Difference between revisions of "Jnimmers Week 4"

From LMU BioDB 2019
Jump to navigation Jump to search
(Link to FDA Database)
(Tag: Replaced)
(Add Week 4 instructions)
Line 1: Line 1:
 
[[File:JnimmersFDAProducts.zip | FDA Database]]
 
[[File:JnimmersFDAProducts.zip | FDA Database]]
 +
Complete your electronic notebook  on your individual journal page. Your notebook entry should contain:
 +
* The '''purpose''':  what was the purpose of your investigations?
 +
* Your '''methods''': what did you actually do?  Give a step by step account for Tasks 1-4 listed above.
 +
** There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
 +
** You may copy protocol instructions on your page and modify them as to what '''''you''''' actually did, as long as you provide appropriate attribution.
 +
** Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
 +
* Your '''results''': the answers to the questions below, plus any other results you gathered.
 +
** Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
 +
* A '''scientific conclusion''':  what was your main finding for today's project?  Did you fulfill the purpose?  Why or why not?
 +
 +
'''[https://support.office.com/en-us/article/access-sql-basic-concepts-vocabulary-and-syntax-444d0303-cde1-424e-9a74-e8dc3e460671 Access SQL: basic concepts, vocabulary, and syntax]'''
 +
 +
For your electronic lab notebook this week, do the following:
 +
# Upload your zipped Microsoft Access FDA database to the wiki and link to it on your individual journal page.
 +
# Write up the methods you used to create the database, load the tables, and write your first query.
 +
 +
We will work with this database for a future assignment in the class.
 +
 +
<!--
 +
''For the questions below, supply (a) the answer to the question and (b) the query that you used to answer the question.''
 +
# What are the names of the drug products that are administered in the ''form'' <code>INJECTABLE;INTRAVENOUS, SUBCUTANEOUS</code>?
 +
# What are the names of the drug products whose active ingredient (''activeingred'') is <code>ATROPINE</code>?
 +
# In what ''form''s and ''dosage''s can the drug product named <code>BENADRYL</code> be administered?
 +
# Which drug products have a name ''ending'' in <code>ESTROL</code>?
 +
# Produce a table listing all of the known values for the ''therapeutic_potential'' column in the ''application'' table and how many ''application'' records there are of each. (''Side note:'' The ''therapeutic_potential'' codes are explained in the ''ReviewClass_Lookup.txt'' file, in case you’re interested.)
 +
# Produce a table listing all of the known values for the ''chemical_type'' column in the ''application'' table and how many ''application'' records there are of each. (''Side note:'' The ''chemical_type'' codes are explained in the ''ChemTypeLookup.txt'' file, in case you’re interested.)
 +
# What are the names of the drug products that are sponsored (''sponsor applicant'' column) by <code>MERCK</code>?
 +
# Which ''sponsor applicant'' companies have the text <code>LABS</code> in their names and have products whose active ingredients (''activeingred'') include ''both'' <code>ASPIRIN</code> and <code>CAFFEINE</code>?
 +
# Also answer, would you have been able to answer these questions using the web interface that the FDA provides to this database ([https://www.accessdata.fda.gov/scripts/cder/daf/index.cfm Drugs@FDA?])
 +
-->
 +
 +
==== Data and Files ====
 +
 +
* References to data and files should be made within the methods and results section of your notebook.
 +
* In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise.  In particular, you will need to zip and upload a compressed version of your MS Access FDA drug database.  Make sure that your filename contains your last name or username to distinguish it from databases created by other students in the class.
 +
 +
==== Acknowledgments ====
 +
 +
In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge. 
 +
# You '''''must''''' acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration.  You should include when and how you met and what content you worked on together.  An appropriate statement could be (but is not limited to) the following:
 +
#* I worked with my homework partner (give name and link name to their user page) in class.  We met face-to-face one time outside of class.  We texted/e-mailed/chatted online three times.  We worked on the <details> portion of the assignment together.
 +
# Acknowledge anyone else you worked with who was not your assigned partner.  This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
 +
# If you copied <code>wiki syntax</code> or a particular ''style'' from another wiki page, acknowledge that here.  Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style. 
 +
# If you need to reference '''''content''''' (such as the methods of a protocol), that belongs in the References section where you will give a include a formal APA-formatted citation (see below).
 +
# You '''must''' also include this statement unless otherwise noted: 
 +
#* '''''"Except for what is noted above, this individual journal entry was completed by me and not copied from another source."'''''
 +
# Sign your Acknowledgments section with your wiki signature.
 +
 +
==== References ====
 +
 +
*In this section, you need to provide properly formatted citations to any '''''content''''' that was not entirely of your own devising.  This includes, but is not limited to:
 +
** methods
 +
** data
 +
** facts
 +
** images
 +
** documents, including the scientific literature
 +
* Do not include extraneous references that you do not cite or use on your page.
 +
* The references in this section should be accompanied by ''in text citations'' on your page that refer to these references.
 +
* The references should be formatted according to the [https://owl.purdue.edu/owl/research_and_citation/using_research/documents/20180719CitationChart.pdf APA guidelines].
 +
* For more detailed guidelines, please see the document [[Media:BIOL367_Fall2019_GuidelinesforLiteratureCitations.pdf | Guidelines for Literature Citations in a Scientific Paper]] that you were given on the first day of class.
 +
* Cite the appropriate weekly Assignment page.  For example, the citation for the [[Week 1]] Assignment page is: LMU BioDB 2019. (2019). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
 +
* Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.

