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Creation of EBI Biome terms #672
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We also need to include mappings to the EBI terms. these don't have IDs, but can be identified by Or we could do these as synonyms. Either way, it is easy to export as a simple TSV as part of each release |
We need something more permissive than xrefs if they don't allow anything other than IDs, and we need this OBO-wide |
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? or is there something more compact? What would the URL/IRI be for something more fine grain (like "Coastal")? |
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) |
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
)
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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.
@cmungall I'm more a fan of the whole URL so there's something actionable right away. |
Obsolete |
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
Perhaps we could create yaml patterns for each of the major biome types, starting with Environmental.
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