ExUniProt-answers - Revision history

Henni at 14:00, 16 September 2025

2025-09-16T14:00:48Z

← Older revision		Revision as of 16:00, 16 September 2025
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	The numbers are found using UniProt on Sep 17, ~~2024~~		The numbers are found using UniProt 2025_03 on Sep 16, 2025

	==Simple text mining==		==Simple text mining==

Henni: /* On your own */

2025-09-16T13:59:53Z

On your own

← Older revision		Revision as of 15:59, 16 September 2025
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	== On your own ==		== On your own ==

	QUESTION 4.1: <tt>(taxonomy_id:562)</tt>, ~~775~~,~~137~~ hits.		QUESTION 4.1: <tt>(taxonomy_id:562)</tt>, 762,443 hits.

	QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 14,~~589~~ hits.		QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 18,197 hits.

	QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, ~~558~~ hits<br>		QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, 602 hits<br>
	(This is a question that does not have one single correct answer)		(This is a question that does not have one single correct answer)

Henni: /* Advanced search */

2025-09-16T13:53:13Z

Advanced search

← Older revision		Revision as of 15:53, 16 September 2025
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	==Advanced search==		==Advanced search==

	'''QUESTION 3.1:''' How many proteins did you find, and what was the search string (the text in the search field)? <br>17,~~883~~,~~532~~, of these 44,~~569~~ from Swiss-Prot<br><tt>(ft_signal:*)</tt>		'''QUESTION 3.1:''' How many proteins did you find, and what was the search string (the text in the search field)? <br>18,656,301, of these 45,100 from Swiss-Prot<br><tt>(ft_signal:*)</tt>

	'''QUESTION 3.2:''' How many proteins do you find now, and what has the search string changed into? <br>3,~~854~~, they are ''all'' from Swiss-Prot<br><tt>(ft_signal_exp:*)</tt><br>Note that the "experimental" evidence is only found in Swiss-Prot entries, not in TrEMBL!		'''QUESTION 3.2:''' How many proteins do you find now, and what has the search string changed into? <br>3,891, they are ''all'' from Swiss-Prot<br><tt>(ft_signal_exp:*)</tt><br>Note that the "experimental" evidence is only found in Swiss-Prot entries, not in TrEMBL!

	'''QUESTION 3.3:''' How many proteins do you find now, and what is the search string? <br>734<br><tt>(ft_signal_exp:*) AND (organism_id:9606)</tt>		'''QUESTION 3.3:''' How many proteins do you find now, and what is the search string? <br>734<br><tt>(ft_signal_exp:*) AND (organism_id:9606)</tt>

	'''QUESTION 3.4:''' How many proteins are there in UniProt from ''Bacillus subtilis'' with the default TaxID [1423]? <br>18,~~684~~ results, of these only 62 from Swiss-Prot<br><tt>(organism_id:1423)</tt>		'''QUESTION 3.4:''' How many proteins are there in UniProt from ''Bacillus subtilis'' with the default TaxID [1423]? <br>18,297 results, of these only 63 from Swiss-Prot<br><tt>(organism_id:1423)</tt>

	'''QUESTION 3.5:''' How many proteins are there in UniProt from ''Bacillus subtilis'' in total (all strains and subspecies)? <br>43,~~300~~, of these 4,~~279~~ from Swiss-Prot<br><tt>(taxonomy_id:1423)</tt>		'''QUESTION 3.5:''' How many proteins are there in UniProt from ''Bacillus subtilis'' in total (all strains and subspecies)? <br>35,762, of these 4,280 from Swiss-Prot<br><tt>(taxonomy_id:1423)</tt>

	'''QUESTION 3.6:''' How many proteins of maximum length 10 do you find? <br>47,~~000~~ <br><tt>(length:[1 TO 10])</tt>		'''QUESTION 3.6:''' How many proteins of maximum length 10 do you find? <br>46,068 <br><tt>(length:[1 TO 10])</tt>

	'''QUESTION 3.7:''' How many proteins are now left? <br>1,~~322~~ <br><tt>(length:[1 TO 10]) AND (existence:1)</tt>		'''QUESTION 3.7:''' How many proteins are now left? <br>1,350 <br><tt>(length:[1 TO 10]) AND (existence:1)</tt>

