ExGenbank-new - Revision history

Carol at 14:46, 28 August 2026

2026-08-28T14:46:36Z

← Older revision		Revision as of 16:46, 28 August 2026
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	:: b) How many search results do you get now?		:: b) How many search results do you get now?
	Notice: There are several possible answers to this question, as it will be a balance between filtering out False Positives (things that are NOT insulin) without filtering out (too many) True Positives (things that are actually insulin). <br/><br/>		Notice: There are several possible answers to this question, as it will be a balance between filtering out False Positives (things that are NOT insulin) without filtering out (too many) True Positives (things that are actually insulin). <br/><br/>

	~~----~~

	==Part 3: On your own==		==Part 3: On your own==

Carol at 14:46, 28 August 2026

2026-08-28T14:46:10Z

← Older revision		Revision as of 16:46, 28 August 2026
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	----		----

	==~~= "Free exercise" =~~==		==Part 3: On your own==
	[[Image:Cogs_brain.png\|50px]]		[[Image:Cogs_brain.png\|50px]]
	Now it's time to perform a number of GenBank searches on your own. It's important to think about the search strategy - discuss this within the group.		Now it's time to perform a number of GenBank searches on your own. It's important to think about the search strategy - discuss this within the group.

Carol: /* Combining search terms using boolean operators: NOT, AND and OR */

2026-08-28T14:43:50Z

Combining search terms using boolean operators: NOT, AND and OR

← Older revision		Revision as of 16:43, 28 August 2026
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	would exclude some real insulin hits that just happened to mention "receptor" in some reference!		would exclude some real insulin hits that just happened to mention "receptor" in some reference!

	* '''The final part of the exercise to continue to ~~find~~ terms to exclude ~~on your own hand~~.~~'''~~ The point is to bring down the number of search results to a level where it's easy to pick the correct ones. '''Remember:''' the task is to find full length insulin genes from as many different organisms as possible using the Title field.		The final part of the exercise is to continue to finding terms to exclude. The point is to bring down the number of search results to a level where it's easy to pick the correct ones. '''Remember:''' the task is to find full length insulin genes from as many different organisms as possible using the Title field.

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]

Carol: /* Combining search terms using boolean operators: NOT, AND and OR */

2026-08-28T14:41:57Z

Combining search terms using boolean operators: NOT, AND and OR

← Older revision		Revision as of 16:41, 28 August 2026
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	Our next task will be to find full length insulin genes from ''as many different organisms as possible'' using the <u>Title</u> field. Note that it might have been easier to use the <u>Protein name</u> or <u>Keyword</u> fields, but with <u>Title</u> we can immediately see the results of what we are doing, so we are using it for pedagogical reasons. We will now type the searches directly into the Search Box without using the Search Builder.		Our next task will be to find full length insulin genes from ''as many different organisms as possible'' using the <u>Title</u> field. Note that it might have been easier to use the <u>Protein name</u> or <u>Keyword</u> fields, but with <u>Title</u> we can immediately see the results of what we are doing, so we are using it for pedagogical reasons. We will now type the searches directly into the Search Box without using the Search Builder.

	* '''Let's start out with a new clean search for Insulin:~~'''~~		Let's start out with a new clean search for Insulin:
	Query:		Query:
	<pre style="overflow:auto;">		<pre style="overflow:auto;">

Carol: /* Advanced search */

2026-08-28T14:38:07Z

Advanced search

← Older revision		Revision as of 16:38, 28 August 2026
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	[[Image:keys1a.png\|right\|frame\|link=http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers\|It's possible to restrict the search to specific fields in the GenBank entires [http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers (click to open the entire list)]]]		[[Image:keys1a.png\|right\|frame\|link=http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers\|It's possible to restrict the search to specific fields in the GenBank entires [http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers (click to open the entire list)]]]

	~~'''~~Now we are going to narrow down the search to specific parts of the annotation.~~'''~~		Now we are going to narrow down the search to specific parts of the annotation.

	* ~~'''~~Click on <u>Advanced</u> in the top of the page.~~'''~~ <br/> This brings up a form with a "<u>Search Builder</u>" that can be used to select and combine terms restricted to specific fields.		* Click on <u>Advanced</u> in the top of the page. <br/> This brings up a form with a "<u>Search Builder</u>" that can be used to select and combine terms restricted to specific fields.
	* Select "<u>Organism</u>" and enter <tt>human</tt>.		* Select "<u>Organism</u>" and enter <tt>human</tt>.
	* Select "<u>Title</u>" and enter <tt>insulin</tt>.		* Select "<u>Title</u>" and enter <tt>insulin</tt>.

Carol: /* Part 2: Searching GenBank */

2026-08-28T14:37:09Z

Part 2: Searching GenBank

← Older revision		Revision as of 16:37, 28 August 2026
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	:: b) Can you find the human insulin entry? (If yes, write down its title and Accession)		:: b) Can you find the human insulin entry? (If yes, write down its title and Accession)
	:: c) How was your search interpreted by the system (the SEARCH DETAILS box)?		:: c) How was your search interpreted by the system (the SEARCH DETAILS box)?

