User:TiagoLubiana/has marker

has positive marker

   Under discussion

Description	a gene or a protein published as a marker of a species-specific cell type
Represents	marker gene (Q2776413) (partially)
Data type	Item
Domain	?subject instance of (P31) cell type (Q189118) . ?subject found in taxon (P703) ?taxon . ?taxon taxon rank (P105) species (Q7432).
Allowed values	{?object instance of (P31) protein (Q8054) .} UNION {?object instance of (P31) gene (Q7187) .} UNION {?object instance of (P31) protein-containing complex (Q22325163) .}
Example 1	human astrocyte (Q67801129) → GFAP (Q14864879) referenced by: stated in (P248) PanglaoDB (Q99936939) retrieved (P813) 08 of November 2020 reference URL (P854) https://panglaodb.se/markers.html
Example 2	human cytotoxic t cell (Q101423166) → CD8 [plasma membrane] (Q50260473) referenced by: retrieved (P813) 09 of November 2020 reference URL (P854) https://www.niaid.nih.gov/research/immune-cells
Example 3	human t helper cell (Q101423298) → CD4 molecule (Q412587) referenced by: retrieved (P813) 09 of November 2020 reference URL (P854) https://www.niaid.nih.gov/research/immune-cells
Source	- PanglaoDB marker database: PanglaoDB (Q99936939) and PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data (Q63664483) - CellMarker marker database: CellMarker (Q64371987) and CellMarker: a manually curated resource of cell markers in human and mouse (Q56984510) - CellPedia-SHOGoiN marker database: CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses (Q35482351)
Planned use	Reconcile knowledge from the PanglaoDB marker database to Wikidata. In the future, expand to other trusted sources of cell type marker information.

Motivation

Even though the concept of a marker gene/protein is not clear cut, it is very important, and widely used in databases and scientific articles.

This property will help us to represent that a gene/protein has been reported as a marker by a credible source, and should always contain a reference.

Some markers are reported as proteins and some as genes. Some genes don`t encode proteins, and some protein markers are actually protein complexes.

The property would be inclusive to these slightly different markers.

Some cell types are marked by absence of expression of genes/proteins/protein expression. As these seem to be less common than positive markers (no organized databases, for example) they are left outside the value range for this property.

TiagoLubiana (talk) 17:33, 8 November 2020 (UTC)