	'''QUESTION 3.8:''' How many proteins are now left? <br>~~877~~ <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false)</tt>		'''QUESTION 3.8:''' How many proteins are now left? <br>905 <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false)</tt>

	'''QUESTION 3.9:''' How many human non-fragment proteins of maximum length 10 do you find in UniProt? <br>6 <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false) AND (organism_id:9606)</tt>		'''QUESTION 3.9:''' How many human non-fragment proteins of maximum length 10 do you find in UniProt? <br>6 <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false) AND (organism_id:9606)</tt>

Henni: /* Simple text mining */

2025-09-16T13:33:53Z

Simple text mining

← Older revision		Revision as of 15:33, 16 September 2025
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	'''QUESTION 1.1:'''		'''QUESTION 1.1:'''
	# How many hits do you find? <br>8,~~061~~		# How many hits do you find? <br>9,722
	# How many of these hits are from Swiss-Prot? <br>1,~~704~~		# How many of these hits are from Swiss-Prot? <br>1,764
	# Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? <br>It's P01308 / INS_HUMAN (not necessarily the top hit, but still on the first page).		# Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? <br>It's P01308 / INS_HUMAN (not necessarily the top hit, but still on the first page).

	'''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot? <br>1,~~769~~ and 1,~~126~~		'''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot? <br>1,915 and 1,181

	'''QUESTION 1.3:''' How many hits are now left? How many of these are from Swiss-Prot? <br>~~201~~ and 60, search string: <tt>(organism_id:9606) AND (protein_name:insulin)</tt>		'''QUESTION 1.3:''' How many hits are now left? How many of these are from Swiss-Prot? <br>202 and 60, search string: <tt>(organism_id:9606) AND (protein_name:insulin)</tt>

	'''QUESTION 1.4:''' How many hits are now left? How many of these are from Swiss-Prot? <br>~~102~~ and 25, search string: <tt>(organism_id:9606) AND (protein_name:insulin) NOT (protein_name:insulin-like)</tt>		'''QUESTION 1.4:''' How many hits are now left? How many of these are from Swiss-Prot? <br>103 and 25, search string: <tt>(organism_id:9606) AND (protein_name:insulin) NOT (protein_name:insulin-like)</tt>

	'''QUESTION 1.5:'''		'''QUESTION 1.5:'''
	# How did you do this? <br>by adding <tt>NOT (protein_name:receptor)</tt> to the query box.		# How did you do this? <br>by adding <tt>NOT (protein_name:receptor)</tt> to the query box.
	# How many hits are now left? How many of these are from Swiss-Prot? <br>52 and 16		# How many hits are now left? How many of these are from Swiss-Prot? <br>53 and 16

	==The contents of UniProt==		==The contents of UniProt==

Henni at 14:54, 17 September 2024

2024-09-17T14:54:13Z

← Older revision		Revision as of 16:54, 17 September 2024
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	The numbers are found using UniProt ~~Beta~~ on Sep 12, ~~2022~~		The numbers are found using UniProt on Sep 17, 2024

	==Simple text mining==		==Simple text mining==

Henni: /* On your own */

2024-09-17T14:49:21Z

On your own

← Older revision		Revision as of 16:49, 17 September 2024
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	QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 14,589 hits.		QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 14,589 hits.

	QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, 558 hits		QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, 558 hits<br>
			(This is a question that does not have one single correct answer)

	QUESTION 4.4: <tt>(protein_name:"alpha globin") AND (taxonomy_id:9845) NOT (protein_name:"transcription factor")</tt>, 17 hits.		QUESTION 4.4: <tt>(protein_name:"alpha globin") AND (taxonomy_id:9845) NOT (protein_name:"transcription factor")</tt>, 17 hits.

	QUESTION 4.5: <tt>(protein_name:"alpha-* globin") AND (taxonomy_id:8932)</tt>, 2 hits.		QUESTION 4.5: <tt>(protein_name:"alpha-* globin") AND (taxonomy_id:8932)</tt>, 2 hits.

Henni: /* On your own */

2024-09-17T14:42:35Z

On your own

← Older revision		Revision as of 16:42, 17 September 2024
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	== On your own ==		== On your own ==

	QUESTION 4.1: <tt>(taxonomy_id:562)</tt>, 1,~~075,614~~ hits.		QUESTION 4.1: <tt>(taxonomy_id:562)</tt>, 775,137 hits.

	QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 14,~~594~~ hits.		QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 14,589 hits.

	QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, ~~545~~ hits		QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, 558 hits

	QUESTION 4.4: <tt>(protein_name:"alpha globin") AND (taxonomy_id:9845) NOT (protein_name:"transcription factor")</tt>, 17 hits.		QUESTION 4.4: <tt>(protein_name:"alpha globin") AND (taxonomy_id:9845) NOT (protein_name:"transcription factor")</tt>, 17 hits.

	QUESTION 4.5: <tt>(protein_name:"alpha-* globin") AND (taxonomy_id:8932)</tt>, 2 hits.		QUESTION 4.5: <tt>(protein_name:"alpha-* globin") AND (taxonomy_id:8932)</tt>, 2 hits.

Henni: /* Advanced search */

2024-09-17T14:37:50Z

Advanced search

← Older revision		Revision as of 16:37, 17 September 2024
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	==Advanced search==		==Advanced search==

	'''QUESTION 3.1:''' How many proteins did you find, and what was the search string (the text in the search field)? <br>18,~~229~~,~~549~~, of these 44,~~113~~ from Swiss-Prot<br><tt>(ft_signal:*)</tt>		'''QUESTION 3.1:''' How many proteins did you find, and what was the search string (the text in the search field)? <br>17,883,532, of these 44,569 from Swiss-Prot<br><tt>(ft_signal:*)</tt>

	'''QUESTION 3.2:''' How many proteins do you find now, and what has the search string changed into? <br>3,~~826~~, they are ''all'' from Swiss-Prot<br><tt>(ft_signal_exp:*)</tt><br>Note that the "experimental" evidence is only found in Swiss-Prot entries, not in TrEMBL!		'''QUESTION 3.2:''' How many proteins do you find now, and what has the search string changed into? <br>3,854, they are ''all'' from Swiss-Prot<br><tt>(ft_signal_exp:*)</tt><br>Note that the "experimental" evidence is only found in Swiss-Prot entries, not in TrEMBL!

	'''QUESTION 3.3:''' How many proteins do you find now, and what is the search string? <br>~~732~~<br><tt>(ft_signal_exp:*) AND (organism_id:9606)</tt>		'''QUESTION 3.3:''' How many proteins do you find now, and what is the search string? <br>734<br><tt>(ft_signal_exp:*) AND (organism_id:9606)</tt>

	'''QUESTION 3.4:''' How many proteins are there in UniProt from ''Bacillus subtilis'' with the default TaxID [1423]? <br>43,~~759~~, of these only 62 from Swiss-Prot<br><tt>(organism_id:1423)</tt>		'''QUESTION 3.4:''' How many proteins are there in UniProt from ''Bacillus subtilis'' with the default TaxID [1423]? <br>18,684 results, of these only 62 from Swiss-Prot<br><tt>(organism_id:1423)</tt>

	'''QUESTION 3.5:''' How many proteins are there in UniProt from ''Bacillus subtilis'' in total (all strains and subspecies)? <br>77,~~776~~, of these 4,279 from Swiss-Prot<br><tt>(taxonomy_id:1423)</tt>		'''QUESTION 3.5:''' How many proteins are there in UniProt from ''Bacillus subtilis'' in total (all strains and subspecies)? <br>43,300, of these 4,279 from Swiss-Prot<br><tt>(taxonomy_id:1423)</tt>

	'''QUESTION 3.6:''' How many proteins of maximum length 10 do you find? <br>46,~~956~~ <br><tt>(length:[1 TO 10])</tt>		'''QUESTION 3.6:''' How many proteins of maximum length 10 do you find? <br>47,000 <br><tt>(length:[1 TO 10])</tt>

	'''QUESTION 3.7:''' How many proteins are now left? <br>1,~~317~~ <br><tt>(length:[1 TO 10]) AND (existence:1)</tt>		'''QUESTION 3.7:''' How many proteins are now left? <br>1,322 <br><tt>(length:[1 TO 10]) AND (existence:1)</tt>

	'''QUESTION 3.8:''' How many proteins are now left? <br>~~873~~ <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false)</tt>		'''QUESTION 3.8:''' How many proteins are now left? <br>877 <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false)</tt>

