Main Page - Revision history

TomHitch: Added list of resources

2026-07-21T06:39:02Z

Added list of resources

← Older revision		Revision as of 06:39, 21 July 2026
Line 21:		Line 21:



			==== <u>Resources used</u> ====
			GTDB = r214

			LTP = 14_10_2024
	==== <u>Projects contributing to TAXA-KG</u> ====		==== <u>Projects contributing to TAXA-KG</u> ====
	<strong>TAXA https://nfdi4microbiota.de/usecases/taxa</strong>		<strong>TAXA https://nfdi4microbiota.de/usecases/taxa</strong>

TomHitch at 03:36, 5 July 2026

2026-07-05T03:36:57Z

← Older revision		Revision as of 03:36, 5 July 2026
Line 14:		Line 14:

	Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.		Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.
	~~'''<u>Understanding the process</u>'''~~

	==== '''<u>Understanding the process</u>''' ====		==== '''<u>Understanding the process</u>''' ====

TomHitch at 03:36, 5 July 2026

2026-07-05T03:36:27Z

← Older revision		Revision as of 03:36, 5 July 2026
Line 16:		Line 16:
	'''<u>Understanding the process</u>'''		'''<u>Understanding the process</u>'''

	'''<u>Understanding the process</u>'''		==== '''<u>Understanding the process</u>''' ====

	TAXA-KG is based on using GTDB as a curated collection of representative genomes for both known and unknown genomes. These are then processed by Protologger2 (https://protologger.bi.denbi.de/), providing taxonomic, ecological, and functional readouts.		TAXA-KG is based on using GTDB as a curated collection of representative genomes for both known and unknown genomes. These are then processed by Protologger2 (https://protologger.bi.denbi.de/), providing taxonomic, ecological, and functional readouts.

TomHitch at 03:35, 5 July 2026

2026-07-05T03:35:50Z

← Older revision		Revision as of 03:35, 5 July 2026
Line 14:		Line 14:

	Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.		Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.
			'''<u>Understanding the process</u>'''

	'''<u>Understanding the process</u>'''		'''<u>Understanding the process</u>'''

	TAXA-KG is based on using GTDB as a curated collection of representative genomes for both known and unknown genomes. These are then processed by Protologger2 (https://protologger.bi.denbi.de/), providing taxonomic, ecological, and functional readouts.		TAXA-KG is based on using GTDB as a curated collection of representative genomes for both known and unknown genomes. These are then processed by Protologger2 (https://protologger.bi.denbi.de/), providing taxonomic, ecological, and functional readouts.

TomHitch: Added explination of the process

2026-07-05T03:35:12Z

Added explination of the process

← Older revision		Revision as of 03:35, 5 July 2026
Line 15:		Line 15:
	Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.		Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.

			'''<u>Understanding the process</u>'''

			TAXA-KG is based on using GTDB as a curated collection of representative genomes for both known and unknown genomes. These are then processed by Protologger2 (https://protologger.bi.denbi.de/), providing taxonomic, ecological, and functional readouts.

			TAXA-KG hosts these outputs for the community to access and use to describe taxa of interest to them. By providing the descriptions on TAXA-KG, these can be collected and used in subsequent publications to name novel taxa according to either the ICNP or SeqCode depending on isolate availability. As a community effort contributors to descriptions will be credited in these publications as "The TAXA-KG Community", with members who have contributed substantial effort being specifically named.


Line 25:		Line 29:
	<strong>Protologger [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</strong>		<strong>Protologger [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</strong>

	==== <strong>How to get in contact:</strong> ====
			==== <strong><u>How to get in contact:</u></strong> ====
	Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de)		Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de)

TomHitch: /* More information */

2026-07-03T08:50:05Z

More information

← Older revision		Revision as of 08:50, 3 July 2026
Line 3:		Line 3:
	</div><strong>Aiming to get the community together and describe novel TAXA.</strong></div></div>		</div><strong>Aiming to get the community together and describe novel TAXA.</strong></div></div>

	~~<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>~~



	'''''<big>~~Descriptions of novel~~ taxonomic lineages</big>'''''		'''''<big>Describing taxonomic lineages</big>'''''

			==== <strong><u>Rationale</u></strong> ====
			A substantial fraction of Prokaryotes (Bacteria and Archaea) are unknown and undescribed, but as genomes exist for these unknown taxa, it is possible to describe them using genome-inferred information. However, the quality of taxonomic descriptions lacks standardisation.

			TAXA-KG fills this gap. The idea it is to use genome-inferred taxonomic, functional, and ecological information from Protologger2 to provide standardised readouts of prokaryotic taxa, which can provide the building blocks for the community to describe them. This information is provided to the community via this Wikibase site, allowing the community to convert the building blocks into fully formed taxonomic descriptions. This tackles the problem of ambiguous descriptions and ensures robust placement of novel taxa due to providing of five different lines of taxonomic evidence for placement.

