Wikipedia:Wiki Ed/Ontario Tech University/CHEM 4610U F19 - Bioinorganic Chemistry (Fall)

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Course name
CHEM 4610U F19 - Bioinorganic Chemistry
Institution
Ontario Tech University
Instructor
Kevin Coulter
Wikipedia Expert
Elysia (Wiki Ed)
Subject
Bioinorganic Chemistry
Course dates
2019-09-05 00:00:00 UTC – 2019-12-04 23:59:59 UTC
Approximate number of student editors
10


Survey of metalloenzymes highlighting their biological occurrence and function, structure-function relationships, and current chemistry research with biomimetic complexes; also an introduction to the specialized inorganic analysis techniques EPR and XAS/EXAFS used to study metalloenzymes. Metalloenzyme examples include (as time permits): biological iron transport and storage, carbonic anhydrase, Marcus Electron-Transfer Theory, iron-sulfur proteins, blue copper proteins, Photosystem II, superoxide dismutase, haemoglobin, cytochrome P450, nitrogenase, vitamin B12, CO2 fixation in methanogens and cofactor F430

Introduction (Wikipedia Assignment)

Our Ontario Tech CHEM 4610 course will be an integral part of WikiEd's important initiative to improve science content on Wikipedia!

Google searches for scientific information routinely return Wikipedia articles in the top five search results, and more and more scientists are recognizing the worthiness of Wikipedia content. As a chemist, I have continually been impressed with the accuracy, quality and range of Wikipedia scientific content, and now use it so much that I have recently made a donation out of appreciation. Every chemistry or physics article I have read so far has been reasonably or very well written and accurate, not only content for which I already have the relevant expertise to pass judgement, but also for content that is new to me which I was later able to verify, for example by reading the primary references listed in the Wikipedia article.

Although Wikipedia does not use the explicit expert peer-review process employed by primary scientific journals, it does have a reasonably effective mechanism to ensure quality and accuracy due to the tireless efforts from the community of many thousands of volunteer editors that not only contribute content but also assess the quality of articles and discuss the best ways to improve them, and assist new editors. In addition, there is the Wiki Education Foundation (https://wikiedu.org/) that supports class assignments and assists instructors and new student editors.

The range of topics covered is impressive, making Wikipedia a preferred resource. While there are other high quality online chemistry information resources, they are either highly specialized or only have a relatively small number of topics/articles, because a small group of chemists at a particular institution can not contribute anywhere near as much content and range of topics as Wikipedia with its many thousands of editors contributing from all over the world. Furthermore, Wikipedia can be relied on to always be there for you, whereas numerous online chemistry information resources that I relied on in the past would at some point disappear off the internet as the staff maintaining the resource either moved on or lost funding that was supporting the resource.

Online video – History of Wikipedia
(https://en.wikipedia.org/wiki/File:The_State_of_Wikipedia_by_JESS3.ogv)

Learning Outcomes

  • Gain experience with writing a scientific article in the neutral encyclopedic style for a general (worldwide) audience, not just for one instructor who is an expert in the field. Your assignment will not just end up archived on your hard drive where no one will see it, instead it will live on as a valuable contribution to a high quality worldwide online encyclopedia read by millions of people.
  • Gain experience with interacting with other editors and experts regarding:
  • feedback on how to improve your content
  • reaching a consensus opinion on how to improve the content of an article
  • justifying your intended contributions with primary source references from peer-reviewed scientific journals
  • objective (and cordial) analysis of existing content from other editors
  • Gain an understanding of the fundamentals of contributing to Wikipedia, and how it involves a large community of editors and volunteers working together to ensure high quality articles and a broad range and depth of content. As future chemistry professionals, this experience may entice you to become a Wikipedia volunteer editor and help contribute quality content in the areas of your expertise.

Student "affidavids":

“With a traditional assignment, your only audience is often your professor, or at most your professor and your classmates. I really liked the fact that this assignment gave me an opportunity to write for a broader audience and make a valuable contribution to a resource that I often use myself.” — Joseph Lapka, San Francisco State University

“Writing for Wikipedia has engaged my students like nothing else. They are some of the most pedagogically powerful assignments I’ve incorporated into my classes.” — Adeline Koh, instructor, Stockton University

“Students do use Wikipedia, and they need to understand what it is and how to trace back to the [cited] sources. It is a valuable tool that is dismissed by too many people.” Faculty participant

Instructor "Affidavids"

" There are few assignments that incorporate all of MY course goals (teaching critical thinking, practicing research skills, writing intensive work, facilitating collaboration between students, teaching practical skills, and incorporating activism/advocacy work) in a succinct manner. The cherry on top was the degree to which students engaged with the project and created thoughtful and significant edits (which in many cases either significantly improved/changed the Wikipedia pages or created totally new and original content)."

Overview of Wikipedia Assignment (25% of Total Course Mark)

Students must contribute a total of 900 “word equivalents” to any Bioinorganic Wikipedia article(s) they choose (create a new Wikipedia article if one does not already exist for your topic), that consists of:

a minimum 500 words of original text content, supported by good quality literature references from reputable peer-reviewed scientific journals.
due dates:

  • the first 250 words of original text content are due for marking Fri Oct 11th 2019 (this is to ensure students get feedback before completing all their contributions)
  • the second 250 words are due Mon Nov 18th 2019.

