Ticket #52 (closed question: fixed)

Opened 5 years ago

Last modified 5 years ago

Change to EnvO

Reported by: guest Owned by: pyilmaz
Priority: minor Component: MIxS general
Version: 3.0 Keywords:
Cc: pbuttigi@… Sensitive: no

Description

Users are having a hard time determining how to use the EnvO ontology to specify the correct biome for host-associated GSC-compliant biosamples. In the past, this was terrestrial biome:

http://www.ncbi.nlm.nih.gov/biosample/778968


A look at the EnvO site (as well as the ontology lookup service at EBI) shows that it has been updated - what should users use for biome when submitting data derived from a host?

We would need to know what to specify for host-associated as well as engineered/synthetic biomes.

thanks!

Change History

comment:1 Changed 5 years ago by pyilmaz

  • Cc pbuttigi@… added

comment:2 Changed 5 years ago by guest

Hi,
I've been using the somewhat unhelpful terms or either "aquatic biome" (ENVO:00002030) or "terrestrial biome" (ENVO:00000446) depending on what the host is. i.e. human hosts are terrestrial, sponge hosts are aquatic etc...
Not the most informative bit of information, but it maintains the compliance with the MIxS.
It would be useful to find an alternative ontology or perhaps get EnvO extended.
Thanks
Chris (Hunter).

comment:3 Changed 5 years ago by pbuttigi

Hi Chris,

Both aquatic and terrestrial biome classes have multiple children which you can use to define your sample's biome more finely. Try to use the most specific term available. We are adding Ellis et al.'s 'Anthropogenic biomes' to EnvO, which should provide some useful terms for built environment studies.

Keep in mind that the biome terms define the coarsest granularity of your sample's environment. Thus, a biome term may refer to the ecosystem the host is embedded in. One would then use an environmental feature term like "human-associated habitat" (ENVO:00009003) or "organ" (ENVO:01000162) to zero in on the more local environment of a sample.

Term requests may be sent to obo-envo@… (a mailing list of the whole EnvO Consortium) or may be submitted through the webpage (http://www.environmentontology.org/contact) to the editorial team.

Best,
PLB

Last edited 5 years ago by pbuttigi (previous) (diff)

comment:4 Changed 5 years ago by guest

Hi,
I think the addition of Anthropogenic biomes will help immensely.
Although it would perhaps also be useful to write a more descriptive set of definitions to the GSC variables Biome, feature and material, especially how they relate to one-another. If I get time I will try to put forward a suggestion as a starting point for discussions at GSC14(if I get there!).
Cheers
Chris

comment:5 Changed 5 years ago by pbuttigi

I'll speed the implementation of the anthromes.
Regarding the definitions of biome/feature/material: we've been working to create top-level definitions that place EnvO in the semantic framework of the Basic Formal Ontology (BFO). We have, more or less, settled on biome, are close to finalising feature, but have some discussions left to nail down the semantics of environmental material. For the moment, treat biome as the descriptor of the broad ecological context of your sample, feature as a descriptor of the more local environment, and material as that in which your sample was embedded.
Best,
PLB

comment:6 Changed 5 years ago by pyilmaz

  • Status changed from new to closed
  • Resolution set to fixed

I guess this is also closed

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