wikibase - User contributions [en]

Item talk:Q44840

2026-07-29T09:21:51Z

TomHitch: /* asked for revision */ Reply

== asked for revision ==

@[[User:TomHitch|TomHitch]] is the label correct? [[User:Admin|Admin]] ([[User talk:Admin|talk]]) 12:54, 21 July 2026 (UTC)

:Yup its one of the placeholders GTDB uses; https://gtdb.ecogenomic.org/searches?s=al&q=CG1-02-47-37 [[User:TomHitch|TomHitch]] ([[User talk:TomHitch|talk]]) 09:21, 29 July 2026 (UTC)

Main Page

2026-07-21T06:39:02Z

TomHitch: Added list of resources

<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>Aiming to get the community together and describe novel TAXA.</strong></div></div>

'''''<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.

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.

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

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

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</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@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>

Item:Q42933

2026-07-06T13:50:38Z

TomHitch: /* wbsetclaim-update:2||1 */ Property:P20: Description of Acidianus copahuensis sp. nov.; Description based on the representative genome (GCF_000632495.1) from GTDB r214 for 'Acidianus copahuensis'. Assignment to Acidianus is based on POCPu of 61.6% to the type species of the genus, Acidianus infernus. ANI values were unable to be calculated to all existing Acidianus species, and 16S rRNA gene sequence identity values were below 50%, defining GCF_000632495.1 as representing a novel specie...

Item:Q42933

2026-07-06T13:46:40Z

TomHitch: /* wbsetclaim-update:2||1 */ Property:P20: Description of Acidianus copahuensis sp. nov.Description based on the representative genome (GCF_000632495.1) from GTDB r214 for 'Acidianus copahuensis'. Assignment to Acidianus is based on POCPu of 61.6% to the type species of the genus, Acidianus infernus. ANI values were unable to be calculated to all existing Acidianus species, and 16S rRNA gene sequence identity values were below 50%, defining GCF_000632495.1 as representing a novel species.

Item:Q42831

2026-07-06T02:49:41Z

TomHitch: /* wbsetclaim-update:2||1 */ Property:P20: Analysis of the representative genome (GCF_000152805.1) for Maritimibacter alkaliphilus confirmed this species as distinct from its closest relatives, with all ANI comparisons being <80% and 16S rRNA gene identity values being <97%.POCPu values >50% were obtained to neighbouring genera (Celeribacter persicus, 54.6%; Roseibacterium elongatum, 54.2%), however GTDB and 16S rRNA gene identity values confirm this species as a member of the genus Marit...

Main Page

2026-07-05T03:36:57Z

TomHitch:

<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>Aiming to get the community together and describe novel TAXA.</strong></div></div>

'''''<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.

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.

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

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</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@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>

Main Page

2026-07-05T03:36:27Z

TomHitch:

<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>Aiming to get the community together and describe novel TAXA.</strong></div></div>

'''''<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>'''

==== '''<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.

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

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</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@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>

Main Page

2026-07-05T03:35:50Z

TomHitch:

<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>Aiming to get the community together and describe novel TAXA.</strong></div></div>

'''''<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>'''

'''<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.

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

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</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@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>

Main Page

2026-07-05T03:35:12Z

TomHitch: Added explination of the process

<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>Aiming to get the community together and describe novel TAXA.</strong></div></div>

'''''<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.

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.

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

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</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@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>

Item:Q42831

2026-07-05T03:25:05Z

Item:Q42831

2026-07-05T03:24:11Z

TomHitch: /* wbsetclaim-update:2||1 */ Property:P20: Analysis of the representative genome (GCF_000152805.1) for <i>Maritimibacter alkaliphilus</i> confirmed this species as distinct from its closest relatives, with all ANI comparisons being <80% and 16S rRNA gene identity values being <97%.POCPu values >50% were obtained to neighbouring genera (''Celeribacter'', 54.6%; ''Roseibacterium'', 54.2%).

Item:Q42831

2026-07-05T03:21:58Z

TomHitch: /* wbsetclaim-update:2||1 */ Property:P20: Analysis of the representative genome (GCF_000152805.1) for ''Maritimibacter alkaliphilus'' confirmed this species as distinct from its closest relatives, with all ANI comparisons being <80% and 16S rRNA gene identity values being <97%.POCPu values >50% were obtained to neighbouring genera (''Celeribacter'', 54.6%; ''Roseibacterium'', 54.2%).

Main Page

2026-07-03T08:50:05Z

TomHitch: /* More information */

<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>Aiming to get the community together and describe novel TAXA.</strong></div></div>

'''''<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>Projects contributing to TAXA-KG</u> ====
<strong>**TAXA** https://nfdi4microbiota.de/usecases/taxa</strong>

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</strong>

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

Main Page

2026-07-02T12:02:40Z

TomHitch: Altered title and email for thitch

<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>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>'''''

==== <strong>Short description</strong> ====
<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 ====
<strong>**TAXA** https://nfdi4microbiota.de/usecases/taxa</strong>

<strong>**MicroBioKGs** https://nfdi4microbiota.de/usecases/microbiokgs</strong>

<strong>**Protologger** [https://protologger.bi.denbi.de/ https://protologger.bi.denbi.de]</strong>

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

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