	~~==== <strong>Short description</strong> ====~~		Using the knowledge-graph behind the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance and screen their associated data.
	~~<strong>A substantial fraction of~~ bacteria ~~are unknown and undescribed, but as genomes exist for these unknown taxa, it is possible~~ to ~~describe them using genome-inferred information. However, the description of novel taxa currently lacks standardized formats~~ and ~~there is limited quality assurance during this process~~.~~</strong>~~

	<strong>TAXA will fill this gap. The idea behind it is to use the published bioinformatic tool Protologger to provide standardized functional and taxonomic readouts of novel taxa using genome sequences, which will provide the building blocks for the community to describe them. This information will be provided to the community via a custom Wiki, allowing members of the community to contribute by converting the building blocks we provide into fully formed taxonomic descriptions. This tackles the problem of ambiguous naming practices in the process of validly describing novel species. Via the Wiki, researchers will be able to identify interesting and relevant bacteria to their research question at a glance.</strong>



	==== ~~More information~~ ====		==== <u>Projects contributing to TAXA-KG</u> ====
	<strong>TAXA https://nfdi4microbiota.de/usecases/taxa</strong>		<strong>TAXA https://nfdi4microbiota.de/usecases/taxa</strong>

Line 27:		Line 29:

	Data Curation, Protologger: Thomas Hitch (thitch@cuhk.edu.hk)		Data Curation, Protologger: Thomas Hitch (thitch@cuhk.edu.hk)


			<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>

TomHitch: Altered title and email for thitch

2026-07-02T12:02:40Z

Altered title and email for thitch

← Older revision		Revision as of 12:02, 2 July 2026
Line 1:		Line 1:
	<div style="width:98%; border:3px solid #0063bf; overflow:hidden; background-color: #FFFFFF; padding:16px 16px 16px 16px"><div style="text-align:left; font-size:1.5em; color: #0063bf"><div style="text-align:left; font-size:1.5em; color: #0063bf">		<div style="width:98%; border:3px solid #0063bf; overflow:hidden; background-color: #FFFFFF; padding:16px 16px 16px 16px"><div style="text-align:left; font-size:1.5em; color: #0063bf"><div style="text-align:left; font-size:1.5em; color: #0063bf">
	<strong>Welcome to TAXA-KG</strong>		<strong>Welcome to TAXA-KG</strong>
	</div><strong>~~a Wikibase instance that aims~~ to get the community together and describe novel TAXA.</strong~~><div style="text-align:left;"></div~~></div></div>		</div><strong>Aiming to get the community together and describe novel TAXA.</strong></div></div>

	<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>		<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>
Line 26:		Line 26:
	Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de)		Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de)

	Data Curation, Protologger: Thomas Hitch (thitch@~~ukaachen~~.de)		Data Curation, Protologger: Thomas Hitch (thitch@cuhk.edu.hk)

LauraSchl at 09:42, 2 July 2026

2026-07-02T09:42:48Z

← Older revision		Revision as of 09:42, 2 July 2026
Line 1:		Line 1:
	<div style="width:98%; border:3px solid #0063bf; overflow:hidden; background-color: #FFFFFF; padding:16px 16px 16px 16px"><div style="text-align:left; font-size:1.5em; color: #0063bf"><div style="text-align:left; font-size:1.5em; color: #0063bf">		<div style="width:98%; border:3px solid #0063bf; overflow:hidden; background-color: #FFFFFF; padding:16px 16px 16px 16px"><div style="text-align:left; font-size:1.5em; color: #0063bf"><div style="text-align:left; font-size:1.5em; color: #0063bf">
	<strong>Welcome to TAXA-KG</strong>		<strong>Welcome to TAXA-KG</strong>
	</div><strong>a Wikibase instance that aims to get the community together and describe novel TAXA.</strong><div style="text-align:left;"~~><strong>More information will follow soon!</strong~~></div></div></div>		</div><strong>a Wikibase instance that aims to get the community together and describe novel TAXA.</strong><div style="text-align:left;"></div></div></div>

	<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>		<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>

Admin at 09:53, 1 July 2026

2026-07-01T09:53:47Z

← Older revision		Revision as of 09:53, 1 July 2026
Line 5:		Line 5:
	<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>		<strong>This is the second and updated version of [https://taxa-kg-v2.wikibase.cloud/wiki/Main_Page TAXA-KG-wikibase-v2]</strong>

	== <~~strong~~>Descriptions of novel taxonomic lineages</~~strong~~> ==

			'''''<big>Descriptions of novel taxonomic lineages</big>'''''

	==== <strong>Short description</strong> ====		==== <strong>Short description</strong> ====

Admin: /* Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de) */

2026-07-01T09:53:00Z

Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de)

← Older revision		Revision as of 09:53, 1 July 2026
Line 14:		Line 14:


	<strong>~~More information about~~ TAXA https://nfdi4microbiota.de/usecases/taxa</strong>		==== More information ====
			<strong>TAXA https://nfdi4microbiota.de/usecases/taxa</strong>

	<strong>~~More information about~~ MicroBioKGs https://nfdi4microbiota.de/usecases/microbiokgs</strong>		<strong>MicroBioKGs https://nfdi4microbiota.de/usecases/microbiokgs</strong>

	<strong>~~More information about~~ Protologger [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</strong>		<strong>Protologger [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</strong>

	<strong>How to get in contact:</strong>		==== <strong>How to get in contact:</strong> ====
			Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de)

	~~==== Data Modelling, Knowledge Graphs: Vanessa Scharf (scharf@zbmed.de) ====~~		Data Curation, Protologger: Thomas Hitch (thitch@ukaachen.de)

	~~====~~ Data Curation, Protologger: Thomas Hitch (thitch@ukaachen.de) ~~====~~