Template:Infobox gene/doc

This is a documentation subpage for Template:Infobox gene.
It may contain usage information, categories and other content that is not part of the original template page.

This template is used on approximately 13,000 pages and changes may be widely noticed. Test changes in the template's /sandbox or /testcases subpages, or in your own user subpage. Consider discussing changes on the talk page before implementing them.

This template uses Lua:

Module:Infobox gene (sandbox)

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.

Data structure

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	SHH	●		●
Aliases	Aliases	HHG1, HLP3, HPE3, MCOPCB5, SMMCI, TPT, TPTPS, sonic hedgehog, Sonic hedgehog, ShhNC, sonic hedgehog signaling molecule	●		●
HGNC gene symbol	P353	SHH	●
Entrez Gene ID	P351	6469	●		●
Image	P18		●
Ensembl Gene ID	P863	ENSG00000164690	●		●
UniProt ID	P352	Q15465		●		●
EC number	P591			●		●
OMIM ID	P492	600725	●
MGI ID	P671	MGI:98297			●
HomoloGene ID	P593	30961	●		●
PDB id	P638	3HO5 3M1N 3MXW		●		●
Gene Atlas Image	P692		●
Gene ontology	P680 P681 P682	• calcium ion binding • metal ion binding • patched binding • peptidase activity • zinc ion binding • laminin-1 binding • glycosaminoglycan binding • morphogen activity • hydrolase activity • protein binding • endopeptidase activity		●		●
RefSeq RNA ID	P639	NM_000193 NM_001310462 NR_132318 NR_132319 XM_011516479 XM_011516480 XM_047420718	●		●
RefSeq Protein ID	P637	NP_000184 NP_001297391 XP_011514781 XP_011514782		●		●
Ensembl Transcript ID	P704	ENST00000472308 ENST00000297261 ENST00000430104 ENST00000435425 ENST00000441114	●		●
Chromosome	P1057	human chromosome 7	●		●
Chromosome number	P1813	7					●
Chromosome length	P2043	159345973					●
Chromosome category	P910						●
Cytogenetic location	P4196	7q36.3	●		●
Genomic start	P644	155592680	●		●
Genomic end	P645	155604967	●		●
Strand orientation	P2548	reverse strand	●		●

Similar templates

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.