			<blockquote style="background-color: lavender; border: solid thin grey;">
			'''But why did the naïve search for "human insulin" go so well?'''
			* If you just need a single (and well-known) gene from one of the well-known model organism, it will indeed work very well to do a simple search. (Much like when you do a Google search and get your desired hit on the first page).
			* However, there are some situations where it's beneficial to specify the search in more details - e.g. for building data sets of the same gene across multiple species, or just trying to locate a slightly more obscure gene. (Same as when the link you were looking for at Google was on page 10+ and you have to provide more accurate search terms).
			</blockquote>

	------		------
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	# Simply writing the advanced search string yourself (e.g. "insulin[title]" - to search in the title field)		# Simply writing the advanced search string yourself (e.g. "insulin[title]" - to search in the title field)
	# Using the "Search builder" to put together the query bit by bit.		# Using the "Search builder" to put together the query bit by bit.

	~~<blockquote style="background-color: lavender; border: solid thin grey;">~~
	~~'''But why did the naïve search for "human insulin" go so well?'''~~
	* If you just need a single (and well-known) gene from one of the well-known model organism, it will indeed work very well to do a simple search. (Much like when you do a Google search and get your desired hit on the first page).
	* However, there are some situations where it's beneficial to specify the search in more details - e.g. for building data sets of the same gene across multiple species, or just trying to locate a slightly more obscure gene. (Same as when the link you were looking for at Google was on page 10+ and you have to provide more accurate search terms).
	~~</blockquote>~~

	[[Image:keys1a.png\|right\|frame\|link=http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers\|It's possible to restrict the search to specific fields in the GenBank entires [http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers (click to open the entire list)]]]		[[Image:keys1a.png\|right\|frame\|link=http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers\|It's possible to restrict the search to specific fields in the GenBank entires [http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers (click to open the entire list)]]]

Carol: /* How the search is interpreted */

2026-08-28T14:30:50Z

How the search is interpreted

← Older revision		Revision as of 16:30, 28 August 2026
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	By default the search term is matched against ALL POSSIBLE fields in the GenBank entries - including almost all text in the HEADER and FEATURE table. It's even possible to pick up entries where the match is to one of the authors names and not a gene name! (Perhaps not an issue for insulin). Luckily it is possible to restrict the search to specific pre-indexed fields in the HEADER and FEATURE table ("''Search fields''"), which makes it possible to make the search much more focused.		By default the search term is matched against ALL POSSIBLE fields in the GenBank entries - including almost all text in the HEADER and FEATURE table. It's even possible to pick up entries where the match is to one of the authors names and not a gene name! (Perhaps not an issue for insulin). Luckily it is possible to restrict the search to specific pre-indexed fields in the HEADER and FEATURE table ("''Search fields''"), which makes it possible to make the search much more focused.

	Now spend a few moments to investigate the HEADER section of the GenBank ~~entry you have all received as a hand-out (<tt>'''X01831'''</tt>)~~ to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).		Now spend a few moments to investigate the HEADER section of one of the GenBank entries to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).

	===Searching for human insulin===		===Searching for human insulin===

Carol: /* How the search is interpreted */

2026-08-28T14:29:16Z

How the search is interpreted

← Older revision		Revision as of 16:29, 28 August 2026
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	:: '''QUESTION 2.1:'''		:: '''QUESTION 2.1:'''
	:: d) How your search for "insulin" has been interpreted?		:: d) How your search for "insulin" has been interpreted?

	By default the search term is matched against ALL POSSIBLE fields in the GenBank entries - including almost all text in the HEADER and FEATURE table. It's even possible to pick up entries where the match is to one of the authors names and not a gene name! (Perhaps not an issue for insulin). Luckily it is possible to restrict the search to specific pre-indexed fields in the HEADER and FEATURE table ("''Search fields''"), which makes it possible to make the search much more focused.

	Try to find a search result that appears NOT to be the real insulin gene, and see why it was picked up by the search. If you have trouble finding one in your own result, search for '''DL142095.1''' which came up around page 200 when the exercise was written.		Try to find a search result that appears NOT to be the real insulin gene, and see why it was picked up by the search. If you have trouble finding one in your own result, search for '''DL142095.1''' which came up around page 200 when the exercise was written.

	The main issue here is that we find entries where "insulin" is mentioned anywhere in the entry, and sometimes it's unrelated genes like "Insulin-receptor", "Insulin inhibitor" etc.		The main issue here is that we find entries where "insulin" is mentioned anywhere in the entry, and sometimes it's unrelated genes like "Insulin-receptor", "Insulin inhibitor" etc.

