Wikipedia talk:Education program archive/University of Toronto/HMB436H Medical and Veterinary Mycology (2014 Fall)/Timeline

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Timeline[edit]

I will reserve a portion of the first few lectures to prepare you for your assignment based on the following schedule.

Week 1: Wikipedia essentials[edit]

In class
  • Overview of the course
  • How will Wikipedia be used in the course?
Homework (please complete this by Friday September 19, 2014)
  • Start the online student orientation. During this training, you will create an account (if you do not already have one), make edits in a sandbox, and learn the basic rules of Wikipedia.
  • Once you have a Wikipedia user account, please email me your user name ([email protected]) - I need to know this in order to mark your assignments.

Week 2: Editing basics[edit]

In class
  • Basics of editing
  • Anatomy of Wikipedia articles, what makes a good article, how to distinguish between good and bad articles
  • Tips on finding the best articles to work on your assignments and to contribute to your classmates' assignments.
  • I will provide you with the enrollment token you will need to register for the course by clicking on the Enroll button at the top of this page.
  • Handouts: Using talk pages, Evaluating Wikipedia article quality, Wikimarkup cheatsheet
Assignment (due Friday September 26, 2013) (worth 5% of your grade)
Milestone
  • All students have Wikipedia user accounts and will be assigned a topic on the course page. All students will also have competed the online training for students (and I will check that you have done it).

Week 3: Citing sources and obeying copyright[edit]

In class
  • We will briefly discuss referencing on Wikipedia and Wikipedia’s copyright policy.
  • I will hand out a topic to each of you that will be the subject of your assignment.
  • Handouts: How to get help
Provisional list of topics (I will assign each student with a topic - you don't get to chose)
Resources

There are a number of excellent online mycology resources you can access to help you with your project. Here are a few:

  • MycoBank - this is an online database that connects you with the most current names of fungi and it provides extensive additional references for many in addition to photographs (so you know what they look like - but remember, you cannot use these photographs in your assignment).
  • University of Alberta Microfungus Collection and Herbarium - This is the world's largest culture collection of biomedically important fungi, and it is located in Canada. The online database contains very detailed records of isolations of fungi from humans and animals, and provides links to the papers where they are documented.
  • Centraalbureau voor Schimmelcultures - this is a very large culture collection of fungi located in The Netherlands. Their website contains a number of searchable databases that provide information on strains of many different species contained in their collection. Lots of these are medically important. The records also provide links to papers where many different aspects of the particular species are described. There are also links to a large number of peer-reviewed publications in the journal Studies in Mycology.
  • Web of Science - This database will help you to locate peer-reviewed papers, including review articles, where you can learn about your fungus. You can access it through the University of Toronto domain through this link, or you can log on through the University of Toronto Library Portal for access. You can search your fungus using its current (and former!) species names in the Topic field. This search will return large numbers of papers (hopefully) which you will need to sort through to find the important ones. Clicking on a paper hyperlink will let you read the abstract, and in many cases, it should provide you a direct link to the full-text paper (again as long as you are logged on through through the university's domain or through the library portal).
  • PubMed is another article search engine which is very useful in searching the biomedical literature. you can access it by following this link. It is not as comprehensive as Web of Knowledge because it is focused mainly on biomedically important topics. But a number of articles can be accessed through PubMed which are absent (or at least hard to find) on Web of Knowledge. PubMed will only provide you links to the full-text of papers that are Open Access.
  • Index Fungorum - This is a search engine similar to MycoBank. Although it is not as comprehensive in some areas, Index Fungorum is still very useful to help you figure out what names your fungus might have had in the past.
  • CMI Descriptions of Pathogenic Fungi and Bacteria – Although many of these profiles are dated (and the names are old), there is still a great deal of useful information in this growing archive. I encourage you to search your fungus (and all of its various historical names) here to see if you find anything worthwhile. Browsing several of these profiles will also give you a clearer idea of how you should approach the writing tone of your article. As long as you are attached to the internet through the University of Toronto backbone, you can follow this link to the CABI portal - Descriptions of Pathogenic Fungi and Bacteria.
  • Doctor Fungus - This is a very helpful website all about medical mycology. Many of the Wikipedia articles that deal with medical fungi cite it, and you will find a great deal of helpful information here. I caution you that the names used on this website may be old or defunct, and so you will always need to check against registries such as MycoBank and Index Fungorum to figure out what things should be called, and also where they belong in the fungal hierarchy.

