NTR: diatomaceous earth

[cmungall]

Needed to define: http://purl.obolibrary.org/obo/AGRO_00000211 ! diatomaceous earth spreading

https://en.wikipedia.org/wiki/Diatomaceous_earth
"a naturally occurring, soft, siliceous sedimentary rock that is easily crumbled into a fine white to off-white powder"

Should we represent the rock, the derivative, or the class union of both? It seems the standard usage of the term is to denote the powdered derivative

Note CHEBI has:

[Term]
id: CHEBI:82661
name: diatomaceous earth
namespace: chebi_ontology
def: "A form of silicon dioxide composed of skeletons of prehistoric diatoms (a type of hard-shelled algae). It can absorb up to four times its weight in water, and is used as an absorbent, filtration aid, and mild abrasive." []
synonym: "Celite" RELATED [ChemIDplus]
synonym: "diatomite" RELATED [ChEBI]
synonym: "fossil flour" RELATED [ChemIDplus]
synonym: "kieselguhr" RELATED [ChemIDplus]
synonym: "siliceous earth" RELATED [ChemIDplus]
xref: ChemIDplus:61790-53-2
xref: CiteXplore:24516665
xref: CiteXplore:24767070
xref: CiteXplore:25024689
xref: Wikipedia:Diatomaceous_earth
is_a: CHEBI:30563  ! silicon dioxide
is_a: CHEBI:46662  ! mineral

But unlike in #456 it's not classified as a mixture but rather as both a molecular entity (SiO2) and a substance (mineral: "In general, a mineral is a chemical substance that is normally crystalline formed and has been formed as a result of geological processes. The term also includes metamict substances (naturally occurring, formerly crystalline substances whose crystallinity has been destroyed by ionising radiation) and can include naturally occurring amorphous substances that have never been crystalline ('mineraloids') such as georgite and calciouranoite as well as substances formed by the action of geological processes on bigenic compounds ('biogenic minerals')")

My suggestion:

Class: ENVO:new1
  Label "diatomaceous earth"
  SubClassOf: ENVO:00002016 ! sedimentary rock,
    composed_primarily_of some ENVO:new2,


Class: ENVO:new2
  Label "diatomaceous earth particle"
  xref: CHEBI:82661
  SubClassOf: ENVO:01000010 ! abiotic mesoscopic physical object,
   has_part some CHEBI:SiO2 and derives from some NCBITaxon:diatom,
   has_part some ...

Perhaps we should have a class 'frustule' in GO

[pbuttigieg]

@cmungall concur with your analysis.

The class has been created with some minor modifications in the editors' version:
http://purl.obolibrary.org/obo/ENVO_01000962

Perhaps we should have a class 'frustule' in GO

Definitely - we're queuing some NTRs for our polar systems and this will be there.

[pbuttigieg]

Sorry - need to add the particles. Will do soon.

[pbuttigieg]

I'm using "diatomite" as the main label, as calling a rock "earth" is a bit confusing. Diatomaceous earth is a related synonym.

We now have:

and

The derives from relation is not exactly right, as it's hard to say that the portion of diatomite ceases to exist if a particle breaks off.

[cmungall]

what's our SOP on abbreviations? In uberon we annotate the axiom https://github.com/obophenotype/uberon/wiki/Using-uberon-for-text-mining

and don't include the periods

[pbuttigieg]

We should adopt this in ENVO. Is there a bulk set of synonym PURLs we could use for import? Moving this to #516