The additional 400 words are due for marking Mon Nov 18th 2019 and can be any combination of:

  • text contributions, supported by good quality literature references from reputable peer-reviewed scientific journals.
  • edits to existing Wikipedia content (see Marking Scheme below for “word equivalents”)
  • Diagrams (see Marking Scheme below for “word equivalents”)
  • Literature References to existing content (ie. not including references that support the student’s text contributions; see Marking Scheme below for “word equivalents”)

(Wikipedia articles often are as much or more in need of high quality diagrams and references than text)

note: text contributions must be submitted to www.turnitin.com to verify its originality.
To submit to Turnitin, log in with your uoit.net (or a personal email account) email address and password and enroll in the CHEM 4610 class using: 

Class ID: see Ass1 file posted to BB
Class enrolment password: see Ass1 file posted to BB

Turnitin: Students are allowed to submit their contributions and view their originality score before the due date and can resubmit (after 24 hrs) which overwrites original submission up until the due date.

Getting Started

Enroll in the 4610 WikiEd course page. DO NOT use your actual name in your username (for security to avoid being identified). To avoid having the enrolment password publicly available, the instructions for enrolling on the CHEM 4610 Wikipedia course page are given in the Ass1 file on BB

Once enrolled, follow the course page timeline (tab above).

the instructor will be able to see:  whether you have completed the training for students  your sandbox  which articles and talk pages you have contributed to  what you have contributed  what files you have uploaded (e.g. figures)  how many views your work has received  and other useful information about your work on Wikipedia.

BEFORE BEGINNING: students must email to obtain approval from the instructor regarding:

 which subtopic(s) you wish to work on (give relevant Wikipedia articles); in the case two or more students choose the same subtopic, only the first student to contact their instructor will get the approval, the others will have to find another subtopic. marks will be deducted if not done

 what type of Wikipedia contribution you wish to make, ie. whether it is to contribute new content, add citations, add media (figures, diagrams, videos), edit existing material, evaluate article quality, or some combination thereof. marks will be deducted if not done

References  must be submitted to instructor (best to put in your Google Drive and share with instructor)  must have the filename format: “name of metalloenzyme/metalloprotein” “one or two keywords indicating topic of article” “(student last name in brackets)” “abbreviated journal name and year of article”, e.g. “Fe transport DMT1 (H_Smith) BiocCellBio1999”  marks will be deducted if references are not submitted to your instructor and/or do not have the requested filename format
Learning How to Contribute to Wikipedia

The total contribution (combination of original text, editing, references and/or diagrams) must be entered into the student’s user page sandbox and the username provided for the instructor to verify.

The content should first be created in the user’s sandbox, and not be placed in the live article until after your instructor has reviewed it and made recommendations, and you have completed any revisions required by your instructor.

use the talk page of the article(s) to which you intend to contribute to identify and justify your intended edits to other Wikipedia editors, and (hopefully) reach a consensus of approval for the edits before making them to the live article.

WikiEdu Assistance and Feedback: Ian, an on-staff Wikipedia content expert, will follow the work that students do throughout the term and provide feedback as they edit. He is signed up on our course page as Ian (Wiki Ed) Also, on your course page, there is a purple "Get Help" button in the upper right corner; students can click on this to access ask.wikiedu.org, the WikiEdu FAQ site, find relevant resources, or reach out to the appropriate member of the Wiki Education team to assist you.

In week2 of the assignment, students will learn about and practice the following features of Wikipedia: • Create account, userpage and sandbox, enroll in course page • Practice (in sandbox) correct use of the following Wikipedia editing and formatting features: Must have at least one example of each of the following in your sandbox  headings, with sublevels  formatting: bold, subscripts, superscripts,  links to other Wikipedia articles and external references (ie. outside Wikipedia)  cited references and a reflist  an uploaded figure with a caption must be an original figure that is not copyrighted, preferably one you have drawn yourself or a photo you have taken  make a table  math formulas  chemical information box see the new F16 chemistry editing brochure from Helaine: our handbook devoted specifically to the topic of editing in the field of chemistry on Wikipedia our handbook devoted specifically to the topic of editing in the field of chemistry on Wikipedia • learn about the following types of pages:  talk pages https://en.wikipedia.org/wiki/Wikipedia:Signatures note: most talk pages now have the “article rating” for its quality (project's quality scale) and importance (project's importance scale.), assessed within the scope of WikiProject Chemistry, a collaborative effort to improve the coverage of chemistry on Wikipedia (and the WikiProject Biology, an effort to build a comprehensive and detailed guide to biology on Wikipedia).  history pages  watchlist

Marking Scheme

TOTAL MARK: /100 

creation of Wikipedia account and user page (submitted to instructor) - [5 marks]

completion of the online training for students - [5 marks]

Learn and Practice Wikipedia Features in your Sandbox - [10 marks]

Assessment of Contributions (text, references, diagrams): [60 marks Total] • first 250 words text contribution [20 marks] • second 250 words text contribution [20 marks] • additional 400 words/word equivalents (text, references, diagrams, edits) [20 marks]

Marking Guide for text contributions:

• Topic/Subtopics (worth ~ 15% of total marks) chosen subtopics are reasonably appropriate, and reasonably important, contributions for the chosen Wikipedia articles

• Quality of Writing (worth ~ 70% of total marks)

Sentence Structure and Grammar

 has been PROOFREAD!! Grammar and spelling are acceptable; no incomplete or run-on sentences  sentence structure is reasonable, understandable and “reads well”, ie. does not leave reader struggling to understand what is being said.

