mianct schema

This schema is CJM's attempt to translate Tiago's minimal info doc into a LinkML schema

The schema is fairly minimal and is in the form of a "checklist" style schema. It is a set of fields mostly associated with this class:

There are a set of examples here:

Currently the examples are YAML, but the YAML is deliberately flat as this is a "checklist" schema, and we could have TSV/CSV/xlsx here

TODO:

include "packages" and "checklists"; e.g.
- a neuron package would have the enum for morphologies constrained
- a transcriptomics package would make it required to enter the set of marker genes
- see MIxS schema for example of how this might work
document how this relates to dosdp/robot templates

When should one provide an entry for a cell type in a MIANCT sheet?

When there is a claim of a new cell class (type or state) that has not been described before
When new information is discovered for a previously cataloged type that might influence its cataloguing (i.e. description of the presence in a different species or in a new location)
When a cell type mentioned in the article has been described before, but is not yet catalogued on an authoritative source like the Cell Ontology.

CellType - Minimal information about a cell type
OrganismTaxon - A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.

develops from
develops into
diagnostic description
id
label - The main label used to refer to a cell type
major class
major life stage - Cells of this type were identified at this stage
morphology
organ or tissue - Cells of this type were identified in an organ of this kind.
previous observations
taxon - Cells of this type were identified in an individual of this taxon. If the cell type is thought to be exclusive for that cell type, note it on the additional information field.

Boolean (Bool) - A binary (true or false) value
Date (XSDDate) - a date (year, month and day) in an idealized calendar
Datetime (XSDDateTime) - The combination of a date and time
Decimal (Decimal) - A real number with arbitrary precision that conforms to the xsd:decimal specification
Double (float) - A real number that conforms to the xsd:double specification
Float (float) - A real number that conforms to the xsd:float specification
Integer (int) - An integer
NarrativeText (str)
Ncname (NCName) - Prefix part of CURIE
Nodeidentifier (NodeIdentifier) - A URI, CURIE or BNODE that represents a node in a model.
Objectidentifier (ElementIdentifier) - A URI or CURIE that represents an object in the model.
String (str) - A character string
Time (XSDTime) - A time object represents a (local) time of day, independent of any particular day
Uri (URI) - a complete URI
Uriorcurie (URIorCURIE) - a URI or a CURIE