MiRPathDB Week 5 - Revision history

Qlanners: fixe links

2017-10-03T06:59:55Z

fixe links

Qlanners: fixed links

2017-10-03T06:59:21Z

fixed links

Qlanners: added file to ppt submission

2017-10-03T06:57:54Z

added file to ppt submission

Qlanners: fixed data

2017-10-03T06:25:44Z

fixed data

Qlanners: word change

2017-10-03T06:12:16Z

word change

Johnllopez616: (John Lopez) Fixed the Week 5 assignment page link

2017-10-03T06:12:12Z

(John Lopez) Fixed the Week 5 assignment page link

Qlanners: made format of headers consistent

2017-10-03T06:11:39Z

made format of headers consistent

Johnllopez616: (John Lopez) Made the template links look more organized, and added titles to the lab notebook.

2017-10-03T06:08:44Z

(John Lopez) Made the template links look more organized, and added titles to the lab notebook.

Johnllopez616: Organized the Links page

2017-10-03T06:04:20Z

Organized the Links page

Johnllopez616: (John Lopez) I added my template

2017-10-03T06:03:26Z

(John Lopez) I added my template

@@ Line 49: / Line 49: @@
 ==Submission==
-[[File:Quinn_Lanners_and_John_Lopez_Biological_Databases_evaluation_of_miRPathDB_Database.pptx]]
+[[Media:Quinn_Lanners_and_John_Lopez_Biological_Databases_evaluation_of_miRPathDB_Database.pptx]]
 ==Acknowledgements==
@@ Line 63: / Line 63: @@
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
-[[Media:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:02, 2 October 2017 (PDT)
+[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:02, 2 October 2017 (PDT)
 ==References==

@@ Line 63: / Line 63: @@
 '''While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.'''
-[[User:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:02, 2 October 2017 (PDT)
+[[Media:Johnllopez616|Johnllopez616]] ([[User talk:Johnllopez616|talk]]) 23:02, 2 October 2017 (PDT)
 ==References==

← Older revision		Revision as of 06:57, 3 October 2017
Line 48:		Line 48:
	After we had both individually researched the answers to our questions, we met for multiple hours on the afternoon of October 2nd to go over the information we have found. After discussing our thoughts on the database, and deciding on how to best present the information, we started a presentation on Google Slides. We began working on the slides together during the remaining time we had together. We then broke up the remaining slides to complete separately in the evening. Through the Chat option on Google Slides and text messaging, we stayed in contact about our progress as we finished the project. Finally, we planned to meet a bit before class on October 3rd to run through the presentation once together.		After we had both individually researched the answers to our questions, we met for multiple hours on the afternoon of October 2nd to go over the information we have found. After discussing our thoughts on the database, and deciding on how to best present the information, we started a presentation on Google Slides. We began working on the slides together during the remaining time we had together. We then broke up the remaining slides to complete separately in the evening. Through the Chat option on Google Slides and text messaging, we stayed in contact about our progress as we finished the project. Finally, we planned to meet a bit before class on October 3rd to run through the presentation once together.

		+	==Submission==
		+	[[File:Quinn_Lanners_and_John_Lopez_Biological_Databases_evaluation_of_miRPathDB_Database.pptx]]