written to Wikipedia standards and well enough to be worthy of the Wikipedia article:

 written at an appropriate level of detail, not too general or vague, not to specific and detailed on a small subtopics that are not so important to the article

 written in the neutral point of view with concise scientific language, and no subjective opinions or persuasion; does not refer to authors by name in the text (ie. unlike the scientific literature, avoid directly naming authors “Jones et al believe this mechanism to be most likely”, just give a subscript to the reference) except where the author is very well known and of great importance to the topic (e.g. “the theory of relativity was developed by Albert Einstein”)

 uses proper Wikipedia formatting and syntax; has heading(s) to identify subtopic(s) ; links to other Wikipedia articles

 chemistry specific terms, parameters, abbreviations and symbols are defined or explained (except when already defined in the existing Wikipedia article)

 follows Wikipedia’s policies and guidelines including the five pillars

• Referencing is Sufficient and Appropriate to support the content (worth ~ 15% of total marks)

pdf files of references must be submitted to your instructor (best to put them in your Google Drive) note: references must have the filename format: “name of metalloenzyme/metalloprotein” “one or two keywords indicating topic of article” “(student last name in brackets)” “abbreviated journal name and year of article”, e.g. “Fe transport DMT1 (H_Smith) BiocCellBio1999” note: marks will be deducted if references are not submitted to your instructor and/or do not have the above filename format

Marking Guide for contribution of references

• Referencing is Sufficient and Appropriate to support the content; references are from the chemical literature and well discuss what is being said in the Wikipedia article.

Marking Guide for contribution of diagrams

• Diagrams are “textbook quality”, have sufficient detail, no mistakes, and look professionally drawn; molecular structures do not have distorted “funny-looking” bond lengths or angles; items in the diagram have appropriate sizing (text is not too small or big, arrows and other graphics are sized appropriately for the diagram) 

Contributing to live article; - [20 marks] Completion of revisions recommended by instructor before contributing; use of talk page to identify and justify your intended edits to other Wikipedia editors;

Word Equivalencies for Non-Text Contributions

• adding diagrams

 the word equivalency of each diagram or table will be decided by the instructor depending on the complexity and relevance of the diagram or table, students must therefore consult (email) with the instructor to determine the equivalency allowed for a diagram or table.

• adding references to existing content:

 adding one reference will be considered equivalent to 20 words of text content, ie. adding 10 references will count as equivalent to contributing 200 words of original text content

 pdf files of all references must be submitted to the instructor to verify their appropriateness; references that do not well support the existing text content will not be counted

• editing existing content:  if more than 50% of a sentence is edited, then count all the words in the sentence  if less than 50% of sentence is edited, then count only the number of words changed or added  there must be a valid reason for each edit and it must be explained in the talk page

NOTEs

• the marks are also indicated in the timeline for each week.

• deciding on Topics and subtopics does not have marks assigned to it but does have due dates with late penalties
Assignment Topics – Guidelines and Instructor Suggestions

Various suitable topics and subtopics identified by your instructor are listed in the "Ass2 Wikipedia Contribution" file posted to BB
Instructor Advice and Student FAQ

see the Ass1 file posted to BB

Student Assigned Reviewing
Bilal.bhatti96 Carbonic anhydrase Copper protein
SushiLover135 Plastocyanin Transferrin
Coordinationchem Iron Sulfur proteins Carbonic anhydrase
Recyclingbin432
ScienceBubble Copper protein Plastocyanin
Mkcm131 Rubredoxin Ferrichrome
Banadoodles Formylmethanofuran dehydrogenase Rubredoxin
Chemistry22 Ferrichrome
Reas0ns11 Carboxypeptidase Carbon monoxide dehydrogenase
KeyLowZip Transferrin Carboxypeptidase
ChemThings&Etc. Carbon monoxide dehydrogenase

Timeline

Week 1

Course meetings
Monday, 9 September 2019   |   Wednesday, 11 September 2019
In class - Introduction to the Wikipedia assignment

Welcome to your Wikipedia assignment's course timeline. This page guides you through the steps you'll need to complete for your Wikipedia assignment, with links to training modules and your classmates' work spaces.

Your course has been assigned a Wikipedia Expert. You can reach them through the Get Help button at the top of this page.

Resources:

During this training, you will learn about:

  • Wikipedia’s policies and guidelines including the five pillars  
  • "edit source" pages and wikimarkup 
  • "edit" pages and the visual editor (relatively new and now the preferred editing method)
  • your userpage and sandbox
  • talk pages, history pages and watchlists

The training consists of units that students take as they proceed with the different stages of their Wikipedia assignment. Each unit covers important aspects of Wikipedia that will set students up for a successful Wikipedia experience, and the instructor can keep track of each student's progress.  Be sure to check the dashboard regularly for upcoming training modules.
 
Wikipedia's Five Pillars:

  • Wikipedia is an online encyclopedia
  • Wikipedia has a neutral point of view
  • Wikipedia is free content
  • Wikipedians should interact in a respectful and civil manner
  • Wikipedia does not have firm rules

 

Assignment - Get started on Wikipedia

Create an account and join this course page, using the enrollment link your instructor sent you. (Because of Wikipedia's technical restraints, you may receive a message that you cannot create an account. To resolve this, please try again off campus or the next day.)

Week1 Tasks (mark = 5%):

  1. Create a Wikipedia account and enroll in the CHEM 4041 assignment page
  2. Initialize your userpage and sandbox
  3. read through the Editing and Evaluating Wikipedia brochures (links above)
  4. do the above Training modules

note: the overall grading scheme is given below the timeline


Resources:
1. Create Account and Enrol
Students can both create their Wikipedia account (username and password) and join the CHEM 4610 F19 Wikipedia course page by clicking the enrollment link provided in the Ass1 file posted to BB.

