Cdomin12 Week 12/13 - Revision history

Cdomin12: /* Milestone 3 */ added replicats

2019-11-21T22:55:30Z

‎Milestone 3: added replicats

Cdomin12: /* Electronic Lab Notebook */ added milestone 3 update

2019-11-21T22:52:57Z

‎Electronic Lab Notebook: added milestone 3 update

Cdomin12: /* Acknowledgments */ added user names

2019-11-21T22:43:06Z

‎Acknowledgments: added user names

Cdomin12: /* Acknowledgments */ added section

2019-11-21T22:42:32Z

‎Acknowledgments: added section

Cdomin12: /* Acknowledgments */ added electronic lab notebook section

2019-11-21T22:40:18Z

‎Acknowledgments: added electronic lab notebook section

Cdomin12: added categories

2019-11-21T22:39:44Z

added categories

Cdomin12: /* 2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)? */ added acknowledmens section

2019-11-18T16:51:00Z

‎2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?: added acknowledmens section

Cdomin12: /* 1.What impact does the choice of keywords have on your results? */ answer

2019-11-16T01:39:34Z

‎1.What impact does the choice of keywords have on your results?: answer

Cdomin12: /* Bibliographic Entries */ added second journal

2019-11-16T01:37:40Z

‎Bibliographic Entries: added second journal

Cdomin12: /* Annotated Bibliography */ answered top questions

2019-11-16T01:20:12Z

‎Annotated Bibliography: answered top questions

@@ Line 73: / Line 73: @@
 *changed "YORF" to "ID" and "Name" to "Standard Name"
 *sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
-*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3,	wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4
+*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3,	wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4 so that replicates are grouped together
 ==Acknowledgments==

← Older revision		Revision as of 22:52, 21 November 2019
Line 69:		Line 69:

	==Electronic Lab Notebook==		==Electronic Lab Notebook==
		+	===Milestone 3===
		+	*deleted Gweight and Eweight since not conducive to our dataset
		+	*changed "YORF" to "ID" and "Name" to "Standard Name"
		+	*sample-data relationship table changed categories to "strain_LogFC_timepoint-replicate number"
		+	*Column Headers were changed to wt_LogFC_t10-1, wt_LogFC_t10-2, wt_LogFC_t20-1, wt_LogFC_t20-2, wt_LogFC_t20-3 , wt_LogFC_t20-4, wt_LogFC_t40-1, wt_LogFC_t40-2, wt_LogFC_t40-3, wt_LogFC_t40-4, wt_LogFC_t60-1, wt_LogFC_t60-2, wt_LogFC_t60-3, wt_LogFC_t60-4, wt_LogFC_t120-1, wt_LogFC_t120-2, wt_LogFC_t120-3, wt_LogFC_t120-4

	==Acknowledgments==		==Acknowledgments==

@@ Line 71: / Line 71: @@
 ==Acknowledgments==
-# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
+# I worked with [[User:ymesfin]], [[User:Jcowan4]], [[User:msamdars]], and [[User:dramir36]] for this assignment.
 [[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)
 ==References==
 *Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

← Older revision		Revision as of 22:42, 21 November 2019
Line 73:		Line 73:
	# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."		# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
	[[User:Cdomin12\|Cdomin12]] ([[User talk:Cdomin12\|talk]]) 08:51, 18 November 2019 (PST)		[[User:Cdomin12\|Cdomin12]] ([[User talk:Cdomin12\|talk]]) 08:51, 18 November 2019 (PST)
		+
		+	==References==
		+	*Week 12/13. Retrieved November 21, 2019, from https://xmlpipedb.cs.lmu.edu/biodb/fall2019/index.php/Week_12/13

@@ Line 67: / Line 67: @@
 *Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
 *Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.
 ==Acknowledgments==
 # "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
 [[User:Cdomin12|Cdomin12]] ([[User talk:Cdomin12|talk]]) 08:51, 18 November 2019 (PST)

← Older revision		Revision as of 22:39, 21 November 2019
Line 1:		Line 1:
	{{template:cdomin12}}		{{template:cdomin12}}
		+
		+	[[category:Group Projects]]
		+	[[category:Skinny Genes]]

	==Annotated Bibliography==		==Annotated Bibliography==

← Older revision		Revision as of 16:51, 18 November 2019
Line 64:		Line 64:
	*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.		*Pubmed: Disadvantages include keywords allowing for specific filters that can limit what is presented as a result. Advantages include a more detailed query for narrowing down searches.
	*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.		*Web of Science: Disadvantages include less up to date results and less relevance in results. Advantages include all articles related to sciences which allows for more diverse results and a university resource. They also have a citation network that allows for connections to all papers referenced.
		+
		+	==Acknowledgments==
		+	# "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."
		+	[[User:Cdomin12\|Cdomin12]] ([[User talk:Cdomin12\|talk]]) 08:51, 18 November 2019 (PST)

@@ Line 58: / Line 58: @@
 ===Reflect===
 ====1.What impact does the choice of keywords have on your results?====
 ====2.What are the advantages and disadvantages of each of the three databases (Pubmed, Google Scholar, Web of Science)?====

