Template:Infobox gene

Infobox Gene documentation[view] [edit] [history] [purge]

This is the Infobox gene template. The data in the infobox is sourced from Wikidata. The Lua implementation of this template is located at Module:Infobox gene.

Usage on a gene page

Add {{infobox gene}} to the top of a gene page. The infobox is populated via the Wikidata item of the page it resides on. To view which Wikidata item is linked to a page, follow the "Wikidata items" link from the "Tools" menu to the left of the article.

Usage on a protein page

Add {{infobox gene}} to the top of a protein page. The infobox is populated by using the Wikidata item of the protein to find the encoded gene item and then uses the gene item to populate the infobox.

Usage on other pages

Any page can display the infobox even if it does not have a gene or protein interwiki link. The Wikidata item must be explicitly added as a parameter and the underlying module is invoked. For instance, appending {{#invoke:Infobox_gene|getTemplateData|QID=Q414043}} to the top of any page will create an infobox for the gene RELN. QID is the Wikidata gene item used to populate the infobox. Substitute the wikidata item id (QID) of interest as the QID parameter.

Error message

"An Error has occurred retrieving Wikidata item for infobox" Indicates a non gene/protein Wikidata item or an incomplete Wikidata item.

Categories

Including this template will automatically result in the addition of relevant categories based on the properties of the gene. These include Category:Human proteins and categories that correspond to the chromosome where the gene is located, such as Category:Genes on human chromosome 19. Other categories added manually to the article apart from the template will work as usual.

Data structure

File:ProteinBoxBot Network Diagram Oct 2016.png

Basic network structure of the ProteinBoxBot wikidata project

Data structure of gene and protein data in Wikidata is a bit complex. Even if there is only one gene/protein article in Wikipedia, there are many data pages in Wikidata.

Basically Wikidata has distinct pages for gene and protein each, for respective species (See the table below). And pages are interconnected based on following rules.

• Wikipedia articles are connected to Wikidata's gene data page (#Case A) or protein data page (#Case B) through d:Help:Sitelinks. In most cases, articles are connected to gene data page.
• Gene and protein pages are interconnected through "encodes (d:P:P688)" and "encoded by (d:P:P702)" property claims (horizontal arrows "→", "←" in the table).
• Gene pages from different species are interconnected through "ortholog (d:P:P684)" property claims (vertical arrows "↑", "↓" in the table).

The data which infobox_gene shows to readers are collected from somewhere of this interconnected Wikidata pages.

Case A

In most cases, Wikipedia article page is connected to Human gene data page. For example, Sonic hedgehog.

	Wikipedia (Article)		Wikidata (Gene)		Wikidata (Protein)
Human	Wikipedia article page Sonic hedgehog	→d:Help:Sitelinks→ ←d:Help:Sitelinks←	Human gene data page SHH (d:Q14860072)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Human protein data page Sonic hedgehog (d:Q2477760)
			↑　　　↓ ortholog (d:P:P684) ↑　　　↓
Mouse			Mouse gene data page Shh (d:Q14860079)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Mouse protein data page Sonic hedgehog (d:Q14860215)
			↑　　　↓ ortholog (d:P:P684) ↑　　　↓
⋮			⋮		⋮

Case B

In some cases, Wikipedia article page is connected to Human protein data page. For example, Reelin.

	Wikidata (Gene)		Wikidata (Protein)		Wikipedia (Article)
Human	Human gene data page RELN (d:Q414043)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Human protein data page Reelin (d:Q13561329)	→d:Help:Sitelinks→ ←d:Help:Sitelinks←	Wikipedia article page Reelin
	↑　　　↓ ortholog (d:P:P684) ↑　　　↓
Mouse	Mouse gene data page Reln (d:Q14331135)	→encodes (d:P:P688)→ ←encoded by (d:P:P702)←	Mouse protein data page Reelin (d:Q14331165)
	↑　　　↓ ortholog (d:P:P684) ↑　　　↓
⋮	⋮		⋮

Data location

The followings are list of data which are used in this template. Showing data example and data location in the case of Sonic hedgehog.

Data	Wikidata property	Data example	Data location				Other
			Human Gene Page	Human Protein Page	Mouse Gene Page	Mouse Protein Page
			Q14860072	Q2477760	Q14860079	Q14860215
Gene name	Label		●		●
Aliases	Aliases		●		●
HGNC gene symbol	P353		●
Entrez Gene ID	P351		●		●
Image	P18		●
Ensembl Gene ID	P594		●		●
UniProt ID	P352			●		●
EC number	P591			●		●
OMIM ID	P492		●
MGI ID	P671				●
HomoloGene ID	P593		●		●
PDB id	P638			●		●
Gene Atlas Image	P692		●
Gene ontology	P680 P681 P682			●		●
RefSeq RNA ID	P639		●		●
RefSeq Protein ID	P637			●		●
Ensembl Transcript ID	P704		●		●
Chromosome	P1057		●		●
Chromosome number	P1813						●
Chromosome length	P2043						●
Chromosome category	P910						●
Cytogenetic location	P4196		●		●
Genomic start	P644		●		●
Genomic end	P645		●		●
Strand orientation	P2548		●		●

Similar templates

• Template:Infobox protein
• Template:Infobox enzyme
• Template:Infobox protein family
• Template:Infobox nonhuman protein
• Template:GNF Protein box - historical

See also

• d:User:ProteinBoxBot - Enormous biomedical data in Wikidata are mostly posted and maintained by this bot
• Wikipedia:Gene Wiki

External links

• BioGPS, a site that allows for automated stub creation for human gene pages using this template
• Huss, Jon W; Orozco, Camilo; Goodale, James; Wu, Chunlei; Batalov, Serge; Vickers, Tim J; Valafar, Faramarz; Su, Andrew I (8 July 2008). "A Gene Wiki for Community Annotation of Gene Function". PLoS Biology. 6 (7): e175. doi:10.1371/journal.pbio.0060175. PMID 18613750.

The above documentation is transcluded from Template:Infobox gene/doc. (edit | history)
Editors can experiment in this template's sandbox (create | mirror) and testcases (create) pages.
Add categories to the /doc subpage. Subpages of this template.