There are a number of great books on medical mycology in the Gerstein Library in the stacks under the call number range in RC117. Also, you may find some worthwhile reference books in the general mycology section at QK603. Besides Gerstein, the Noranda Library at the Earth Sciences Centre has lots of mycology books too. A few that I think are particularly good include:

  • Barron G.L. 1968. The genera of Hyphomycetes from soil. Baltimore, MD: Williams and Wilkins. 364 pp. Embed this reference: <ref name=barron1968>{{cite book|last1=Barron|first1=G.L.|title=The genera of Hyphomycetes from soil|date=1968|publisher=Williams & Wilkins|location=Baltimore, MD|isbn=9780882750040}}</ref>
  • Domsch K.H., Gams W., Anderson T.H. 1980. Compendium of soil fungi. Vol. 1. London, UK: Academic Press. 859 pp. Embed this reference: <ref name="domsch1980">{{cite book|last=Domsch|first=K.H.; W. Gams, W.; Andersen, T.-H.|title=Compendium of soil fungi|year=1980|publisher=Academic Press|location=London, UK|isbn=9780122204029|edition=2nd}}</ref>
  • Howard D.H. 2002. Pathogenic fungi in humans and animals, 2nd ed. New York, NY: Marcel Dekker. 800 pp. Embed this reference: <ref name=howard2003>{{cite book|last1=Howard|first1=ed. by Dexter H.|title=Pathogenic fungi in humans and animals|date=2003|publisher=Dekker|location=New York, NY|isbn=0824706838|edition=2nd}}</ref>
  • Kane J., Summerbell R.C., Sigler J., Krajden S, Land G. 1997. Laboratory handbook of dermatophytes: a clinical guide and laboratory handbook of dermatophytes and other filamentous fungi from skin, hair, and nails. Belmont, CA: Star Pub. Embed this reference: <ref name=kane1997>{{cite book|last=Kane|first=Julius; Summerbell, Richard; Sigler, Lynne; Krajden, Sigmund.; Land, Geoffrey|title=Laboratory handbook of dermatophytes: a clinical guide and laboratory handbook of dermatophytes and other filamentous fungi from skin, hair, and nails|year=1997|publisher=Star Pub.|location=Belmont, CA|isbn=978-0898631579}}</ref>
  • Kirk P.M. et al. (eds) 2008. Ainsworth & Bisby's Dictionary of the Fungi, 10th ed. Wallingford, UK: CABI International. (This is a fungal "encyclopedia" that defines terms & concepts, provides overviews of different taxa and lists important references.)
  • Kwon-Chung K.J., Bennett J.E. 1992. Medical mycology. Philadelphia, PA: Lea & Febinger. Embed this reference: <ref name=kwon-chung1992>{{cite book|last=Kwon-Chung|first=K.J.; Bennett, J.E.|title=Medical mycology|year=1992|publisher=Lea & Febiger|location=Philadelphia|isbn=0812114639|author2=Bennett, John E.}}</ref>
  • Onions, A.H.S.; Allsopp, D.; Eggins, H.O.W. (1981). Smith's introduction to industrial mycology (7th ed.). London, UK: Arnold. ISBN 0-7131-2811-9. Embed this reference: <ref name=onions1981>{{cite book|last1=Onions|first1=A.H.S.|last2=Allsopp|first2=D.|last3=Eggins|first3=H.O.W.|title=Smith's introduction to industrial mycology|date=1981|publisher=Arnold|location=London, UK|isbn=0-7131-2811-9|edition=7th}}</ref>
  • Rippon J.W. 1988. Medical mycology, 3rd ed. Philadelphia: WB Saunders. 797 pp. Embed this reference: <ref name=rippon1988>{{cite book|last=Rippon|first=John Willard|title=Medical mycology : the pathogenic fungi and the pathogenic actinomycetes|year=1988|publisher=Saunders|location=Philadelphia, PA|isbn=0721624448|edition=3rd}}</ref>
  • Samson R.A., Hoekstra E.S., Oorschot C.A.N v. 1984. Introduction to food-borne fungi, 2nd ed. Baarn, The Netherlands: Centraalbureau voor Schimmelcultures, Institute of the Royal Netherlands Academy of Arts and Sciences.
  • Watanabe T. 2011. Pictorial atlas of soil and seed fungi, 3rd ed. Boca Raton, FL: CRC Press. (The second edition will work if that's all we have.)

