Creation of EBI Biome terms

[kaiiam]

I have been tasked with the creation of ENVO terms for the EBI biomes hierarchy, so that EBI which can better link to ENVO. They have major biome hierarcies for environmental, host-associated, and engineered systems. I have created a spreadsheet for the Environmental biomes hierarchy which has columns for

environmental feature	environmental material (or material entity for CHEBI, FOODON or other)	environmental system

Perhaps we could create yaml patterns for each of the major biome types, starting with Environmental.

[cmungall]

We also need to include mappings to the EBI terms. these don't have IDs, but can be identified by > Foo > Bar > Baz descriptors. Normally we would do mappings as xrefs but xrefs should be IDs with no spaces, so maybe we want to a specific property here.

Or we could do these as synonyms.

Either way, it is easy to export as a simple TSV as part of each release

[pbuttigieg]

We need something more permissive than xrefs if they don't allow anything other than IDs, and we need this OBO-wide

[pbuttigieg]

Perhaps @mscheremetjew, @olatarkowska, or @mb1069 from over at https://github.com/EBI-Metagenomics / https://github.com/EBI-Metagenomics/ebi-metagenomics-webkit can help:

Do the EBI biomes have IRIs or some other kind of web-accessible ID?
Is this valid: https://www.ebi.ac.uk/metagenomics/browse?lineage=root:Environmental:Aquatic:Marine

or is there something more compact? What would the URL/IRI be for something more fine grain (like "Coastal")?

[mb1069]

Gladly! Our biomes are constructed as colon separated strings, though these can sometimes contain spaces (eg: root:Engineered:Wastewater:Activated Sludge). We also have duplicated biome names which is why we not yet investigated a simplified biome URI (eg root:Engineered:Solid waste:Composting:Bioreactor and root:Engineered:Solid waste:Composting:Wood:Bioreactor). So @pbuttigieg you have a correct URI, though this is also exposed via our API (https://www.ebi.ac.uk/metagenomics/api/latest/biomes?lineage=root:Environmental:Aquatic:Marine)

[cmungall]

OK, thanks! In this case we should encode the xref with identical fragment to the URL, e.g. MGNIFY:Foo:Bar:Baz+Biz, or we can just use the URL directly as the xref (these should get translated to equivalence axioms in the release)

…

On Wed, Mar 6, 2019 at 4:55 AM Miguel Boland ***@***.***> wrote: Gladly! Our biomes are constructed as colon separated strings, though these can sometimes contain spaces (eg: root:Engineered:Wastewater:*Activated Sludge*). We also have duplicated biome names which is why we not yet investigated a simplified biome URI (eg root:Engineered:Solid waste:Composting:*Bioreactor* and root:Engineered:Solid waste:Composting:Wood:*Bioreactor*). So @pbuttigieg <https://github.com/pbuttigieg> you have a correct URI, though this is also exposed via our API ( https://www.ebi.ac.uk/metagenomics/api/latest/biomes?lineage=root:Environmental:Aquatic:Marine ) — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#672 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AADGOaaGvAkP4jG8W4OlYRBpDn6NwPqWks5vT5CrgaJpZM4bV0bC> .

[pbuttigieg]

Many thanks @mb1069 ! Our work here (Rob's in the loop on this) aims to give you another tool to do this with semantic web tech.

OK, thanks! In this case we should encode the xref with identical fragment
to the URL, e.g. MGNIFY:Foo:Bar:Baz+Biz, or we can just use the URL
directly as the xref (these should get translated to equivalence axioms in
the release)

@cmungall I'm more a fan of the whole URL so there's something actionable right away.

[pbuttigieg]

Obsolete