	==Acknowledgements==		==Acknowledgements==

@@ Line 22: / Line 22: @@
 *# Does the content appear to completely cover its content domain? '''Answer:''' This database seems to have very strong coverage of the targets and pathways of mRNAs, but has not information on the mRNAs themselves. While this does align with what the database claims to cover, information on the mRNAs themselves would allow for a more full coverage of the field. '''Source:''' (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)
-*#* How many records does the database contain? '''Answer:''' Contains records for primarily ''Homo sapiens'' but also has records on ''Mus musculus'' for comparison purposes. There are a total of 2,599 human mRNAs contained in the DB with 14,773 experimentally validated target genes and 19281 predicted targets genes. Also a total of 12,875 biochemical pathway categories. As for ''Mus musculus'', there are 1,933 miRNA covered and 8,201 biochemical pathways categories. '''Source:''' (https://mpd.bioinf.uni-sb.de/overview.html) (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
+*#* How many records does the database contain? '''Answer:''' Contains records for primarily ''Homo sapiens'' but also has records on ''Mus musculus'' for comparison purposes. There are a total of 2,599 human mRNAs contained in the DB with 14,773 experimentally validated target genes and 19281 predicted targets genes. Also a total of 12,875 biochemical pathway categories. As for ''Mus musculus'', there are 1,933 miRNA covered and 9,741 biochemical pathways categories. '''Source:''' (https://mpd.bioinf.uni-sb.de/overview.html) (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
 *#* What claims do the database owners make about coverage in the corresponding paper? '''Answer:''' They claim to cover a broad range of mRNAs (primarily in ''Home sapiens'') in regards to target genes, and functional pathways for mRNAs to show how they function. '''Source:''' (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target)
 *# What species are covered in the database? '''Answer:''' Primarily ''Homo sapiens'' with some information on ''Mus musculus'' for comparison purposes. '''Source:''' (https://mpd.bioinf.uni-sb.de/overview.html)

@@ Line 41: / Line 41: @@
 # There are no restrictions on access nor is there a license agreement to use the database. '''Source:''' (https://mpd.bioinf.uni-sb.de/about.html)
-* '''Summary judgment:''' (retrieved on October 2nd by Quinn)
+* '''Summary judgment:''' (answered on October 2nd by Quinn)
 *# Would you direct a colleague unfamiliar with the field to use it? '''Answer''' I would definitely not direct a colleague unfimiliar with the field of miRNA to this website. This website has a very specific function and thus contains very specific data that is only useful to a trained professional that understands how to use the data. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)
 *# Is this a professional or hobby database? '''Answer:''' Branching off of the previous answer, this is most certainly a professional database. The data is so specific and narrow that it really only serves a purpose for a professional who needs this kind of information for research purposes. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)

@@ Line 1: / Line 1: @@
 ==Lab Notebook==
 ===Planning the Project===
-As homework partner, [[User:Qlanners|Quinn Lanners]] and [[User:johnllopez616|John Lopez]] worked together to analyze the [https://mpd.bioinf.uni-sb.de miRPathDB] database by following the template laid out on the [[Weel5|week 5 assignment page]].
+As homework partner, [[User:Qlanners|Quinn Lanners]] and [[User:johnllopez616|John Lopez]] worked together to analyze the [https://mpd.bioinf.uni-sb.de miRPathDB] database by following the template laid out on the [[Week 5|week 5 assignment page]].
 To start this weeks assignment, we selected a database from one of the ones on the [https://academic.oup.com/nar/issue/45/D1 ''Nucleic Acids Research'' Database Issue Table of Contents 2017]. After we had selected a database, and it was approved by [[User:Kdahlquist|Dr. Dahlquist]], we began work on the assignment.

@@ Line 8: / Line 8: @@
 ===Questions===
-*General Information: (answered on October 1st by John)
+*'''General Information:''' (answered on October 1st by John)
 # The name of the database is miRPathDB '''Source:'''  (https://mpd.bioinf.uni-sb.de/overview.html)
 # Two answers:
@@ Line 17: / Line 17: @@
 I aimed to answer the following questions regarding our database:
-* '''Scientific quality of the database''' (answered on October 1st by Quinn)
+* '''Scientific quality of the database:''' (answered on October 1st by Quinn)
 In order to answer these questions I read the [https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target article] covering the miRPathDB from the ''Nucleic Acids Research'' and by analyzing the actual miRPathDB website.
@@ Line 33: / Line 33: @@
 *#* When was the last update? '''Answer:''' Biological categories: 11 Jan 2016. miRNA Targets: 09 Sept 2016. And several of their source databases have been updated since them. '''Source:''' (https://mpd.bioinf.uni-sb.de/documentation.html) (http://www.genome.jp/kegg/pathway.html) (http://reactome.org/cgi-bin/toc?DB=gk_current)
-*General Utility: (answered on October 1st by John)
+*'''General Utility:''' (answered on October 1st by John)
 #Whenever a search is performed for an miRNA molecule, the database provides a link to that molecule from the following sites: (http://www.mirbase.org/). It also directs you to a link that tells you what tissue that molecule might be located in using the following site: (https://ccb-web.cs.uni-saarland.de/tissueatlas/patterns). NOTE: It will link you to these databases whether or not you search a mouse or human miRNA. '''Sources:''' (https://mpd.bioinf.uni-sb.de/mirna.html?mirna=hsa-miR-1976&organism=hsa), (https://mpd.bioinf.uni-sb.de/mirna.html?mirna=hsa-miR-1976&organism=mmu)
@@ Line 41: / Line 41: @@
 # There are no restrictions on access nor is there a license agreement to use the database. '''Source:''' (https://mpd.bioinf.uni-sb.de/about.html)
-* '''Summary judgment''' (retrieved on October 2nd by Quinn)
+* '''Summary judgment:''' (retrieved on October 2nd by Quinn)
 *# Would you direct a colleague unfamiliar with the field to use it? '''Answer''' I would definitely not direct a colleague unfimiliar with the field of miRNA to this website. This website has a very specific function and thus contains very specific data that is only useful to a trained professional that understands how to use the data. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)
 *# Is this a professional or hobby database? '''Answer:''' Branching off of the previous answer, this is most certainly a professional database. The data is so specific and narrow that it really only serves a purpose for a professional who needs this kind of information for research purposes. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)