	'''QUESTION 3.9:''' How many human non-fragment proteins of maximum length 10 do you find in UniProt? <br>6 <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false) AND (organism_id:9606)</tt>		'''QUESTION 3.9:''' How many human non-fragment proteins of maximum length 10 do you find in UniProt? <br>6 <br><tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false) AND (organism_id:9606)</tt>

Henni: /* Simple text mining */

2024-09-17T14:24:00Z

Simple text mining

← Older revision		Revision as of 16:24, 17 September 2024
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	'''QUESTION 1.1:'''		'''QUESTION 1.1:'''
	# How many hits do you find? <br>4,~~796~~		# How many hits do you find? <br>8,061
	# How many of these hits are from Swiss-Prot? <br>1,~~667~~		# How many of these hits are from Swiss-Prot? <br>1,704
	# Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? <br>It's P01308 / INS_HUMAN (not the top hit, but still on the first page).		# Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? <br>It's P01308 / INS_HUMAN (not necessarily the top hit, but still on the first page).

	'''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot? <br>1,~~569~~ and 1,~~101~~		'''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot? <br>1,769 and 1,126

	'''QUESTION 1.3:''' How many hits are now left? How many of these are from Swiss-Prot? <br>~~203~~ and 60, search string: <tt>(organism_id:9606) AND (protein_name:insulin)</tt>		'''QUESTION 1.3:''' How many hits are now left? How many of these are from Swiss-Prot? <br>201 and 60, search string: <tt>(organism_id:9606) AND (protein_name:insulin)</tt>

	'''QUESTION 1.4:''' How many hits are now left? How many of these are from Swiss-Prot? <br>~~101~~ and 25, search string: <tt>(organism_id:9606) AND (protein_name:insulin) NOT (protein_name:insulin-like)</tt>		'''QUESTION 1.4:''' How many hits are now left? How many of these are from Swiss-Prot? <br>102 and 25, search string: <tt>(organism_id:9606) AND (protein_name:insulin) NOT (protein_name:insulin-like)</tt>

	'''QUESTION 1.5:'''		'''QUESTION 1.5:'''

WikiSysop: Created page with " The numbers are found using UniProt Beta on Sep 12, 2022 ==Simple text mining== '''QUESTION 1.1:''' # How many hits do you find?
4,796 # How many of these hits are from Swiss-Prot?
1,667 # Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)?
It's P01308 / INS_HUMAN (not the top hit, but still on the first page). '''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot?
2024-03-15T08:42:52Z

Created page with " The numbers are found using UniProt Beta on Sep 12, 2022 ==Simple text mining== '''QUESTION 1.1:''' # How many hits do you find? 4,796 # How many of these hits are from Swiss-Prot? 1,667 # Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? It's P01308 / INS_HUMAN (not the top hit, but still on the first page). '''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot? <b..."

New page

The numbers are found using UniProt Beta on Sep 12, 2022

==Simple text mining==

'''QUESTION 1.1:'''
# How many hits do you find? 4,796
# How many of these hits are from Swiss-Prot? 1,667
# Can you identify the correct hit (''i.e.'' see which one is actually human insulin and not something else)? It's P01308 / INS_HUMAN (not the top hit, but still on the first page).

'''QUESTION 1.2:''' How many hits are now left? How many of these are from Swiss-Prot? 1,569 and 1,101

'''QUESTION 1.3:''' How many hits are now left? How many of these are from Swiss-Prot? 203 and 60, search string: <tt>(organism_id:9606) AND (protein_name:insulin)</tt>

'''QUESTION 1.4:''' How many hits are now left? How many of these are from Swiss-Prot? 101 and 25, search string: <tt>(organism_id:9606) AND (protein_name:insulin) NOT (protein_name:insulin-like)</tt>

'''QUESTION 1.5:'''
# How did you do this? by adding <tt>NOT (protein_name:receptor)</tt> to the query box.
# How many hits are now left? How many of these are from Swiss-Prot? 52 and 16

==The contents of UniProt==

'''QUESTION 2.1:'''
# How many references are there in the insulin entry? 36
# Why do you think insulin is such a highly investigated protein? Because it is linked to a common and serious disease (diabetes) and used as a drug.