(Because of Wikipedia's technical restraints, you may receive a message that you cannot create an account. To resolve this, please try again off campus or the next day.)


Once enrolled, the instructor will be able to see:

  • whether you have completed the training for students
  • your sandbox
  • which articles and talk pages you have contributed to
  • how much and what you have contributed 
  • what files you have uploaded (e.g. figures)
  • how many views your work has received
  • and other useful information about your work on Wikipedia.

 

Milestones

This week, everyone should have a Wikipedia account.

Week 2

Course meetings
Monday, 16 September 2019   |   Wednesday, 18 September 2019
Assignment - Training
Edit and Evaluate Wikipedia (5% of Total Mark)

Exercise

Evaluate an article

Week 3

Course meetings
Monday, 23 September 2019   |   Wednesday, 25 September 2019
Assignment - Assignment Tasks - Practice Editing (10% of Total Mark)

 

Week3 Tasks (Mark = 10%)

 

1. Practice the following in your sandbox (mark = 7%)
(see detailed instructions below)

  • Editing and formatting etc. with the Visual Editor 
  • Practice citing internal and external references and creating a reflist
  • Practice uploading figures
  • Practice making a table
  • Practice entering a formula
  • Practice making a chemical information box ("ChemBox")


2. View and learn how to use: talk pages, history pages, watchlists (mark = 3%)
(see detailed instructions below) 


Detailed Instructions and Resources:

Instructions

1. Practice the following formatting features in your sandbox; inform your instructor when the tasks are complete for marking


For the items below, choose one chemical compound for which there is no Wikipedia article or only a stub article that does not list the chemical and physical properties, check these sources:

 

  • look through the Sigma-Aldrich chemical database (or Fisher or VWR) 
  • you may know of a literature article that reports the chemical properties of a compound
  • search for the chemical properties using SciFinder (which gives the CAS number) and/or the CAS number; (see course syllabus for instructions how to use Scifinder)
  • choose one of the following examples identified by your instructor:  
    1.  tri(2,2'-bipyridine)iron(II) chloride; see PubChem tris(bipyridine)iron(II) chloride chemical and physical properties; there is no Wikipedia article for [Fe(bipy)3]2+ and Wikipedia 2,2'-bipyridine article only gives the formula, nothing else
    2. Chromium(III) acetate (CRAC) tris(aquo)hexa-μ2-acetato-μ3-oxo-trichromium(III) chloride hexahydrate; see PubChem chromic acetate data and literature references from CHEM 3510 lab manual posted to BB 4610 Ass1 folder
    3.  nickel(II) cyclam perchlorate (cyclam = 1,4,8,11-tetraazacyclotetradecane); see the PubChem [Ni(cyclam)(ClO4)2 data] and the literature references from the CHEM 3510 lab manual posted to BB 4610 Ass1 folder
    4.  Fe(TAML) green oxidation catalyst developed by Terrence Collins (Carnegie-Mellon); probably can get physical properties from the patents listed on his GreenOx Catalysts company website, and/or the primary literature (see Chem. Rev., 2017, 117 (13), pp 9140–9162 and Science, 315, 835-838, 2007)

    5. ;;

      vanadyl tartrate, vanadyl citrate (as per literature articles in Ass2 folder and Wikipedia vanadate article) tetrachlorozincate , 2-methyl-3-heptanol , bee pheromones: 4-Hydroxy-3-methoxy phenylethanol (HVA) and methyl oleate ,  ?  .  do not have a cheminfo box

      dibutyltin diacetate used to make FTO glass does not have a Wikipedia article

for example N,N'-dimethyl-1,3-propanediamine is listed in the Sigma-Aldrich polyamines list and has only a stub Wikipedia article
Most of the well known common compounds do have Wikipedia articles, so best to check less common examples; be sure to search for them on Wikipedia until you find a compound that has no article or only a stub article that does not give the chemical properties asked for below. 
note that the WikiProject Chemicals links to the project worklist which has a comprehensive list of Wikipedia chemical articles being worked on (and their status).

 

1.1. In your sandbox, use the Visual Editor to make: 

  • the Heading: "Week3 Tasks - Info for {name of your compound}"
  • the subheading: "Properties of {name of your compound}"
  • a bullet list of the following properties:  molecular formula ; molar mass ; m.p. ; b.p. ; solubility in water.  

Note if the compound is a metal salt, e.g. most metal complexes, the m.p. and b.p. will likely be not available since salts usually do not melt or boil and instead just decompose on heating to high temperatures (> 250 dec C)


1.2. repeat the name of your chosen compound in bold and again in italics

1.3. give an internal Wikipedia link to any chemistry article of your choosing

1.4. give an external link to the Sigma-Aldrich catalogue entry for your above chosen compound, or to the literature article or CAS entry etc, whichever is the source you used for the chemical properties. 
For example, the Sigma-Aldrich catalog entry for N,N'-dimethyl-1,3-diaminopropane.

1.5.  Practice making citations
Google Search or use SciFinder (see course syllabus for instructions how to use Scifinder) for three different chemistry literature articles not listed in the Wikipedia article for any of the topics below.  Give the title of each article and make a citation at the end of each title to the journal article.  If your articles are directly relevant to the content of the article, then they can serve as part of your assignment contribution.