@@ Line 1: / Line 1: @@
-As homework partner, [[User:Qlanners|Quinn Lanners]] and [[User:johnllopez616|John Lopez]] worked together to analyze the [https://mpd.bioinf.uni-sb.de miRPathDB] database by following the template laid out on the [[Weel_5|week 5 assignment page]].
+==Lab Notebook==
 To start this weeks assignment, we selected a database from one of the ones on the [https://academic.oup.com/nar/issue/45/D1 ''Nucleic Acids Research'' Database Issue Table of Contents 2017]. After we had selected a database, and it was approved by [[User:Kdahlquist|Dr. Dahlquist]], we began work on the assignment.
@@ Line 5: / Line 7: @@
 To make better use of our time, we decided on Thursday to break up the questions between ourselves. Then we could work separately on our own time to find the answers before coming together to put all of the information into a PowerPoint presentation. We decided that John would handle the questions "General Utility" questions of the database, while Quinn would handle the "Scientific Quality" questions of the database. As for the "General Information", which we figured would be easier to determine, we decided to answer those questions each individually as we looked into our specific part. Since the database research was broken up in this manner, the following section of the electronic journal is comprised of two separate accounts from each of us about how we retrieved the answers to our assigned questions.
 *General Information: (answered on October 1st by John)
 # The name of the database is miRPathDB '''Source:'''  (https://mpd.bioinf.uni-sb.de/overview.html)
@@ Line 42: / Line 45: @@
 *# Is this a professional or hobby database? '''Answer:''' Branching off of the previous answer, this is most certainly a professional database. The data is so specific and narrow that it really only serves a purpose for a professional who needs this kind of information for research purposes. (https://academic.oup.com/nar/article/45/D1/D90/2290890/miRPathDB-a-new-dictionary-on-microRNAs-and-target) (https://mpd.bioinf.uni-sb.de/overview.html)
 After we had both individually researched the answers to our questions, we met for multiple hours on the afternoon of October 2nd to go over the information we have found. After discussing our thoughts on the database, and deciding on how to best present the information, we started a presentation on Google Slides. We began working on the slides together during the remaining time we had together. We then broke up the remaining slides to complete separately in the evening. Through the Chat option on Google Slides and text messaging, we stayed in contact about our progress as we finished the project. Finally, we planned to meet a bit before class on October 3rd to run through the presentation once together.
@@ Line 64: / Line 68: @@
 miRPathDB. (2016). Retrieved on October 1, 2017, from https://mpd.bioinf.uni-sb.de/documentation.html
-==Links==
+==QLanners Links==
 {{Template:QLannersLinks}}
 {{Template:johnllopez616}}

← Older revision		Revision as of 06:03, 3 October 2017
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	==QLanners Links==		==QLanners Links==
	{{Template:QLannersLinks}}		{{Template:QLannersLinks}}
		+
		+	==John Lopez Links==
		+	{{Template:johnllopez616}}