Mbalducc Week 9 - Revision history

Mbalducc: /* Acknowledgements */

2017-10-31T01:52:15Z

‎Acknowledgements

Mbalducc: /* Web Service API Exploration */

2017-10-31T01:50:13Z

‎Web Service API Exploration

Mbalducc: /* Web Service API Exploration */

2017-10-31T01:47:37Z

‎Web Service API Exploration

Mbalducc: /* References */

2017-10-31T01:45:54Z

‎References

Mbalducc: /* Acknowledgements */

2017-10-31T01:36:46Z

‎Acknowledgements

Mbalducc: /* Notes */

2017-10-31T01:34:58Z

‎Notes

Mbalducc: /* Web Service API Exploration */

2017-10-31T01:32:48Z

‎Web Service API Exploration

Mbalducc: /* Notes */

2017-10-31T01:29:15Z

‎Notes

Mbalducc: /* Notes */

2017-10-31T01:22:36Z

‎Notes

Mbalducc: /* Notes */

2017-10-31T01:17:41Z

‎Notes

@@ Line 132: / Line 132: @@
 =Acknowledgements=
-I worked with my homework partner, [[User:Qlanners|Quinn Lanners]], on this assignment. We were not able to meet in person, but we did communicate over text to make sure we got the same result. For the Web API Exploration, we used the same gene as examples to make sure we both were using the same URLs and that they worked for both of us.
+I worked with my homework partner, [[User:Qlanners|Quinn Lanners]], on this assignment. We were not able to meet in person, but we did communicate over text to make sure we got the same results. For the Web API Exploration, we used the same genes as examples to make sure we both were using the same URLs and that they worked for both of us.
 While I worked with the people noted above, this individual entry was completed by me and not copied from another source.

@@ Line 101: / Line 101: @@
 =Web Service API Exploration=
 *We were assigned the database [https://www.ncbi.nlm.nih.gov/gene NCBI Gene], which uses the data format XML.
-*The first link we used was to go from the gene name to the gene ID. This was:
+*The first link we used was to go from the gene name to the gene ID. This was: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=<gene_name>[gene]+AND+Saccharomyces+cerevisiae[Organism]
 =Notes=

@@ Line 100: / Line 100: @@
 =Web Service API Exploration=
-*We were assigned the database [https://www.ncbi.nlm.nih.gov/gene NCBI Gene], which uses XML
+*We were assigned the database [https://www.ncbi.nlm.nih.gov/gene NCBI Gene], which uses the data format XML.
 =Notes=

@@ Line 134: / Line 134: @@
 =References=
 LMU BioDB 2017. (2017). Week 9. Retrieved October 24, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_9
 {{template:mbalducc}}

@@ Line 127: / Line 127: @@
 =Acknowledgements=
-I worked with my homework partner, [[User:Qlanners|Quinn Lanners]], on this assignment.
+I worked with my homework partner, [[User:Qlanners|Quinn Lanners]], on this assignment. We were not able to meet in person, but we did communicate over text to make sure we got the same result. For the Web API Exploration, we used the same gene as examples to make sure we both were using the same URLs and that they worked for both of us.
 While I worked with the people noted above, this individual entry was completed by me and not copied from another source.

@@ Line 120: / Line 120: @@
 *We then tried this again replacing the "pbs2" term with other genes.
 **This worked to give their IDs as well.
-*The final step was to take the gene ID from that result page and use it to link to the page for that gene, we used another URL from the [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] page to do this.
+*The final step was to take the gene ID from that result page and use it to link to the page for that gene, we used the NCBI URL found in the ajax starter files to do this.
 **We used this link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&id=<query>
 ***The <query> is the gene ID

← Older revision		Revision as of 01:32, 31 October 2017
Line 100:		Line 100:

	=Web Service API Exploration=		=Web Service API Exploration=
		+	*We were assigned the database [https://www.ncbi.nlm.nih.gov/gene NCBI Gene], which uses XML

	=Notes=		=Notes=

@@ Line 102: / Line 102: @@
 =Notes=
-'''Part 1:'''
+'''GRNSight Tests:'''
 *I used the '''21-genes_31-edges_Schade-data_estimation_output.graphml''', '''21-genes_31-edges_Schade-data_estimation_output.sif''', and '''21-genes_31-edges_Schade-data_estimation_output.xlsx''' files for the tests.
 *I checked with my partner to make sure that he got the same results for each test as I did.
-'''Part 2:'''
+'''API Exploration:'''
 *We started by using this [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] page
 *We used the general search link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>
@@ Line 114: / Line 115: @@
 *To narrow down, we added the organism name, ''Saccharomyces cerevisiae'' to the term field, so that the URL became: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2+AND+Saccharomyces+cerivisiae
 **This did narrow the results to 492, but did not get us what we wanted.
-*We searched the [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] page again and found that adding bracketed categories to the terms would give us the results we wanted, so the next URL we tried was: <nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]</nowiki>
+*We searched the [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] page again and found that adding bracketed categories to the terms would give us the results we wanted, so the next URL we tried was: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]
 **This gave only one result, with the ID for PBS2 in ''Saccharomyces cerevisiae'', which was 853313.
 *We then tried this again replacing the "pbs2" term with other genes.
 **This worked to give their IDs as well.
 =Acknowledgements=

@@ Line 108: / Line 108: @@
 *We started by using this [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] page
 *We used the general search link: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=<database>&term=<query>
-**the <database> we were looking in was gene.
+**The <database> we were looking in was gene.
-**the <query> is whatever gene you are looking for.
+**The <query> is whatever gene you are looking for.
 *The example we used first was https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2
 **This gave 539 results, so we had to narrow this down to genes contained within one organism, ''Saccharomyces cerevisiae''.
@@ Line 115: / Line 115: @@
 **This did narrow the results to 492, but did not get us what we wanted.
 *We searched the [https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database| Searching a Database] page again and found that adding bracketed categories to the terms would give us the results we wanted, so the next URL we tried was: <nowiki>https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=gene&term=pbs2[gene]+AND+Saccharomyces+cerevisiae[Organism]</nowiki>
 =Acknowledgements=