  • article(s) on the nitrogenase enzyme that are not listed in the Wikipedia nitrogenase article.  
  • article(s) on Photosystem II that are not listed in the Wikipedia Photosystem II article
  •  

make a reflist with the heading "references" below the list of articles (use the visual editor "cite" and "insert/references list" buttons, but note that the wikimarkup syntax is in the wikimarkup quick reference "cheatsheet".  

1.6.  Practice Uploading Figures 

  • Use ChemDraw to draw the chemical structure of your chosen compound above
  • use "save as" to save the ChemDraw file as a jpeg file (can also save as a pdf but might not be as good resolution)
  • upload the jpeg figure to the Wikimedia Commons
  • display the figure with a caption in your sandbox


1.7.  Practice making a table
make a table, with a minimum two columns and three rows, listing any kind of chemical data of your choosing, suggestions are:

  • NMR or IR data (check the Aldrich catalog or the SDBS database for NMR spectra)
  • search for a compound on the NIST chemistry webBook and list chemical properties and/or spectroscopic data
  • the chemical properties for your chosen compound above
  •  


1.8. Practice entering a formula
enter any formula or calculation of your choosing that includes:

  • at least one term with a fraction (numerator and denominator)
  • at least one number with an exponent
  • at least one variable with a subscript  


1.9. Practice making a chemical information box ("ChemBox")

make a chembox for your chosen chemical compound (above) for which there is no Wikipedia article and fill in what information in the chembox template that you have (name, IUPAC name, formula, molar mass, m.p., b.p. etc)

2.1.  View and learn how to use talk pages,

2.2.  View and learn how to use history pages

2.3.  View and learn how to use watchlists

 

====
Resources: ====

 

(Wiki Ed) (Ian Ramjohn / ian@wikiedu.org) Wikipedia Content Expert in the Sciences
Ian is our content expert from Wiki Ed, he will help students throughout the term.

 

the Basics of how to Contribute to Wikipedia
About [https://en.wikipedia.org/wiki/Wikipedia:Policies_and_guidelines Wikipedia Policies and Guidelines

]
Help: Wikipedia: The Missing Manual
 Wikipedia: The Missing Manual is a how-to guide that explains the process of contributing to the English Wikipedia, both for novice users and experienced editors. It was originally written in 2008 by John Broughton, but has since been expanded and updated by many other Wikipedia contributors.

 

=====
Editing and Markup: =====

About Editing Wikipedia (a downloadable pdf file that is also posted to the BB Ass1 folder)

[https://en.wikipedia.org/wiki/Help:Cheatsheet a quick reference on wikimarkup syntax

]

 

NOTE: to see "Edit Source", in the "edit" tab, there is an "edit pen" button on the top right that toggles between the "visual editor" and "edit source" 

====== in some cases, like a chembox, there is no visual editor option so you will likely want to view the edit source syntax of an existing chembox to know what syntax is needed 

======
 
How to make a Table:

====== Advice from Ian (our mentor from Wiki Ed, see above):
if you are using the VisualEditor (which you should be), creating a table is actually as easy as clicking the Insert button and selecting Table.
If you want to learn how to do it "properly", using wikicode, you should check out Help:Table on Wikipedia. It probably tells you more than you want to know about table formatting, but it does give you an awful lot of control over what you want to do. ======

A convenient in-between option is to use a tool that lets you convert Excel into a wikicode table. Here's a good example http://tools.wmflabs.org/magnustools/tab2wiki.php

 

 

How to make a formula:

Advice from Ian (our mentor from Wiki Ed, see above):
When it comes to mathematical notation in Wikipedia, you can find everything you'd ever want to know (and a lot more) at Help:Displaying a formula. A specific extension to the <math> tags that are specifically designed for chemistry were introduced this summer - see Help:Displaying a formula#Chemistry. There are still issues with that extension though, and for that reason some Chemistry editors have mixed feelings about whether to use it or not. I'd say use it if it works, but bear in mind that it will sometimes fail to display anything but an error message. So warn your students to double-check things after they save a page.

VisualEditor also has a decent tool for building formulae. I haven't played with it much, but it seems pretty powerful. You can access it by clicking the More button on the drop-down menu from Insert, as shown in the screen shot. This might be sufficient to your students needs.

 

 

How to Upload images and diagrams:
Uploading Images, includes the "Illustrating Wikipedia" Guide (a downloadable pdf file that is also posted to the BB Ass1 folder)


for further details on chemistry illustrations, see the “Editing Wikipedia articles on Chemistry (Wiki Ed)” handbook, you can download the pdf (it is also posted in the 4610 Ass1 folder and hardcopies are available from your instructor; and it is also posted in the Wikimedia Commons for download), see p. 3 where it says: “If you’d like to create and share images of chemical structures or reaction schemes, check out | shortcut WP:CSDG -  for details on how to upload them (don’t upload freehand drawings).”

Tips for Wikipedia chem-art: no words, uniform font (sans serif), no "a" and "b", the two mechanisms should be separate figures to ensure versatility. Wikipedia would probably only show one mechanism.