'''QUESTION 2.2:'''
# Where do you find insulin? It is secreted from the cell (this is written just below the section heading. Under GO - Cellular component you can find additional locations mentioned, such as endoplasmic reticulum lumen, but these are temporary stages on the way to secretion).
# Why do you think is it found there? Because it is a hormone - it has to travel through the bloodstream to influence other cells.

'''QUESTION 2.3:''' How long is the signal peptide and the propeptide, respectively? 24 and 31 amino acids.

'''QUESTION 2.4:''' Which positions are in β-sheet conformation in insulin? Positions 26-29, 48-50, 56-58, 74-76, and 98-101.

===Other databases linked from UniProt===

''No questions asked here.''

===Text format===

''No questions asked here.''

==Advanced search==

'''QUESTION 3.1:''' How many proteins did you find, and what was the search string (the text in the search field)? 18,229,549, of these 44,113 from Swiss-Prot <tt>(ft_signal:)</tt>

'''QUESTION 3.2:''' How many proteins do you find now, and what has the search string changed into? 3,826, they are ''all'' from Swiss-Prot <tt>(ft_signal_exp:)</tt> Note that the "experimental" evidence is only found in Swiss-Prot entries, not in TrEMBL!

'''QUESTION 3.3:''' How many proteins do you find now, and what is the search string? 732 <tt>(ft_signal_exp:) AND (organism_id:9606)</tt>

'''QUESTION 3.4:''' How many proteins are there in UniProt from ''Bacillus subtilis'' with the default TaxID [1423]? 43,759, of these only 62 from Swiss-Prot <tt>(organism_id:1423)</tt>

'''QUESTION 3.5:''' How many proteins are there in UniProt from ''Bacillus subtilis'' in total (all strains and subspecies)? 77,776, of these 4,279 from Swiss-Prot <tt>(taxonomy_id:1423)</tt>

'''QUESTION 3.6:''' How many proteins of maximum length 10 do you find? 46,956 <tt>(length:[1 TO 10])</tt>

'''QUESTION 3.7:''' How many proteins are now left? 1,317 <tt>(length:[1 TO 10]) AND (existence:1)</tt>

'''QUESTION 3.8:''' How many proteins are now left? 873 <tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false)</tt>

'''QUESTION 3.9:''' How many human non-fragment proteins of maximum length 10 do you find in UniProt? 6 <tt>(length:[1 TO 10]) AND (existence:1) AND (fragment:false) AND (organism_id:9606)</tt>

'''QUESTION 3.10:'''

Here they are in FASTA format:

>sp|P0DPR3|TRDD1_HUMAN T cell receptor delta diversity 1 OS=Homo sapiens OX=9606 GN=TRDD1 PE=1 SV=1
EI
>sp|P01858|TUFT_HUMAN Phagocytosis-stimulating peptide OS=Homo sapiens OX=9606 PE=1 SV=1
TKPR
>sp|P02729|GLUR_HUMAN Urine glycopeptide OS=Homo sapiens OX=9606 PE=1 SV=1
CEHSHDGA
>sp|P01358|GAJU_HUMAN Gastric juice peptide 1 OS=Homo sapiens OX=9606 PE=1 SV=1
LAAGKVEDSD
>sp|P02728|GLEM_HUMAN Erythrocyte membrane glycopeptide OS=Homo sapiens OX=9606 PE=1 SV=1
CEGHSHDHGA
>sp|P22103|PNEU_HUMAN Pneumadin OS=Homo sapiens OX=9606 PE=1 SV=1
AGEPKLDAGV

== On your own ==

QUESTION 4.1: <tt>(taxonomy_id:562)</tt>, 1,075,614 hits.

QUESTION 4.2: <tt>(taxonomy_id:83334)</tt>, 14,594 hits.

QUESTION 4.3: <tt>(protein_name:insulin) AND (gene:ins) NOT (protein_name:insulin-like) NOT (protein_name:"insulin related")</tt>, 545 hits

QUESTION 4.4: <tt>(protein_name:"alpha globin") AND (taxonomy_id:9845) NOT (protein_name:"transcription factor")</tt>, 17 hits.

QUESTION 4.5: <tt>(protein_name:"alpha- globin") AND (taxonomy_id:8932)</tt>, 2 hits.