Wikidata:Property proposal/has positive marker

has positive markerEdit

Originally proposed at Wikidata:Property proposal/Natural science

   Done: has marker (P8872) (Talk and documentation)
Descriptiona gene or a protein published as a marker of a species-specific cell type
RepresentsMarker gene (Q2776413) (partially)
Data typeItem
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) macromolecular complex (Q22325163) .}
Example 1human astrocyte (Q67801129)GFAP (Q14864879)

referenced by:

Example 2human cytotoxic t cell (Q101423166)CD8 [plasma membrane] (Q50260473)

referenced by:

Example 3human t helper cell (Q101423298)CD4 molecule (Q412587)

referenced by:

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 useReconcile knowledge from the PanglaoDB marker database to Wikidata. In the future, expand to other trusted sources of cell type marker information.

MotivationEdit

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) 14:39, 17 November 2020 (UTC)

DiscussionEdit

<ping project should not be used in an indented reply> Andrew Su
Marc Robinson-Rechavi
Pierre Lindenbaum
Michael Kuhn
Boghog
Emw
Chandres
Dan Bolser
Pradyumna
Chinmay
Timo Willemsen
Salvatore Loguercio
Tobias1984
Daniel Mietchen
Optimale
Mcnabber091
Ben Moore
Alex Bateman
Klortho
Hypothalamus
Vojtěch Dostál
Gtsulab
Andra Waagmeester
Sebotic
Mvolz
Toniher
Elvira Mitraka
David Bikard
Dan Lawson
Francesco Sirocco
Konrad U. Förstner (talk)
Chris Mungall (talk)
Kristina Hettne
Hardwigg
i9606
Putmantime
Tinm
Karima Rafes
Finn Årup Nielsen
Jasper Koehorst
Till Sauerwein
Crowegian
Nothingserious
Okkn
AlexanderPico
Amos Bairoch
Gstupp
DePiep
Was a bee
SarahKeating
Muhammad Elhossary
Ptolusque
Netha
Damian Szklarczyk
Kpjas
Thibdx
Juliansteinb
TiagoLubiana
SCIdude
Photocyte
Yusra Haider
JS
Hannes Röst
Kritika Dusad
T.Shafee(evo&evo) (talk)
GoEThe
  Notified participants of WikiProject Molecular biology --TiagoLubiana (talk) 14:43, 17 November 2020 (UTC)

@TiagoLubiana, Jvcavv, Bmeldal, Tinker Bell:   Done has marker (P8872) Pamputt (talk) 07:24, 27 November 2020 (UTC)