[NTR] Liver abscess

[ipediez]

Preferred term label

Liver abscess

Synonyms

Hepatic abscess

Textual definition

An abscess in the liver

Suggested parent term

Abscess (MONDO:0005227)

Use case

This pathology is listed as one of the pathologies of a human donor for a liver single-cell project

Attribution

0000-0002-2658-1136

[ipediez]

I would need a new term also for Intersphincteric abscess. That would be for the same use case and would fall under the same parent term and have a similar description. I haven't created the ticket yet, in case you want to discuss here if there are already terms available or that we can import. Both terms would have similar ones available on SNOMEDCT: Abscess of liver (27916005) and Intersphincteric abscess (235795007). Do you want me to create a new ticket for Intersphincteric abscess?

[paolaroncaglia]

@ipediez no need to open a separate ticket, thanks. I'll look into both terms today.

[paolaroncaglia]

@ipediez I double-checked Mondo (including potential synonyms of your requested terms) and I confirm that there are no specific terms currently available. (EFO imports 'Liver abscess' from the Human Phenotype Ontology, so as a phenotype term that's not available in HCAO.)

• [x] I will ask Mondo to create 'liver abscess' and 'intersphincteric abscess' (this ticket)
• [ ] I'll comment back here when they are available to you (update 06/04/22: the Mondo terms have been created but not released yet; they'll be public with the early May Mondo release, and available to you with the HCAO release scheduled for May 17th)

In the meantime, if you need to annotate for a release before that date, you could use Abscess (MONDO:0005227) and combine that with the anatomy terms UBERON:0002107 'liver' and UBERON:0004916 'anal sphincter', respectively. (Though, strictly speaking, the abscess occurs in the space between the two sphincters.)

[paolaroncaglia]

@ipediez The 2 new disease terms you requested have been created in Mondo, but not released yet. As anticipated, they will be public with the next Mondo release, and available to HCA wranglers after May 17th. Here are the IDs for future reference: MONDO:0700051 liver abscess (disease) MONDO:0700052 intersphincteric abscess

[dosumis]

Pending.

[paolaroncaglia]

@ipediez MONDO:0700051 liver abscess (disease) and MONDO:0700052 intersphincteric abscess will be available in HCAO as soon as the new release is in the OLS instance, pending https://github.com/ebi-ait/hca-ebi-dev-team/issues/487. Thank you.