Week 4: Develop a bibliography[edit]

Assignment (due Friday October 17, 2014) (worth 5% of your grade)
  • If an article on your fungus already exists, copy its source code and paste it into your sandbox page below the sandbox template at the top {{User sandbox|YourName}} ← Do not delete this from the top of your sandbox page
  • Compile a bibliography of relevant references in your sandbox, linking each reference to the point-formed facts you plan to use that reference to support. I expect at least 20-30 "facts" (hopefully more) supported by at least 10 references. You're annotated bibliography might look something like this:
Markup Renders as 
==''Fungus name''==
*fast-growing,<ref name=barron1968 /> yellow colonies<ref name=onions1981 />
*[[conidium|conidia]] 1-celled,<ref name=howard2003 /> rough-walled<ref name=barron1968 />
*nutrition, uses [[fructose]],<ref name=domsch1980 /> [[sorbitol]]<ref name=barron1968 /> and [[sucrose]]<ref name=domsch1980 />
*reported from dermatophytosis-like infection,<ref name=rippon1988 /> heart valve infection<ref name=kwon-chung1992 />
*resistant to [[amphotericin B]]<ref name=kane1997 />
*etc, etc.
==References==
{{Reflist|30em|refs=
<ref name=barron1968>{{cite book|last1=Barron|first1=G.L.|title=The genera of Hyphomycetes from soil|date=1968|publisher=Williams & Wilkins|location=Baltimore, MD|isbn=9780882750040}}</ref>

<ref name="domsch1980">{{cite book|last1=Domsch|first1=K.H.|last2=Gams|first2=Walter|last3=Andersen|first3=Traute-Heidi|title=Compendium of soil fungi|year=1980|publisher=Academic Press|location=London, UK|isbn=9780122204029|edition=2nd}}</ref>

<ref name=howard2003>{{cite book|last1=Howard|first1=ed. by Dexter H.|title=Pathogenic fungi in humans and animals|date=2003|publisher=Dekker|location=New York, NY|isbn=0824706838|edition=2nd}}</ref>

<ref name=kane1997>{{cite book|last1=Kane|first1=Julius|last2=Summerbell|first2=Richard|last3=Sigler|first3=Lynne|last4=Krajden|first4=Sigmund|last5=Land|first5=Geoffrey|title=Laboratory handbook of dermatophytes: a clinical guide and laboratory handbook of dermatophytes and other filamentous fungi from skin, hair, and nails|year=1997|publisher=Star Pub.|location=Belmont, CA|isbn=978-0898631579}}</ref>

<ref name=kwon-chung1992>{{cite book|last1=Kwon-Chung|first1=K.J.|last2=Bennett|first2=J.E.|title=Medical mycology|year=1992|publisher=Lea & Febiger|location=Philadelphia|isbn=0812114639}}</ref>

<ref name=onions1981>{{cite book|last1=Onions|first1=A.H.S.|last2=Allsopp|first2=D.|last3=Eggins|first3=H.O.W.|title=Smith's introduction to industrial mycology|date=1981|publisher=Arnold|location=London, UK|isbn=0-7131-2811-9|edition=7th}}</ref>

<ref name=rippon1988>{{cite book|last=Rippon|first=John Willard|title=Medical mycology: the pathogenic fungi and the pathogenic actinomycetes|year=1988|publisher=Saunders|location=Philadelphia, PA|isbn=0721624448|edition=3rd}}</ref>
}}
Fungus name
References
  1. ^ a b c Barron, G.L. (1968). The genera of Hyphomycetes from soil. Baltimore, MD: Williams & Wilkins. ISBN 9780882750040.
  2. ^ Onions, A.H.S.; Allsopp, D.; Eggins, H.O.W. (1981). Smith's introduction to industrial mycology (7th ed.). London, UK: Arnold. ISBN 0-7131-2811-9.
  3. ^ Howard, ed. by Dexter H. (2003). Pathogenic fungi in humans and animals (2nd ed.). New York, NY: Dekker. ISBN 0824706838. {{cite book}}: |first1= has generic name (help)
  4. ^ a b Domsch, K.H.; Gams, Walter; Andersen, Traute-Heidi (1980). Compendium of soil fungi (2nd ed.). London, UK: Academic Press. ISBN 9780122204029.
  5. ^ Rippon, John Willard (1988). Medical mycology: the pathogenic fungi and the pathogenic actinomycetes (3rd ed.). Philadelphia, PA: Saunders. ISBN 0721624448.
  6. ^ Kwon-Chung, K.J.; Bennett, J.E. (1992). Medical mycology. Philadelphia: Lea & Febiger. ISBN 0812114639.
  7. ^ Kane, Julius; Summerbell, Richard; Sigler, Lynne; Krajden, Sigmund; Land, Geoffrey (1997). Laboratory handbook of dermatophytes: a clinical guide and laboratory handbook of dermatophytes and other filamentous fungi from skin, hair, and nails. Belmont, CA: Star Pub. ISBN 978-0898631579.
Selecting the right references