			By default the search term is matched against ALL POSSIBLE fields in the GenBank entries - including almost all text in the HEADER and FEATURE table. It's even possible to pick up entries where the match is to one of the authors names and not a gene name! (Perhaps not an issue for insulin). Luckily it is possible to restrict the search to specific pre-indexed fields in the HEADER and FEATURE table ("''Search fields''"), which makes it possible to make the search much more focused.

	Now spend a few moments to investigate the HEADER section of the GenBank entry you have all received as a hand-out (<tt>'''X01831'''</tt>) to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).		Now spend a few moments to investigate the HEADER section of the GenBank entry you have all received as a hand-out (<tt>'''X01831'''</tt>) to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).


	===Searching for human insulin===		===Searching for human insulin===

Carol: /* Part 2: Searching GenBank */

2026-08-28T14:28:16Z

Part 2: Searching GenBank

← Older revision		Revision as of 16:28, 28 August 2026
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	Why does such a simple search return so many different entries?		Why does such a simple search return so many different entries?

	By default the search term is matched against ALL POSSIBLE fields in the GenBank entries - including almost all text in the HEADER and FEATURE table. It's even possible to pick up entries where the match is to one of the authors names and not a gene name! (Perhaps not an issue for insulin). Luckily it is possible to restrict the search to specific pre-indexed fields in the HEADER and FEATURE table ("''Search fields''"), which makes it possible to make the search much more focused.

	===How the search is interpreted===		===How the search is interpreted===
	When you do a naïve search ~~(without specifying any field)~~ GenBank ~~tried~~ to interpret what you most likely meant, it is has a behind-the-scene scheme to sorting the results to push the most interesting ones to the top. It is actually possible to see exactly how your search query is interpreted by locating the '''SEARCH DETAILS''' box.		When you do a naïve search GenBank tries to interpret what you most likely meant, it is has a behind-the-scene scheme to sorting the results to push the most interesting ones to the top. It is actually possible to see exactly how your search query is interpreted by locating the '''SEARCH DETAILS''' box.

	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
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	:: d) How your search for "insulin" has been interpreted?		:: d) How your search for "insulin" has been interpreted?

	~~Spend a few moments~~ to ~~investigate~~ the ~~HEADER section~~ of the ~~GenBank entry you have all received as~~ a ~~hand-out~~ (~~<tt>'''X01831'''</tt>~~) to ~~get an idea of how~~ the ~~data is related~~ to specific ~~sections~~ (~~e.g. <tt>~~'''~~KEYWORDS~~'~~''</tt> and <tt>'''ORGANISM'''</tt>~~ which ~~we will use in a moment)~~.		By default the search term is matched against ALL POSSIBLE fields in the GenBank entries - including almost all text in the HEADER and FEATURE table. It's even possible to pick up entries where the match is to one of the authors names and not a gene name! (Perhaps not an issue for insulin). Luckily it is possible to restrict the search to specific pre-indexed fields in the HEADER and FEATURE table ("''Search fields''"), which makes it possible to make the search much more focused.

	Try to find a search result that appears NOT to be the real insulin gene, and see why it was picked up by the search. If you have trouble finding one in your own result, search for '''DL142095.1''' which came up around page 200 when the exercise was written.		Try to find a search result that appears NOT to be the real insulin gene, and see why it was picked up by the search. If you have trouble finding one in your own result, search for '''DL142095.1''' which came up around page 200 when the exercise was written.

	The main issue here is that we find entries where "insulin" is mentioned anywhere in the entry, and sometimes it's unrelated genes like "Insulin-receptor", "Insulin inhibitor" etc.		The main issue here is that we find entries where "insulin" is mentioned anywhere in the entry, and sometimes it's unrelated genes like "Insulin-receptor", "Insulin inhibitor" etc.

			Now spend a few moments to investigate the HEADER section of the GenBank entry you have all received as a hand-out (<tt>'''X01831'''</tt>) to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).


	===Searching for human insulin===		===Searching for human insulin===

Carol: /* How the search is interpreted */

2026-08-28T14:18:52Z

How the search is interpreted

← Older revision		Revision as of 16:18, 28 August 2026
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	[[Image:Office-notes-line_drawing.png\|30px\|left]]		[[Image:Office-notes-line_drawing.png\|30px\|left]]
	:: '''QUESTION 2.1:'''		:: '''QUESTION 2.1:'''
	:: d) ~~What have~~ your search for "insulin" been ~~expanded into~~?		:: d) How your search for "insulin" has been interpreted?

	Spend a few moments to investigate the HEADER section of the GenBank entry you have all received as a hand-out (<tt>'''X01831'''</tt>) to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).		Spend a few moments to investigate the HEADER section of the GenBank entry you have all received as a hand-out (<tt>'''X01831'''</tt>) to get an idea of how the data is related to specific sections (e.g. <tt>'''KEYWORDS'''</tt> and <tt>'''ORGANISM'''</tt> which we will use in a moment).