper, with 3-4 sources open before you, moving the present table columns around to a unique table form you decide, and so create a new original WP table, making your work truly unique and encyclopedic? Cheers, for now. Leprof 7272 (talk) 20:57, 14 April 2015 (UTC)
I found a similar table from Creighton University. I will use it, and hopefully additional fitting sources if any are found, to make this table a novel, amalgamated one. However, it may take a couple of weeks. Mikael Häggström (talk) 04:36, 15 April 2015 (UTC)
Bravo, @[[User:Mikael Häggström, but better, for both your training, and the readers here, if you go with a referred (appropriate non-web, secondary source)—another textbook or two. Your work here is admirable, and I will call attention to it as a positive example when completed. Cheers. Leprof 7272 (talk) 17:34, 18 April 2015 (UTC)
Leprof 7272, see Mdennis (WMF), the WMF person most known for making comments on copyright, and you could contact her if you like, but the usual first step is to post to a noticeboard and get other comments. Wikipedia:Copyright problems seems like a good choice, or Wikipedia:Close_paraphrasing#Addressing could be another.
I should not comment further because I have not seen the original source. When I first commented I was imagining the copying of data like in a chemistry infobox (like silicon), which happens often, and which I imagined to be analogous. It seems feasible to me that if someone rewrote this even from a single source then all the data could be presented on Wikipedia because there are limited ways to do this. In the source shared, there is a different presentation, but the first few column headings on the Wikipedia version (Genus, species, gram staining, Shape, Capsulation) match the order of the information presented in this other source. Without seeing the source I cannot make an opinion, but it is not unthinkable to me that many sources would be similar and there is already an example here. Blue Rasberry (talk) 21:52, 16 April 2015 (UTC)
I made an entry at Wikipedia:Copyright problems/2015 April 14, requesting further comments:
Pathogenic bacteria was tagged for possible copyright infringement (Talk:Pathogenic_bacteria#Copyright tags placed), because of the tables of basic laboratory and clinical characteristics of pathogenic bacteria. The source textbook presented similar short descriptions of each type of bacterial group, including gram staining, shape, capsulation etc, as well as for individual species by transmission, diseases, treatment etc. However, it didn't put all bacterial groups and species, respectively, in rows to make up as large and comprehensive tables as can be seen in the Wikipedia article. Individual box entries are expressed as to avoid close paraphrasing, but there really aren't many ways to express for example "Capsulation: Encapsulated", so a major question is whether the layout itself, with the given column titles, is copyrightable. Please provide additional input at Talk:Pathogenic_bacteria#Copyright tags placed. Mikael Häggström (talk) 11:56, 18 April 2015 (UTC)
Approving comment, @[[User:Mikael Häggström, placed at the entry. Cheers. Le Prof Leprof 7272 (talk) 17:34, 18 April 2015 (UTC)

Hi! I'm not Mdennis (WMF), nor anywhere remotely near in her class at this sort of thing; but I thought I'd take a look here to see if this can easily be resolved. It seems to me that both sides of the discussion have a case, and that each is partly right.

  • Unless this table is copied from a similar table in the source that I haven't seen (it's a large book), I can't see that taking various bits of data and compiling them into a presentation in a new form is an infringement; the information in the book is not copyrightable, the copyright covers the form of expression used to present that information; or that's my take. There can be copyright in lists, but the the criterion of "creative compilation" does not apply here.
  • There are copyright problems here: I looked, at random, at Treponema; our description of it reads "Long, slender, flexible, spiral- or corkscrew-shaped rods"; the description in the book reads "Long, slender, flexible, spiral- or corkscrew-shaped rods". That's a copyright infringement and needs to be rewritten in entirely new words (it isn't enough just to invert the order of a couple of words, for example).

May I make some suggestions?

  • All the descriptive entries need to be checked against the content of the source to ensure that they do not copy it, and rewritten as new text if they do
  • Instead of repeating a word such as "encapsulated" or "motile" ad infinitum, could the column not be headed, say, "Encapsulated?" or "Motile?", and the various entries be filled in with "yes", "no", "partly", "highly" etc? That would reduce the amount of overlap with the source, and improve the layout and readability of the table at the same time. (Could you use " + " and " − " instead of writing "Gram positive" again and again?)

