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Latest revision as of 06:39, 21 July 2026

Welcome to TAXA-KG

Aiming to get the community together and describe novel TAXA.

Describing taxonomic lineages

Rationale

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.

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.

Understanding the process

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.

Resources used

GTDB = r214

LTP = 14_10_2024

Projects contributing to TAXA-KG

**TAXA** https://nfdi4microbiota.de/usecases/taxa

**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs

**Protologger** https://protologger.bi.denbi.de

How to get in contact:

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

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

This is the second and updated version of TAXA-KG-wikibase-v2

@@ 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">
 <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>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.
+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.
-==== <strong>Short description</strong> ====
+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.
-<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>
+==== <u>Resources used</u> ====
+GTDB = r214
-==== More information ====
+LTP = 14_10_2024
+==== <u>Projects contributing to TAXA-KG</u> ====
 <strong>**TAXA** https://nfdi4microbiota.de/usecases/taxa</strong>
@@ Line 23: / Line 33: @@
 <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 Curation, Protologger: Thomas Hitch (thitch@ukaachen.de)
+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>