Using the Taxonomy database - Revision history

Raz: /* The NCBI Taxonomy Database */

2026-08-30T19:13:25Z

The NCBI Taxonomy Database

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	'''Main link:''' https://www.ncbi.nlm.nih.gov/datasets/taxonomy/		'''Main link:''' https://www.ncbi.nlm.nih.gov/datasets/taxonomy/

	(''2026 note: NCBI is in process of migrating to this new site - if you find the old ~~Ncbi~~ Tax homepage via Google, make sure to press the link they provide to jump to the new site'').		(''2026 note: NCBI is in process of migrating to this new site - if you find the old NCBI Tax homepage via Google (or other means), make sure to press the link they provide to jump to the new site'').
	</div>		</div>

Raz: /* The NCBI Taxonomy Database */

2026-08-30T19:12:53Z

The NCBI Taxonomy Database

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	[[File:NcbiTax2026.jpg\|800px\|center\|border]]		[[File:NcbiTax2026.jpg\|800px\|center\|border]]


			<div style="background-color: lavender; border: solid thin grey;">
	'''Main link:''' https://www.ncbi.nlm.nih.gov/datasets/taxonomy/		'''Main link:''' https://www.ncbi.nlm.nih.gov/datasets/taxonomy/

	(''2026 note: NCBI is in process of migrating to this new site - if you find the old Ncbi Tax homepage via Google, make sure to press the link they provide to jump to the new site'').		(''2026 note: NCBI is in process of migrating to this new site - if you find the old Ncbi Tax homepage via Google, make sure to press the link they provide to jump to the new site'').
			</div>
	~~----~~

	As mentioned above NCBI Taxonomy will serve as our '''Ground Truth''' for everything related to taxonomy. The NCBI Tax database provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (''Homo sapiens'') has the ID "'''9606'''" and Yeast (''Saccharomyces cerevisiae'') as the ID "'''4932'''".		As mentioned above NCBI Taxonomy will serve as our '''Ground Truth''' for everything related to taxonomy. The NCBI Tax database provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (''Homo sapiens'') has the ID "'''9606'''" and Yeast (''Saccharomyces cerevisiae'') as the ID "'''4932'''".

Henni: /* Example: Homo sapiens */

2026-08-28T12:39:13Z

Example: Homo sapiens

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	## "'''Full lineage'''": Click this to view a FULL list of all the groups leading "down" to human. Notice, that you can "mouse over" the groups to see a pop-up with the taxonomical rank. NOTICE: The rank "CLADE" is used whenever a group does not have a common English name ("Clade" is the generic name for a uniquely defined taxonomical group).		## "'''Full lineage'''": Click this to view a FULL list of all the groups leading "down" to human. Notice, that you can "mouse over" the groups to see a pop-up with the taxonomical rank. NOTICE: The rank "CLADE" is used whenever a group does not have a common English name ("Clade" is the generic name for a uniquely defined taxonomical group).

	Play around with the Homo sapiens page for a bit to familiarize ~~you~~ with the interface, and answer the following questions along the way:		Play around with the Homo sapiens page for a bit to familiarize yourself with the interface, and answer the following questions along the way:
	* '''QUESTION 1a''': What is the TaxID of "''Metazoa''"?		* '''QUESTION 1a''': What is the TaxID of "''Metazoa''"?
	* '''QUESTION 1b''': What is the family that contains humans?		* '''QUESTION 1b''': What is the family that contains humans?

Raz at 12:30, 28 August 2026

2026-08-28T12:30:14Z

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	Exercise written by: '''Rasmus Wernersson''' and '''Henrik Nielsen'''.		Exercise written by: '''Rasmus Wernersson''' and '''Henrik Nielsen'''.

	~~'''UNDER CONSTRUCTION!!!!'''~~

	~~'''UNDER CONSTRUCTION!!!!'''~~

	~~'''UNDER CONSTRUCTION!!!!'''~~

	~~'''UNDER CONSTRUCTION!!!!'''~~

	~~'''UNDER CONSTRUCTION!!!!'''~~

	~~'''UNDER CONSTRUCTION!!!!'''~~

	~~'''UNDER CONSTRUCTION!!!!'''~~


	==Background==		==Background==

Raz: /* The need for a Ground Truth */

2026-08-27T19:45:17Z

The need for a Ground Truth

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	===The need for a Ground Truth===		===The need for a Ground Truth===
	Luckily, modern taxonomy is very well established and there an internationally recognized organization that makes revisions in a highly regulated manner. This '''taxonomy standard''' is captured in '''NCBI Taxonomy''' database we'll be working with in the sections below. For all molecular data NCBI Taxonomy is THE standard reference.		Luckily, modern taxonomy is very well established and there an internationally recognized organization that makes revisions in a highly regulated manner. This '''taxonomy standard''' is captured in the '''NCBI Taxonomy''' database we'll be working with in the sections below. For all molecular data NCBI Taxonomy is THE standard reference.

