Name of the (nano) material JSON schema about isa-api HOT 13 CLOSED

Hi @vedina, what about nano_material_schema.json? Otherwise, doesn't the ISA-Tab nano spec suggest a name?

from isa-api.

We thought about creating the extensions in separate folders under:
https://github.com/ISA-tools/isa-api/tree/master/isatools/schemas/isa_model_version_1_0_schemas
(where we also have the 'core' schemas)

Would that work for you?
Thanks

from isa-api.

• ISA-TAB-Nano uses i_material.txt , hence we named the new schema material_schema.json in a subfolder material (in the forked repo).

However, in ISA there already is material_schema.json, describing quite a different object. I'm concerned using the same name for two different schema may confuse the parsers (if not people).

from isa-api.

@vedina I still think it would be better to name the schema nano_material_schema.json - in the ISA model (and the schemas we have been working on), the concept of material is generic - then sources/samples are special cases (to be strict, they are material elements that play specific roles). The serialisation to a particular format (e.g. ISA-Tab nano) could use the required filename (i_material.txt) if needed.

I will close the issue now, but @vedina or @proccaserra, do re-open it if you think this requires further discussion.

Many thanks

from isa-api.

We avoided naming it "nano", because what we are working on is rather generic way to describe the composition of chemical substances (with nanomaterial a special case). Perhaps we should use "composition" in the schema name.

from isa-api.

Actually, I think that @proccaserra was thinking along those same lines... We looked at 'composite material' but we found this: https://en.wikipedia.org/wiki/Composite_material

What about 'composition material'? would that work?

from isa-api.

not sure it's the same (similar, yes).

at the moment we need support for chemical substances (including nanomaterials), as per these definitons for example.

NPO chemical substance

More ontology definitions in BioPortal

IUPAC substance definition

Matter of constant composition best characterized by the entities 
(molecules, formula units, atoms) it is composed of. 
Physical properties such as density, refractive index, 
electric conductivity, melting point etc. characterize the chemical substance.

REACH substance definition

a chemical element and its compounds in the natural state or obtained by any
manufacturing process, including any additive necessary to preserve its stability and
any impurity deriving from the process used, but excluding any solvent which may be
separated without affecting the stability of the substance or changing its
composition

from isa-api.

Hi @vedina, what about calling mcm_material_extension, where mcm would stand for 'mixture & complex molecular entity' for now. the name could be altered as the schema is created, which would clarify our appreciation of the envelop of cases it is supposed to support?

from isa-api.

sounds good, thanks @proccaserra

from isa-api.

Great! But maybe remove 'extension' from the name (as we know this won't be part of the core, and it will be in a separate folder for extensions)? so, it would be mcm_material_schema.json.

from isa-api.

Done enanomapper@e32a213

from isa-api.

Thanks @vedina, send us a pull request when you are ready (do consider that we have been pushing many updates to our repo).

from isa-api.

we try to merge with yours, will send a pull request when ready.

from isa-api.