 

How to make a ChemBox:

see the “Editing Wikipedia articles on Chemistry (Wiki Ed)” handbook, you can download the pdf (it is also posted in the 4610 Ass1 folder and hardcopies are available from your instructor; and it is also posted in the Wikimedia Commons for download):  p. 3 gives the chembox template and the link to the Template:Chembox,

General info on Infoboxes:  Wikipedia:infoboxes , Wikipedia:List of Infoboxes

 

 

 

 

Guide(s) for writing articles in your topic area

Chemistry

Week 4

Course meetings
Monday, 30 September 2019   |   Wednesday, 2 October 2019
Milestones

Week4 Tasks - Start Choosing Topics/Subtopics and Type of Contribution

  1. Start Deciding on Topics and Subtopics and what types of contributions you will make, esp for the first 250 word contribution due Fri Oct 11th
  2. Begin Searching the Literature and Reading References. 
  3. Obtain Instructor Approval (email a list of the topics/subtopics you have chosen); must obtain approval for the first 250 word contribution by Mon Oct 8th (or marks may be deducted)
  4. Assign the articles you will edit to your name on dashboard

 

Detailed Instructions
  • Choose one or more topics of interest to you and assess the Wikipedia articles.              Various suitable topics and subtopics identified by your instructor are listed in the "Ass1 Wikipedia Contribution" file posted to BB
  • Perform a literature search for the most relevant literature articles from reputable peer-reviewed scientific journals on the topic; focus on finding the most recent review articles which give an overview of the topic and are usually written at a level appropriate for Wikipedia; also the introductions of research articles often give a good overview.  Look up the most relevant references from the most recent articles to get a more complete view of the topic. In addition to search engines such as Google Scholar you can use our UOIT licensed SciFinder Scholar (instructions in the Course Syllabus on BB).  Check the course textbook (BGSV-06) for literature references (if the topic is discussed in the course textbook).

References

·        must be submitted to instructor (best to put in your Google Drive and share with instructor)

·        must have the filename format:

“name of metalloenzyme/metalloprotein” “one or two keywords indicating topic of article” “(student last name in brackets)” “abbreviated journal name and year of article”,

e.g.  “Fe transport DMT1 (H_Smith) BiocCellBio1999”

·        marks will be deducted if references are not submitted to your instructor and/or do not have the requested filename format

 

  • Be sure to look for the most recent articles also, to be sure the content of earlier articles is still considered accurate and relevant. Many bioinorganic topics involve very active areas of research where fundamental aspects such as the structure or mechanism are still not known or proven, such that new experiments and insights are being reported every year. For example, the exact structure of the CaMn4O5 cluster in photosystem II has only been determined as of 2011 (well after the current edition of the textbook BGSV-06) and the mechanism is not "settled" with several different proposed mechanisms in the recent literature, likewise the structure of the FeMoco (MoFe7S9C) cofactor in nitrogenase was not fully resolved until 2011 and currently the mechanism is still not known, even the initial binding site of the N2 substrate is not known
  • decide on what subtopics you will contribute, ie. for example do not just decide to work on "hemoglobin", instead identify very specific subtopics that are missing or incomplete within the Wikipedia hemoglobin article such as "how Fe3+ high spin-low spin conversions trigger the conformational switching mechanism of hemoglobin" or "carbonate binding mechanism of hemoglobin" or "current methods of isolating hemoglobin"
  • decide what type(s) of contribution you will make, ie. whether it is to contribute new content, add citations, add media (figures and diagrams), edit existing material, evaluate article quality, or some combination thereof.

 

How to Search the Literature

 

For Wikipedia contributions, you should be primarily using textbooks and Review articles from the literature, because they are usually written at the level of detail appropriate for Wikipedia articles.  Therefore, take care to look Review articles and the review articles will have lots of references that you can look to for more detail.  That being said, some research articles do have good discussions at a level appropriate for Wikipedia, so do not be dimissive of a research article if it looks like it has good discussion of the topic/subtopic you want, just that usually the best strategy is to look at the review articles first to get a good overview of the topic.

 

Downloading Articles

On the Ontario Tech Library website, select the "Journal Titles" tab/portal which allows access to online articles from a large number of chemistry journals for which Ontario Tech has a subscription.

If Ontario Tech does not have a subscription to the journal such that the journal website will not allow you to download the article, you can order the article using "RACER":

- go to the Ontario Tech Library front page, from the "services" drop-down list in the top right, select "Interlibrary Loan - (IIL) RACER"

- must create a RACER account, from the "how to use RACER" drop-down list, select "creating an account (first time users must register)"

- select "log in to RACER if you have already registered"

- on the left side of the page, select "blank request form"

- fill our the form (select "Ontario Tech email delivery), and submit

- you will be emailed a .pdf of the scanned article, usually takes 2 days - 1 week

 

 

Searching the Chemistry/Science Journals:

 

NOTE: often a reference will only give the abbreviation of the journal title, so to find the full title, the UBC library kindly provides a search feature:

Chemistry/Science Journal Abbreviations, a Comprehensive list from UBC

http://www.library.ubc.ca/scieng/coden.html

 

Google Scholar

is an excellent search engine for Science/Chemistry articles; you can enter keywords for your topic and subtopics and sort by relevance or by date; however it does not allow any futher refining, for example to filter the search results for review articles only.

 

SciFinder Scholar

The Ontario Tech Library website provides a sophisticated (and expensive!) literature searching software called "SciFinder Scholar" which searches ALL the Chemistry/Biology/Biochemistry and other Science Literature (and even conference presentations and patents), much more convenient than searching the individual (e.g. ACS, RSC etc) journal websites.  

SciFinder Scholar access (2018):

to register (username and password) or to login, go to http://guides.library.uoit.ca/chemistry which has a box on the left side with the link "go to registration page" if you are a new user. 

Alternatively, use Access SciFinder Scholar starting on the Ontario Tech Library website front page, select "databases by subject" then "chemistry" then "SciFinder (CAS)" and login to use SciFinder Scholar.

