Johnllopez Week 14 - Revision history

Johnllopez616: Added link to github

2017-12-05T07:08:59Z

Added link to github

Johnllopez616: /* Acknowledgements and References */ Added acknowledgements

2017-12-05T07:07:00Z

‎Acknowledgements and References: Added acknowledgements

Johnllopez616: Added references

2017-12-05T07:02:57Z

Added references

Johnllopez616: Finished the XML section

2017-12-05T03:30:54Z

Finished the XML section

Johnllopez616: Explained how I got NCBI

2017-12-05T03:25:28Z

Explained how I got NCBI

Johnllopez616: Explained how I used jquery

2017-12-05T03:19:10Z

Explained how I used jquery

Johnllopez616: Added my template

2017-12-05T01:46:51Z

Added my template

Johnllopez616: Added a template for the page structure

2017-12-05T01:46:12Z

Added a template for the page structure

Johnllopez616: /* Pulling Data */ Added how to get the data

2017-11-30T08:50:18Z

‎Pulling Data: Added how to get the data

Johnllopez616: Added table for what information needs to be pulled from where

2017-11-30T08:02:03Z

Added table for what information needs to be pulled from where

New page

==Pulling Data==
Thanks to [[User:cwong34 | 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
*Gene ID

'''UniProt'''
*Protein type/name
*Protein sequence
*Gene ID
*Similar proteins

'''Ensembl'''
*DNA sequence
*Gene description
*Gene ID

'''SGD'''
*Gene ID
*Gene expression
*Gene regulation
*Gene ontology

'''JASPAR'''
*Sequence logo
*Frequency matrixon her

@@ Line 43: / Line 43: @@
 There was one piece of data that I could unfortunately not figure out how to extract because I could not find the API call for it. This is something I will discuss with my partners on Tuesday.
-===Working with JSON===
+You may see the work I completed on github [https://github.com/bhamilton18/GRNsight/blob/gene-database-apis/XML/XMLfunction.js here].
 ==Acknowledgements and References==
 ===Acknowledgements===

@@ Line 46: / Line 46: @@
 ==Acknowledgements and References==
 ===Acknowledgements===
 ===References===
-  MDN. '''Document Object Model'''. Retrieved December 1, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
+  MDN. ''Document Object Model''. Retrieved December 1, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
   LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
   LMU BioDB 2017. (2017). Week 7. Retrieved December 1, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
 {{Template:johnllopez616}}

@@ Line 47: / Line 47: @@
 ===Acknowledgements===
 ===References===
-  https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_7
+  MDN. '''Document Object Model'''. Retrieved December 1, 2017, from https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
-  https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model
+ LMU BioDB 2017. (2017). Week 14. Retrieved December 4, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_14
 {{Template:johnllopez616}}

@@ Line 33: / Line 33: @@
 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.
-I then figured out since XML was a markup language like HTML, I could use the same Document Object Model functions that I would to parse HTML. Of course, I had no idea how to do either, so I used [[https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model | MDN]] to explain certain aspects of it.
+I then figured out since XML was a markup language like HTML, I could use the same Document Object Model functions that I would to parse HTML. Of course, I had no idea how to do either, so I used [https://developer.mozilla.org/en-US/docs/Web/API/Document_Object_Model | MDN] to explain certain aspects of it.
 I figured that the serializeToString() and getElementsByTagName() were useful, so that allowed me to pull lines of XML.
@@ Line 39: / Line 39: @@
 One problem was, such in the case of extracting the LOTUS tag and Other Names data from NCBI, the string that returned contained both pieces of data! The way I got around this was by taking the data as a string, using the split() function to make each word a node of an array, then further manipulating this array using the splice() function to remove the LOTUS tag once it was called.
 ===Working with JSON===

@@ Line 32: / Line 32: @@
 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===
 {{Template:johnllopez616}}

← Older revision		Revision as of 01:46, 5 December 2017
Line 33:		Line 33:
	===Acknowledgements===		===Acknowledgements===
	===References===		===References===
		+	{{Template:johnllopez616}}

@@ Line 1: / Line 1: @@
-==Pulling Data==
+==Electronic Lab Notebook==
 Thanks to [[User:cwong34 | 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:
@@ Line 26: / Line 27: @@
 *Sequence logo
 *Frequency matrixon her

@@ Line 3: / Line 3: @@
 '''NCBI'''
-*Locus tag
+*Locus tag < Parse from page https://www.ncbi.nlm.nih.gov/gene/854068
-*Gene ID
+*Gene ID < Parse from conversion algorithm
 '''UniProt'''
-*Protein type/name
+*Protein type/name <Parse XML?
-*Protein sequence
+*Protein sequence <Parse XML
-*Gene ID
+*Gene ID <Parse XML
-*Similar proteins
+*Similar proteins <Could not find on XML, found on Page
 '''Ensembl'''
-*DNA sequence
+*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
+*Gene description < Pulled from JSON
-*Gene ID
+*Gene ID < Pulled from JSON / Conversion Necessary
 '''SGD'''
-*Gene ID
+*Gene ID < Pulled from JSON/ Possible conversion necessary
-*Gene expression
+*Gene expression < NO IDEA HOW WE CAN PULL THIS
-*Gene regulation
+*Gene regulation <Pull from page https://www.yeastgenome.org/locus/S000005446
-*Gene ontology
+*Gene ontology <SUummary in JSON
 '''JASPAR'''
 *Sequence logo
 *Frequency matrixon her