As you may have already suspected, all sources are not equal. Some are objective and neutral, based on evidence and analysis; others are subjective and biased, based on opinion and spin. Although this distinction may seem straightforward, it is not always easy to distinguish between the two types of sources. For the purposes of writing an encyclopedia entry on a species of fungus, the very best sort of information is kind that comes from secondary and tertiary sources, based on research findings that were published in peer-reviewed primary sources. Ultimately if you need to use a primary reference to support a fact because there are no alternatives, go ahead and use it, but because of the particular sensitivity of health-related topics, you should only cite secondary sources when it comes to issues related to treatment. For more information I encourage you to read the articles on editing medicine and health topics and identifying reliable sources.

I hope you have gathered by now that writing an encyclopedia entry is quite different from writing a term paper in many ways, one of which is the need to select references carefully to support facts. And although many references may support the same fact, some references are much more suitable than others given the situation.

Week 5: Expand your article in your Wikipedia sandbox[edit]

Homework
  • Write a 3–4 paragraph summary of your article —with citations— on your Wikipedia sandbox.
  • Do not edit the article in the main space.
Milestone
  • All students have started editing draft articles in their Wikipedia sandboxes.

Week 6: Helping your peers[edit]

Assignment (due Friday October 31, 2014) (worth 5% of your grade)
  • Review and comment on the draft articles of at least 2–3 your classmates (last week's homework). Provide comments and constructive criticism to help them polish their articles and fix any major issues. Do not just say "Nice job! That looks great!!". You can suggest additional or better references, ways that they can organize the headings and subheadings of their articles to improve the flow, other articles on Wikipedia that they could look at that might help them to build their article, essays on Wikipedia they could read that might help them to overcome issues they might be having, etc. The more, the better.
  • Leave your comments on their user talk page, do not edit their sandbox.
  • Continue to work on your article and integrate the comments you receive.
Milestone
  • All articles have been reviewed by others. All students have reviewed articles by their several of their classmates.

Week 7: Your midterm exam is this week[edit]

Homework
  • Continue to work on your article

Week 8: Polishing your article[edit]

Homework
  • Continue research on your article.
  • Take a look at several of the articles of your peers and comment on them.

Week 9: Final due date[edit]

Assignment (due Friday November 14, 2014) (worth 15% of your grade)
  • Email me a MS-Word file containing the full text of your article ([email protected])
  • Leave your article in your sandbox and I will grade it there.
  • Frequently asked questions:
1. What do I need to hand in?
I plan to grade your assignment based on what is in your sandbox at midnight on the due date. I've asked that you send me a file (MS Word or Notepad is OK), but this is just as a back-up. I plan to do all the marking from your Wikipedia sandbox. So all you really need to do is make sure that you're happy with what's in your sandbox by the end of the day the assignment is due, and I'll grade the sandbox revision based on the last time-stamp.
2. Do I need to "submit" my article in Wikipedia by clicking Submit your draft for review!?
No. It's not necessary. It might actually be better if I have a chance to go through your article first to make sure there are no major errors and that it's adequately written before it gets submitted to the editors. Having said that, if you've confident and want to submit it, please feel free. But before you click the button, please check to see if a "stub" page already exists for your fungus.
a. If an article on your fungus already exists (and about half of your fungi already have stubs), my advice is to not use the "Submit your draft for review" feature. Rather, you might better click Edit source in your sandbox, copy everything below the <!-- EDIT BELOW THIS LINE --> tag, then go to the article stub in the main space, click Edit source there, delete the content and paste in yours. Then make a note in your edit summary that your edit was a major revision to a stub as part of a WP:Education project, and sign it ~~~~.
b. If your fungus does not already have a stub in the main space, the best option is to use the Submit your draft for review! feature.
3. What happens if I don't submit my article in Wikipedia?
Once I have taken a look at it, I'll follow-up with you about any questions I have. In most cases I'll also do some light editing. After this, either of us can go through the process of submitting it (I'm happy to do it if you feel the lack of a pending grade causes you to lose interest). Yu've all done quite good work, and I fully intend to make sure it all gets into the main encyclopedia.
4. I still want a photograph but you haven't given me one.
That means that I don't have one, at least not right now. That won't affect your grade. But I do plan to try to grow some of these species and obtain photographs in the next several weeks at which time I will attach them to your article.
Milestone
  • Students have finished all their work on Wikipedia that will be considered for grading.


(Click to return to your main course page and continue.)

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