	==The NCBI Taxonomy Database==		==The NCBI Taxonomy Database==

Raz: /* The NCBI Taxonomy Database */

2026-08-27T19:38:32Z

The NCBI Taxonomy Database

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	As mentioned above NCBI Taxonomy will serve as our '''Ground Truth''' for everything related to taxonomy. The NCBI Tax database provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (''Homo sapiens'') has the ID "'''9606'''" and Yeast (''Saccharomyces cerevisiae'') as the ID "'''4932'''".		As mentioned above NCBI Taxonomy will serve as our '''Ground Truth''' for everything related to taxonomy. The NCBI Tax database provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (''Homo sapiens'') has the ID "'''9606'''" and Yeast (''Saccharomyces cerevisiae'') as the ID "'''4932'''".

	NCBI Tax is perhaps not a database you would browse for fun (depending on ~~you~~ level of geekiness). It's good for looking up definitions, and for comparing the taxonomical position of multiple organisms (since the information is so densely presented).		NCBI Tax is perhaps not a database you would browse for fun (depending on your level of geekiness). It's good for looking up definitions, and for comparing the taxonomical position of multiple organisms (since the information is so densely presented).

	===Example: Homo sapiens===		===Example: Homo sapiens===

Raz: /* The NCBI Taxonomy Database */

2026-08-27T19:38:05Z

The NCBI Taxonomy Database

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	----		----

	As mentioned above NCBI Taxonomy will serve as ~~out~~ '''Ground Truth''' for everything related to taxonomy. The NCBI Tax database provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (''Homo sapiens'') has the ID "'''9606'''" and Yeast (''Saccharomyces cerevisiae'') as the ID "'''4932'''".		As mentioned above NCBI Taxonomy will serve as our '''Ground Truth''' for everything related to taxonomy. The NCBI Tax database provides the numerical enumeration of species (and other taxonomical levels) that is used and referenced in most Sequence databases, such as GenBank (DNA) and UniProt (Protein). For example human (''Homo sapiens'') has the ID "'''9606'''" and Yeast (''Saccharomyces cerevisiae'') as the ID "'''4932'''".

	NCBI Tax is perhaps not a database you would browse for fun (depending on you level of geekiness). It's good for looking up definitions, and for comparing the taxonomical position of multiple organisms (since the information is so densely presented).		NCBI Tax is perhaps not a database you would browse for fun (depending on you level of geekiness). It's good for looking up definitions, and for comparing the taxonomical position of multiple organisms (since the information is so densely presented).

Raz: /* AI investigation */

2026-08-27T19:23:24Z

AI investigation

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	We do realize that the AI field is rapidly evolving, and answers will vary. We will recommend you to play around with the prompt to make the system generate an answer with the best possible scientific rigor. You are welcome to either use the list of species (+human) as we did above, or ask the AI to find relevant data itself.		We do realize that the AI field is rapidly evolving, and answers will vary. We will recommend you to play around with the prompt to make the system generate an answer with the best possible scientific rigor. You are welcome to either use the list of species (+human) as we did above, or ask the AI to find relevant data itself.

			*'''QUESTION 6:''' Provide your final prompt + answer from the AI (+ info about which version you used). Reflect upon the correctness of the answer (how much do you trust it, ''anything fishy?'')

Raz: /* AI investigation */

2026-08-27T19:20:04Z

AI investigation

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	'''QUESTION 5b:''' Can the gene tree be made to comply with the Common tree by swapping two species? If so, which two?		'''QUESTION 5b:''' Can the gene tree be made to comply with the Common tree by swapping two species? If so, which two?

			-----
	===AI investigation===		===AI investigation===
	As the final step, use your favorite AI (ChatGPT etc) to try to get as '''detailed and comprehensive''' an answer to QUESTION 4f as possible: ''Does the category "fish" make any scientific sense?''		As the final step, use your favorite AI (ChatGPT etc) to try to get as '''detailed and comprehensive''' an answer to QUESTION 4f as possible: ''Does the category "fish" make any scientific sense?''

	We do realize that the AI field is rapidly evolving, and answers will vary. We will recommend you to play around with the prompt to make the system generate an answer with the best possible scientific rigor. You are welcome to either use the list of species (+human) as we did above, or ask the AI to find relevant data itself.		We do realize that the AI field is rapidly evolving, and answers will vary. We will recommend you to play around with the prompt to make the system generate an answer with the best possible scientific rigor. You are welcome to either use the list of species (+human) as we did above, or ask the AI to find relevant data itself.

Raz: /* Comparing trees */

2026-08-27T19:19:39Z

Comparing trees

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	'''QUESTION 5b:''' Can the gene tree be made to comply with the Common tree by swapping two species? If so, which two?		'''QUESTION 5b:''' Can the gene tree be made to comply with the Common tree by swapping two species? If so, which two?

			===AI investigation===
			As the final step, use your favorite AI (ChatGPT etc) to try to get as '''detailed and comprehensive''' an answer to QUESTION 4f as possible: ''Does the category "fish" make any scientific sense?''

			We do realize that the AI field is rapidly evolving, and answers will vary. We will recommend you to play around with the prompt to make the system generate an answer with the best possible scientific rigor. You are welcome to either use the list of species (+human) as we did above, or ask the AI to find relevant data itself.