Does that help? Justlettersandnumbers (talk) 22:28, 24 April 2015 (UTC)

Thanks Face-smile.svg With these comments in mind, I will now start to re-write the tables to avoid copyright infringement in individual boxes. Mikael Häggström (talk) 08:11, 2 May 2015 (UTC)

Before you get too far with altering the tables, I would like to add some more comments:

  • This article is about bacterial pathogens, but the information in the tables is strongly weighted towards identification of bacteria in a clinical microbiology laboratory rather than the actual pathogenic properties of the bacteria. Several of the columns could be combined or even removed entirely, and the two tables could be merged. In my opinion, the columns "bonding tendency," "oxygen requirement," "growth medium," "treatment," "prevention," and "laboratory diagnosis" can be removed since they provide little information about why the bacteria listed are pathogens. At least one column is needed to describe the bacteria's pathogenic properties (pathogenic mechanism, target organs, etc.). Some of these bacteria produce toxins critical to the disease process, yet toxins aren't mentioned in the tables.
  • It may be helpful to readers if the disease is listed in a column immediately after the genus/species. The first thing a reader would like to know is what disease a pathogen causes, but this important piece of information is missing in the first table. Again, combining the tables would help. If that's not possible, maybe the order of the tables can be flipped.
  • Why have separate columns for the genus and species? It's confusing trying to relate the bacteria to the diseases because some genera consist of species causing different diseases. The "genus" column could be removed without losing any information.
  • Be careful relying too heavily on Lippincott’s Illustrated Reviews Microbiology for the content in the table. If you look at my edits, you'll see that I corrected some mistakes and outdated information about Leptospira and Borrelia (I still need to add references). I didn't take a close look at the other bacteria, but I suspect that additional mistakes that were transferred over to the tables from the source material. CatPath (talk) 17:26, 2 May 2015 (UTC)
I think it's important to have the current columns in "basic laboratory characteristics" in order to display characteristics that are used to identify bacteria by microscopy. I changed the title to "List of genera of pathogenic bacteria and microscopy features" to emphasize this. I did, on the other hand, remove the "laboratory diagnosis" in the table on clinical characteristics, because the actual diagnosis of the bacterial infections are largely based on the symptoms of the disease as well. I'd prefer to simply have a "Diagnosis" column, but I will first focus on fixing more urgent issues in the tables. Mikael Häggström (talk) 07:37, 3 May 2015 (UTC)

Copyright issues on the Pathogenic bacteria article[edit]

Thank you to all the editors for the hard work that you have put into the Pathogenic bacteria article. Unfortunately, much of it is a copyright infringement because is directly quoted from a google book. Not to worry! In the whole idea of "being bold" and WP:JUSTDOIT, I am re-wording and re-formatting in my best attempts to resolve this and almost all the content you have worked so hard to put into the article will probably remain intact. I will only need to reword the content. I will certainly retain the references that you have added and I have added even more myself. I am not critical of anything that you have done with this article, I am only trying to get rid of the copyright problems. Feel free to go to the article after I am done with my heavy editing and reword things better to your liking. I only suggest that you not copy and past tables or contents from a book directly into an article to create the appearance of violating copyrights. Best Regards,

  Bfpage |leave a message  13:42, 7 June 2015 (UTC)
Another round of formatting to eliminate copyvio issues...
  Bfpage |leave a message  07:12, 13 June 2015 (UTC)
Great thanks! I see some experimenting with the layout of the table as well. However, I personally think the text size is to small at the beginning of the table of clinical characteristics. Also, having a separate column gives a fragmented and spacy look. Most included genera only have one species, and for those entries it is easy to mistake the characteristics for applying to the entire genus. We can link to bacterial nomenclature for those who are particularly interested in that subject. Mikael Häggström (talk) 04:46, 8 September 2015 (UTC)