@@ Line 38: / Line 38: @@
 # Impact factor: 7.98
 # Primary research article
-# [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/] at bottom of page titled "electronic supplementary material"
+# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"
-# Schade, B., Jansen, G., Whiteway, M., Entian, K.D., & Thomas, D.Y. (2004). Cold Adaptation in Budding Yeast.  ''Molecular Biology of the Cell'', 15, 5492-5502.  doi:  10.1091/mbc.E04-03-0167
+# Martínez, J. L., Luna, C., & Ramos, J. (2012). Proteomic changes in response to potassium starvation in the extremophilic yeast Debaryomyces hansenii. FEMS yeast research, 12(6), 651-661. doi: 10.1111/j.1567-1364.2012.00815.x
-# PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/15483057
+# PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
-# PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
+# PubMed Central: N/A
-# Publisher Full Text (HTML):  http://www.molbiolcell.org/content/15/12/5492.long
+# Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
-# Publisher Full Text (PDF):  http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
+# Publisher Full Text (PDF): https://watermark.silverchair.com/12-6-651.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAmswggJnBgkqhkiG9w0BBwagggJYMIICVAIBADCCAk0GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMS28Gc_64lo0S5ZOsAgEQgIICHmtxEUsoWIF-rzLhH5zoeHZxIody_Cm7QuaVy4dTveZ3QOXd9gDTSDhNWBw3xiiuZ2pmj64dx5LkWYNWeyP99QGzYAD7PHaKm2l96qRjDZYeD_sfIwSfa9LAXr8olcrLKJPjR4uiZtIy7MXncNkU3991cc7PRZWxnTS994vQd0a5rwVFrrwhR3L7Y77HzHxN8Pza3TSHWhxNVxeV4tMiI9pAkH5wlS_EuqKI_6w8RXRQ6NNnswgPr2ky4pjnPY9GSdpcqSVCFkgkJZG4lvXAb-IoYDdMpnZ-DPXIiwC3cbFXrYso8ie9tX8z7i83vv9Hv9GLaEKy9sWIHOq2ig8O0ihELO_td8YEVW-E4c3C2WJCGlaLRlLRrcCHR395-qHDFjnLHaHgiyzIu6KwxloyUS9iFEqp1oLXses5nD9zE_2145xnfA-741mK-a2YWhitStQjtBp7U4xVXL_gF3vxryGy2GK3Ea6n7nvm8faWZGFyvc89MuerMkH4PiCSD6Rh_vcCpcMkweUzxhtWUlTxbobLWAo3CdbxfwQ4S-8Umwf2QrHd7oC9HywBgyRYa3EKxwRWadK_16F8zBE79qd1yFLZhoKovVza7UAJ-2PcuI3enya1zcND1dt-wU_86hdFsOM8bElprCn9gCI4RImIesFpXLJEuHgmdLVpHBNeLoEqAUQj33bcDfggizIRta4f3npaE_6syWqBesGnKw-g
-# Copyright:  2004 by the American Society for Cell Biology (information found on PDF version of article);
+# Copyright:  Federation of European Microbiological Societies
-# Article is not Open Access, but is freely available 2 months after publication, published in the United States, LMU did not pay for the article
+# Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
-# Availability:  in print and online
+# Availability: online
-# Publisher:  American Society for Cell Biology (scientific society), non-profit, not a member of the OAPA
+# Publisher:  Blackwell Publishing, for profit, not a member of the OAPA
-# The journal begain in 1989
+# The journal begain in 1922
-# Peer-reviewed articles: yest
+# Peer-reviewed articles: yes
-# [https://www.molbiolcell.org/editorial-board Editorial board].
+# https://fems-microbiology.org/about_fems/organization/
-# Impact factor: 3.512 (2017)
+# Impact factor: 1.994 (2019)
 # Primary research article
 ===Reflect===

@@ Line 11: / Line 11: @@
 *#** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search? By doing an advanced search of "potassium starvation" and "yeast" gave 4,560 results
 *#* Web of Science
-*#** What original keyword(s) did you use?  How many results did you get?
+*#** What original keyword(s) did you use?  How many results did you get? "potassium starvation" which gave 427 results
-*#** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
+*#** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search? "potassium starvation" and "yeast" gave 60 results
 *# Use the advanced search functions for each of these three databases/tools and answer the following:
 *#* PubMed
@@ Line 19: / Line 19: @@
 *#** Which advanced search functions were most useful to narrow down the search?  How many results did you get? I used "since 2018" to sort more recent studies which gave 9,520 results.
 *#* Web of Science
-*#** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
+*#** Which advanced search functions were most useful to narrow down the search?  How many results did you get? searching "potassium starvation" in abstract yielded 27 results.
 *#* Perform a prospective search on your article in the Web of Science and answer the following:
-*#** How many articles does this article cite?
+*#** How many articles does this article cite? 41 articles
-*#** How many articles cite this article?
+*#** How many articles cite this article? 13 articles
 ===Bibliographic Entries===