Using the Taxonomy database - Revision history

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

← Older revision		Revision as of 21:38, 27 August 2026
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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.

Raz: /* Comparing trees */

2026-08-27T19:13:04Z

Comparing trees

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	You will later learn how to make trees like these in the [[Exercise: Phylogeny\|Phylogenetic trees exercise]]. For now, you only need to know that such a tree is not necessarily 100% correct, since it is based on a limited amount of data.		You will later learn how to make trees like these in the [[Exercise: Phylogeny\|Phylogenetic trees exercise]]. For now, you only need to know that such a tree is not necessarily 100% correct, since it is based on a limited amount of data.

	'''QUESTION 9a:''' Are there any differences in the branching pattern between the gene tree and the Common tree from the previous question?		'''QUESTION 5a:''' Are there any differences in the branching pattern between the gene tree and the Common tree from the previous question?

	'''QUESTION 9b:''' 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?

Raz: /* Fishing in NCBI Tax using the Common Tree function */

2026-08-27T19:12:27Z

Fishing in NCBI Tax using the Common Tree function

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	[[Image:NcbiCommonTree2026.jpg \|400px\|frame\|center\|'''Direct link:''' [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/common-tree/ Common Tree tool (2026)] ]]		[[Image:NcbiCommonTree2026.jpg \|400px\|frame\|center\|'''Direct link:''' [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/common-tree/ Common Tree tool (2026)] ]]

	'''IMPORTANT:''' The 2026 version of the tool is quite good at automatically detecting the shared groups to display, but you can ask the tool to display a full lineage, if needed: You can test this by clicking "'''View in Taxonomy Browser'''" after the Common Tree has been populated (but return to the standard view for answering the questions below).		'''IMPORTANT:''' The 2026 version of the tool is quite good at automatically detecting the shared groups to display, but you can ask the tool to display a full lineage, if needed: You can test this by clicking "'''View in Taxonomy Browser'''" after the Common Tree has been populated (but '''return to the standard view''' for answering the questions below).

	'''QUESTION 4a:''' In this selection of species, what is the sister group (nearest neighbour) to the Zebrafish? What is the sister group to the lungfish?		'''QUESTION 4a:''' In this selection of species, what is the sister group (nearest neighbour) to the Zebrafish? What is the sister group to the lungfish?

Raz: /* Fishing in NCBI Tax using the Common Tree function */

2026-08-27T19:12:02Z

Fishing in NCBI Tax using the Common Tree function

← Older revision		Revision as of 21:12, 27 August 2026
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	[[Image:NcbiCommonTree2026.jpg \|400px\|frame\|center\|'''Direct link:''' [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/common-tree/ Common Tree tool (2026)] ]]		[[Image:NcbiCommonTree2026.jpg \|400px\|frame\|center\|'''Direct link:''' [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/common-tree/ Common Tree tool (2026)] ]]

	'''IMPORTANT:''' The 2026 version of the tool is quite good at automatically detecting the shared groups to display, but you can ask the tool to display a full lineage, if needed.		'''IMPORTANT:''' The 2026 version of the tool is quite good at automatically detecting the shared groups to display, but you can ask the tool to display a full lineage, if needed: You can test this by clicking "'''View in Taxonomy Browser'''" after the Common Tree has been populated (but return to the standard view for answering the questions below).

	'''QUESTION 4a:''' In this selection of species, what is the sister group (nearest neighbour) to the Zebrafish? What is the sister group to the lungfish?		'''QUESTION 4a:''' In this selection of species, what is the sister group (nearest neighbour) to the Zebrafish? What is the sister group to the lungfish?

Raz: /* Fishing in NCBI Tax using the Common Tree function */

2026-08-27T19:08:16Z

Fishing in NCBI Tax using the Common Tree function

← Older revision		Revision as of 21:08, 27 August 2026
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	[[Image:NcbiCommonTree2026.jpg \|400px\|frame\|center\|'''Direct link:''' [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/common-tree/ Common Tree tool (2026)] ]]		[[Image:NcbiCommonTree2026.jpg \|400px\|frame\|center\|'''Direct link:''' [https://www.ncbi.nlm.nih.gov/datasets/taxonomy/common-tree/ Common Tree tool (2026)] ]]

	'''IMPORTANT:''' ~~Tick~~ the ~~box labeled "include unranked (phylogenetic) taxa"~~ to ~~get a maximally resolved tree. Note that~~ you can ~~click~~ the ~~small boxes with~~ a ~~"+" to see the~~ full ~~lineages~~, if ~~you want~~.		'''IMPORTANT:''' The 2026 version of the tool is quite good at automatically detecting the shared groups to display, but you can ask the tool to display a full lineage, if needed.

	'''QUESTION 8a:''' In this selection of species, what is the sister group (nearest neighbour) to the Zebrafish? What is the sister group to the lungfish?		'''QUESTION 4a:''' In this selection of species, what is the sister group (nearest neighbour) to the Zebrafish? What is the sister group to the lungfish?

	Now try to add yourself (i.e. Human) to the tree, using either the Latin name or the TaxID. Any surprises?		Now try to add yourself (i.e. Human) to the tree, using either the Latin name or the TaxID. Any surprises?

	'''QUESTION 8b:''' What is now the sister group to the lungfish?		'''QUESTION 4b:''' What is now the sister group to the lungfish?

	'''QUESTION 8c:''' Which of the following is most closely related to the "Blue fish": the cod, or you?		'''QUESTION 4c:''' Which of the following is most closely related to the "Blue fish": the cod, or you?

	'''QUESTION 8d:''' Which of the following is most closely related to the cod: the shark, or you?		'''QUESTION 4d:''' Which of the following is most closely related to the cod: the shark, or you?

	'''QUESTION 8e:''' Which of the following is most closely related to the shark: the lamprey, or you?		'''QUESTION 4e:''' Which of the following is most closely related to the shark: the lamprey, or you?

	'''QUESTION 8f:''' Does the category "fish" make any scientific sense?		'''QUESTION 4f:''' Does the category "fish" make any scientific sense?

	Leave the browser window with the Common tree open for the next question.		Leave the browser window with the Common tree open for the next question.