deprecated ENVO terms

[zhengj2007]

We are working on database holding microbes and their genes data. See: http://microbiome.org/

The Mixs standards were used on guiding data collection and ENVO terms were used in data annotation. We found some terms used in the annotation were deprecated in ENVO, such as: ENVO:animal-associated habitat ENVO:anthropogenic environmental material ENVO:human-associated habitat ENVO:insecta-associated habitat

We'd like to know whether there are replaced terms we can use for the deprecated ENVO terms.

Thanks,

Jie

[pbuttigieg]

ENVO:anthropogenic environmental material

This is a live term available here. Please note, that this will become a defined class once we have more manufacturing and human-mediated processes in the ontology. This shouldn't affect annotation, however.

ENVO:human-associated habitat ENVO:insecta-associated habitat ENVO:animal-associated habitat

These were not replaced by another term, but we can create classes like "Metazoan environment" using NCBITaxon_33208, for example.

[zhengj2007]

Thanks Pier for your quick reply.

Sorry I forgot to remove term 'anthropogenic environmental material' from the deprecated list.

Thanks a lot if you can create classes like "Metazoan environment". So, we can use these ENVO terms in our database. How long shall we wait for it?

Thanks!

[pbuttigieg]

How long shall we wait for it?

I'll create the class for tagging now, but we'll have to think a little about the axioms behind it. Once those are settled (we'll keep discussion in this issue), it may be worth post-composing the terms you need. If this is about MIxS compliance, then I understand the need for pre-composed terms, however.

@cmungall, may need your assist here.

Could we extend the TermGenie to work with the NCBI taxonomy import? The PersonaID login isn't supported anymore. We'd create a pattern like: e.g. [Taxon] environment = "An environmental system determined by an instance of taxon X"

Further, given that NCBI classes refer to the entire taxon rather than an individual, how would we express that we're talking about an individual in the logical def? Is this an issue?

[zhengj2007]

@pbuttigieg Thanks a lot! If you can make the terms available are good enough for us since current we only need consistent annotation for the project especially when the terms are part of Mixs standards and have been used by microbiome researchers.

[cmungall]

Yes, first task is to create a organism_environment.yaml in https://github.com/EnvironmentOntology/envo/tree/master/src/envo/patterns