NOTE: you must be on campus to use SciFinder Scholar but it is easy to save search results when on campus so you can then look up articles of interest off campus using the Library Portal.

 

 

 

 

Article Finder Tool

 

Finding articles for your students to work on can often be one of the trickiest parts of the Wikipedia assignment. To help them in this process, we just launched a new article finder tool on the Dashboard. The new article finder can be found under the articles tab of your course page.

After typing in keywords, students can sort the results by quality, completeness, or daily page views so they can more easily find the articles where they can have the most impact. You can read more about the new article finder tool here.

In conjunction with our finding articles training module, students can learn to identify those articles that are both relevant to their coursework and in need of improvement.

 


How to find Stub articles:

https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Stub_sorting/Stub_types#Physical_sciences

 

 

FYI: the Wikiproject_chemistry classifies chemistry articles and identifies what changes are needed, however it does not have anything on bioinorganic articles so not very useful to the 4610 assignment

https://en.wikipedia.org/wiki/Wikipedia:WikiProject_Chemistry

click on “open tasks” and/or “things you can do” for a listing of chemistry articles that need editing

 

 

Add to an article

Exercise

Add a citation

Week 5

Course meetings
Monday, 7 October 2019   |   Wednesday, 9 October 2019
Assignment - Start drafting your contributions

Reach out to your Wikipedia Expert if you have questions using the Get Help button at the top of this page.

Resource: Editing Wikipedia, pages 7–9

Week 5 Tasks

  1. Make final Decisions on what exact contributions you will make for your first 250 words, and obtain instructor approval:   (due Fri Oct 11th; 5% penalty per day late to max 20%) 
    • specify (in your sandbox) what subtopics you will contribute, do not just say "hemoglobin", instead say  "how Fe3+ high spin-low spin conversions trigger the conformational switching mechanism of hemoglobin"  or "carbonate binding mechanism of hemoglobin" or "method of isolating hemoglobin"
    • specify (in your sandbox) what type(s) of contribution you will make, ie. whether it is to contribute new content, add citations, add media (figures and diagrams), edit existing material, evaluate article quality, or some combination thereof. 
    • place the literature articles that you will be using as sources for your contributions in a folder on your Google drive; use the filename format indicated in the Marking Scheme and Week4 above; share with your instructor
  2.   Start writing your contributions and format them in your Sandbox, and clearly label what contribution it is (first 250 words, second 250 words, additional 400 words/word equivalents etc.)
  3. View the talk pages of the articles you intend to contribute to and inform other editors what contributions you wish to make in the near future, invite constructive comments and suggestions to improve your contributions.  This is an important part of the process as it avoids unnecessarily taking editors by surprise.
  4. Continue looking for and deciding on Subtopics for the second 250 words, and types of contributions (text, references, diagrams, edits) for the additional 400 words/word equivalents; the earlier you start writing/drawing the easier it will be for you!

 

Reach out to your Wikipedia Expert if you have questions using the Get Help button at the top of this page.

Resource: Editing Wikipedia, pages 7–9

 

 


 

Milestones

Everyone has begun writing their article drafts.

Week 6

Course meetings
Monday, 14 October 2019   |   Wednesday, 16 October 2019
Assignment - Instructor Marking and Revisions (20% of Total Mark; 5% penalty per day lat

Week 6 Tasks

1. Peer Review (due Oct 21st 2019)

Be sure your contribution is started and well identified in your sandbox so it can be peer reviewed by another student

Peer Review the Sandbox Contribution from another student as per below. 

 

2. Submit your first 250 Word Contribution (due Oct 11th 2019)

1.  In your sandbox, clearly identify your first 250 words contributions and inform (email) your instructor it is ready for marking and revisions (5% penalty per day late to max 20%)

2.  check the talk pages for editor comments on the contributions you wish to make; if there are any editor suggestions you agree will improve the contributions, then revise accordingly; likewise with the student peer review

Assignment - Peer review an article (5% penalty if not done)

Guiding framework

Milestones

Week 7

Course meetings
Monday, 21 October 2019   |   Wednesday, 23 October 2019
Reading Week

No work required but will serve you well if you take some time to make Preliminary Decisions on what exact contributions you will make for your second 250 words and additional 400 words, and obtain instructor approval:

Respond to your peer review (optional)

You probably have some feedback from other students and possibly other Wikipedians. Consider their suggestions, decide whether it makes your work more accurate and complete, and edit your draft to make those changes.

Resources:

  • Editing Wikipedia, pages 12 and 14
  • Reach out to your Wikipedia Expert if you have any questions.

Week 8

Course meetings
Monday, 28 October 2019   |   Wednesday, 30 October 2019
Assignment - Complete Revisions, Moving to Wikipedia (10% of mark)

Week 8 Tasks (10% of Total Mark for tasks 1,2,3) due Oct 31 2019:

1.  Complete Instructor Revisions on first 250 words contribution in your sandbox;

2.  check the talk pages again for editor comments on the contributions you wish to make; if there are any editor suggestions you agree will improve the contributions, then revise accordingly; likewise with the student peer review

3.  Copy your contributions (at least the parts that were deemed "Wikipedia worthy" by your instructor) to the live Wikipedia articles (the "mainspace.") (due date Nov 1st but may be extended by instructor according to when marking is completed)

4.  Make final Decisions on what exact contributions you will make for your second 250 words and additional 400 words, and obtain instructor approval:   (due date Mon Nov 4th; 5% penalty per day late to max 20%); the due date is Nov 4th but the earlier you decide the easier it will be for you.

specify (in your sandbox) what subtopics you will contribute, do not just say "hemoglobin", instead say "how Fe3+ high spin-low spin conversions trigger the conformational switching mechanism of hemoglobin"  or "carbonate binding mechanism of hemoglobin" or "method of isolating hemoglobin"

specify (in your sandbox) what type(s) of contribution you will make, ie. whether it is to contribute new content, add citations, add media (figures and diagrams), edit existing material, evaluate article quality, or some combination thereof.

place the literature articles that you will be using as sources for your contributions in a folder on your Google drive; use the filename format indicated in the Marking Scheme and Week4 above; share with your instructor

Start writing/drawing your contributions and format them in your Sandbox, and clearly label what contribution it is (second 250 words, additional 400 words/word equivalents etc.)

