Difference between revisions of "Johnllopez Week 14"

Revision as of 03:19, 5 December 2017

Electronic Lab Notebook

Pulling Data

Thanks to Corrine Wong, I was able to use the following table to figure out what processes had to be made in order to pull certain data from the functions:

NCBI

• Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
• Gene ID < Parse from conversion algorithm

UniProt

• Protein type/name <Parse XML?
• Protein sequence <Parse XML
• Gene ID <Parse XML
• Similar proteins <Could not find on XML, found on Page

Ensembl

• DNA sequence < Pull from http://www.ensembl.org/Saccharomyces_cerevisiae/Transcript/Sequence_cDNA?db=core;g=YJL128C;r=X:178097-180103;t=YJL128C
• Gene description < Pulled from JSON
• Gene ID < Pulled from JSON / Conversion Necessary

SGD

• Gene ID < Pulled from JSON/ Possible conversion necessary
• Gene expression < NO IDEA HOW WE CAN PULL THIS
• Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
• Gene ontology <SUummary in JSON

JASPAR

• Sequence logo
• Frequency matrixon her

Learning XML DOM

I was first tasked to figure out how to extract data from XML files. This was necessary to pull the pieces above marked "XML". I did so by using aspects from the jQuery library and XML Document Object Model.

The functions I used from jQuery were $get and $append, and I learned how to use these thanks to the Week 7 assignment. They allowed me to directly pull XML files from a query and append to a webpage. The next challenge was figuring out how to parse the data given to me and extract what I need.

Working with JSON

Acknowledgements and References

Acknowledgements

References

Individual Journal Entries and Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14
• Week 15

Class Assignments

• Week 1
• Week 2
• Week 3
• Week 4
• Week 5
• Week 6
• Week 7
• Week 8
• Week 9
• Week 10
• Week 11
• Week 12
• Week 14
• Week 15

Class Weekly Journal Entries / Project Weekly Journal Entries

• Class Weekly Journal 1
• Class Weekly Journal 2
• Class Weekly Journal 3
• Class Weekly Journal 4
• Class Weekly Journal 5
• Class Weekly Journal 6
• Class Weekly Journal 7
• Class Weekly Journal 8
• Class Weekly Journal 9
• Class Weekly Journal 10
• Class Weekly Journal 11
• Project Journal Week 12
• Project Journal Week 14
• Project Journal Week 15

My Page

• My User Page