Cdomin12 Week 12/13

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Assignment Page	Individual Journal Entries	Class Journal
Week 1	cdomin12 Week 1	Class Journal Week 1
Week 2	cdomin12 Week 2	Class Journal Week 2
Week 3	RAD53 / YPL153C Week 3	Class Journal Week 3
Week 4	cdomin12 Week 4	Class Journal Week 4
Week 5	IMG/VR Week 5	Class Journal Week 5
Week 6	cdomin12 Week 6	Class Journal Week 6
Week 7	cdomin12 Week 7	Class Journal Week 7
Week 8	cdomin12 Week 8	Class Journal Week 8
Week 9	cdomin12 Week 9	Class Journal Week 9
Week 10	cdomin12 Week 10	Class Journal Week 10
Week 11	cdomin12 Week 11	Skinny Genes
Week 12/13	Skinny Genes Quality Assurance	Skinny Genes
Week 15	Skinny Genes Deliverables	Skinny Genes

Annotated Bibliography

• 1. Use a keyword search for the first three databases/tools and answer the following:
     • PubMed
       • What original keyword(s) did you use? How many results did you get? "potassium starvation" which got 521 results
       • 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 31 results
     • Google Scholar
       • What original keyword(s) did you use? How many results did you get? "potassium starvation" gave 133,000 results
       • 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? "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? "potassium starvation" and "yeast" gave 60 results
  2. Use the advanced search functions for each of these three databases/tools and answer the following:
     • PubMed
       • Which advanced search functions were most useful to narrow down the search? How many results did you get? 31 results with "potassium starvation" in title/abstract search
     • Google Scholar
       • 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? 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? 41 articles
       • How many articles cite this article? 13 articles

Bibliographic Entries

1. Anemaet, I. G., & van Heusden, G. P. H. (2014). Transcriptional response of Saccharomyces cerevisiae to potassium starvation. BMC genomics, 15(1), 1040. doi:10.1186/1471-2164-15-1040
2. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/25432801
3. PubMed Central: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/
4. Publisher Full Text (HTML): http://sq4ya5rf2q.search.serialssolutions.com/?V=1.0&sid=PubMed:LinkOut&pmid=25432801
5. Publisher Full Text (PDF): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/pdf/12864_2014_Article_6863.pdf
6. Copyright: BioMed Central. This is an Open Access article.
7. Availability: online
8. Publisher: BioMedCentral, for profit, not a member of the OAPA, in United Kingdom
9. The journal began in 2000
10. Peer-reviewed articles: yes
11. https://bmcbiol.biomedcentral.com/about/editorial-board
12. Impact factor: 7.98
13. Primary research article
14. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4289377/ at bottom of page titled "electronic supplementary material"

1. 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
2. PubMed Abstract: https://www.ncbi.nlm.nih.gov/pubmed/22612992
3. PubMed Central: N/A
4. Publisher Full Text (HTML): https://academic.oup.com/femsyr/article/12/6/651/528233
5. 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
6. Copyright: Federation of European Microbiological Societies
7. Article is not Open Access, does not discuss when it becomes available, published in Europe, LMU did pay for the article
8. Availability: online
9. Publisher: Blackwell Publishing, for profit, not a member of the OAPA
10. The journal begain in 1922
11. Peer-reviewed articles: yes
12. https://fems-microbiology.org/about_fems/organization/
13. Impact factor: 1.994 (2019)
14. Primary research article

Reflect

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

Adding the type of organism that you want results on makes a major difference in the specificity of the results. I found that there has been a lot of work on plants and less work on yeast. Adding that I wanted it for yeast made a difference to find articles that were more relatable.

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

• Google Scholar: Disadvantages include limited capability of narrowing down search and not including DOI number in citations. Advantages include formatted citations and a familiar interface that is user friendly.
• 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.

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

1. I worked with User:ymesfin, User:Jcowan4, User:msamdars, and User:dramir36 for this assignment.
2. "Except for what is noted above, this individual journal entry was completed by me and not copied from another source."

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