5. View the talk pages of the articles you intend to contribute to and inform other editors what contributions you wish to make in the near future, invite constructive comments and suggestions to improve your contributions.  This is an important part of the process as it avoids unnecessarily taking editors by surprise and gives time to reach an agreement before drafting and contributing.

Resource: Editing Wikipedia, page 13


Week 9

Course meetings
Monday, 4 November 2019   |   Wednesday, 6 November 2019
Assignment - Finalize Subtopics/References and Draft Second Contribution

Exercise

[[../../../training/students/continue-improving-exercise/link-articles|Add links to your article]]

Week 9 Tasks (Task#1 must be completed by Nov 4th)

1. Make final Decisions on what exact contributions you will make for your second 250 words and additional 400 words/word equivalents, and obtain instructor approval:  

due Mon Nov 4th; 5% penalty per day late to max 20%

  • specify (in your sandbox) what subtopics you will contribute, do not just say "hemoglobin", instead say  "how Fe3+ high spin-low spin conversions trigger the conformational switching mechanism of hemoglobin"  or "carbonate binding mechanism of hemoglobin" or "method of isolating hemoglobin"
  • specify (in your sandbox) what type(s) of contribution you will make, ie. whether it is to contribute new content, add citations, add media (figures and diagrams), edit existing material, evaluate article quality, or some combination thereof. 
  • place the literature articles that you will be using as sources for your contributions in a folder on your Google drive; use the filename format indicated in the Marking Scheme and Week4 above; share with your instructor

3.  Ask you Instructor for help if you are having trouble deciding on what to contribute and/or whether references are appropriate to use

4.  Continue drafting contributions in your sandbox

2.  check the talk pages again for editor comments on the contributions you wish to make; if there are any editor suggestions you agree will improve the contributions, then revise accordingly; this is an important part of the process as it avoids unnecessarily taking editors by surprise and will allow you to know if there is any resistance to your proposed contributions.

6.  Be sure you are progressing well enough to meet the Nov 18 due date

Now's the time to revisit your text and refine your work. You may do more research and find missing information; rewrite the lead section to represent all major points; reorganize the text to communicate the information better; or add images and other media.

Week 10

Course meetings
Monday, 11 November 2019   |   Wednesday, 13 November 2019
Draft Your Contributions (250 words + 400 words/word equivalents)

Week 10 Tasks:

1.  Try to complete all your drafts in your sandbox.

2.  Be sure you are progressing well enough to meet the Nov 18 due date

3.  check the talk pages again for editor comments on the contributions you wish to make; if there are any editor suggestions you agree will improve the contributions, then revise accordingly.

  • Read Editing Wikipedia page 15 to review a final check-list before completing your assignment.
  • Don't forget that you can ask for help from your Wikipedia Expert at any time!


Week 11

Course meetings
Monday, 18 November 2019   |   Wednesday, 20 November 2019
Assignment - Instructor Marking and Revisions (40% of Total Mark; 5% penalty per day lat

Week 11 Tasks - Submit Second 250 Word Contribution and Additional 400 words/word equivalents (Due Mon Nov 18)

1. In your sandbox, clearly identify your second 250 words contributions and additional 400 words/word equivalents; and inform (email) your instructor it is ready for marking and revisions (5% penalty per day late to max 40%)

2. View the talk pages of the articles you intend to contribute to and inform other editors what contributions you wish to make in the near future, invite constructive comments and suggestions to improve your contributions.  This is an important part of the process as it avoids unnecessarily taking editors by surprise.

Everyone should have finished all of the work they'll do on Wikipedia, and be ready for grading.

 

Final Polishing

It's the final week to develop your article.

  • Read Editing Wikipedia page 15 to review a final check-list before completing your assignment.
  • Don't forget that you can ask for help from your Wikipedia Expert at any time!

Week 12

Course meetings
Monday, 25 November 2019   |   Wednesday, 27 November 2019
Assignment - Complete Revisions, Moving to Wikipedia (10% of mark)

Week 12 Tasks (10% of total Ass mark) Due Mon Dec 2nd:

1.  Complete Instructor Revisions on second 250 words and 400 word/word equivalents contributions in your sandbox;

2.  check the talk pages again for editor comments on the contributions you wish to make; if there are any editor suggestions you agree will improve the contributions, then revise accordingly

3.  Copy your contributions (at least the parts that were deemed "Wikipedia worthy" by your instructor) to the live Wikipedia articles (the "mainspace.")

 

Week 13

Course meetings
Monday, 2 December 2019   |   Wednesday, 4 December 2019
Milestones
Recommended Task (no marks allotted)

Check the Wikipedia live article to see if your contributions have "survived" the initial "vetting" by other Wikipedia editors for that article.  They likely will give constructive critizism/advice for your changes to the article in the Talk Page

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