Revision as of 16:41, 25 September 2019

File:JnimmersFDAProducts.zip Complete your electronic notebook on your individual journal page. Your notebook entry should contain:

  • The purpose: what was the purpose of your investigations?
  • Your methods: what did you actually do? Give a step by step account for Tasks 1-4 listed above.
    • There should be enough detail provided so that you or another person could re-do it based solely on your notebook.
    • You may copy protocol instructions on your page and modify them as to what you actually did, as long as you provide appropriate attribution.
    • Take advantage of the electronic nature of the notebook by providing screenshots, links to web pages, links to data, etc.
  • Your results: the answers to the questions below, plus any other results you gathered.
    • Usually it makes sense to embed your answers to the questions/results in the "methods" in the order in which you obtained them.
  • A scientific conclusion: what was your main finding for today's project? Did you fulfill the purpose? Why or why not?

Access SQL: basic concepts, vocabulary, and syntax

For your electronic lab notebook this week, do the following:

  1. Upload your zipped Microsoft Access FDA database to the wiki and link to it on your individual journal page.
  2. Write up the methods you used to create the database, load the tables, and write your first query.

We will work with this database for a future assignment in the class.


Data and Files

  • References to data and files should be made within the methods and results section of your notebook.
  • In addition to these inline links, create a "Data and Files" section of your notebook to make a list of the files generated in this exercise. In particular, you will need to zip and upload a compressed version of your MS Access FDA drug database. Make sure that your filename contains your last name or username to distinguish it from databases created by other students in the class.

Acknowledgments

In this section, you need to acknowledge anyone who assisted you with your assignment, either in person, electronically, or even anonymously without their knowledge.

  1. You must acknowledge your homework partner or team members with whom you worked, giving details of the nature of the collaboration. You should include when and how you met and what content you worked on together. An appropriate statement could be (but is not limited to) the following:
    • I worked with my homework partner (give name and link name to their user page) in class. We met face-to-face one time outside of class. We texted/e-mailed/chatted online three times. We worked on the <details> portion of the assignment together.
  2. Acknowledge anyone else you worked with who was not your assigned partner. This could be Dr. Dahlquist (for example, via office hours), the TA, other students in the class, or even other students or faculty outside of the class.
  3. If you copied wiki syntax or a particular style from another wiki page, acknowledge that here. Provide the user name of the original page, if possible, and provide a link to the page from which you copied the syntax or style.
  4. If you need to reference content (such as the methods of a protocol), that belongs in the References section where you will give a include a formal APA-formatted citation (see below).
  5. You must also include this statement unless otherwise noted:
    • "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
  6. Sign your Acknowledgments section with your wiki signature.

References

  • In this section, you need to provide properly formatted citations to any content that was not entirely of your own devising. This includes, but is not limited to:
    • methods
    • data
    • facts
    • images
    • documents, including the scientific literature
  • Do not include extraneous references that you do not cite or use on your page.
  • The references in this section should be accompanied by in text citations on your page that refer to these references.
  • The references should be formatted according to the APA guidelines.
  • For more detailed guidelines, please see the document Guidelines for Literature Citations in a Scientific Paper that you were given on the first day of class.
  • Cite the appropriate weekly Assignment page. For example, the citation for the Week 1 Assignment page is: LMU BioDB 2019. (2019). Week 1. Retrieved August 27, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_1
  • Even if you have nothing else to cite, the References section must be present and include the citation to the appropriate weekly assignment page.
Retrieved from "https://xmlpipedb.lmucs.io/biodb/fall2019/index.php?title=Jnimmers_Week_4&oldid=3009"