User:Was a bee/Infobox gene/doc

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

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[edit]

Append {{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[edit]

Append {{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[edit]

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 {{Infobox_gene|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[edit]

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

Categories[edit]

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[edit]

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. Foe example,

Human gene location data is from "Human gene page"
Mouse UniProt id data is from "Mouse protein page"

and so on.

To get QID of each pages, User:Was a bee/Infobox gene/sub is used.

Case A[edit]

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[edit]

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[edit]

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

Data	Wikidata property	Code example	Output	Data location				Other
				Human Gene Page	Human Protein Page	Mouse Gene Page	Mouse Protein Page
				Q14860072	Q2477760	Q14860079	Q14860215

Gene name	Label	{{wikidata\|label\|{{User:Was a bee/Infobox gene/sub\|getPageQID\|Human\|Gene}} }}	SHH	●		●
Aliases	Aliases	{{wikidata\|aliases\|{{User:Was a bee/Infobox gene/sub\|getPageQID\|Human\|Gene}} }}	HHG1, HLP3, HPE3, MCOPCB5, SMMCI, TPT, TPTPS, sonic hedgehog, Sonic hedgehog, ShhNC, sonic hedgehog signaling molecule	●		●
HGNC gene symbol	P353	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P353}}	SHH	●
Entrez Gene ID	P351	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P351}}	6469	●		●
Image	P18	{{#invoke:InfoboxImage\|InfoboxImage\|image={{wikidata\|property\|raw\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P18}}\|size=50px}}		●
Ensembl Gene ID	P594	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P594}}	ENSG00000164690	●		●
UniProt ID	P352	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Protein}}\|P352}}	Q15465		●		●
EC number	P591	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Protein}}\|P591}}			●		●
OMIM ID	P492	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P492}}	600725	●
MGI ID	P671	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Mouse\|Gene}}\|P671}}	MGI:98297			●
HomoloGene ID	P593	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P593}}	30961	●		●
PDB id	P638	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Protein}}\|P638\|format=\[http://www.rcsb.org/pdb/explore/explore.do?pdbId=%p %p\]\|sep =<br/>}}	3HO5 3M1N 3MXW		●		●
Gene Atlas Image	P692	{{wikidata\|properties\|raw\|{{User:Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P692\|format=\[\[File:%p{{!}}100px\]\]\|sep=<br><br>}}		●
Gene ontology	P680 P681 P682	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Protein\|{{{QID\|}}} }}\|P680\|format=• %p\|sep =<br/>}}	• 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	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P639\|format=\[https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=%p %p\]\|sep =<br/>}}	NM_000193 NM_001310462 NR_132318 NR_132319 XM_011516479 XM_011516480 XM_047420718	●		●
RefSeq Protein ID	P637	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Protein}}\|P637\|format=\[https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=%p %p\]\|sep =<br/>}}	NP_000184 NP_001297391 XP_011514781 XP_011514782		●		●
Ensembl Transcript ID	P704	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}} \|P704\|format=\[http://identifiers.org/ensembl/%p %p\]\|sep =<br/>}}	ENST00000472308 ENST00000297261 ENST00000430104 ENST00000435425 ENST00000441114	●		●
Chromosome	P1057	{{wikidata\|property\|linked\|references\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P1057}}	human chromosome 7^[1]	●		●
Chromosome number	P1813	{{wikidata\|property\| {{wikidata\|property\|raw\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P1057}} \|P1813}}	7					●
Chromosome length	P2043	{{wikidata\|property\| {{wikidata\|property\|raw\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P1057}} \|P2043}}	159345973					●
Chromosome category	P910	{{wikidata\|property\| {{wikidata\|property\|raw\|{{Infobox gene/sub\|getPageQID\|Human\|Gene\|Q14860072}}\|P1057}} \|P910\|format=\[\[:%p\]\]}}						●
Cytogenetic location	P4196	{{wikidata\|property\|references\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P4196}}	7q36.3^[2]	●		●
Genomic start	P644	{{wikidata\|property\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P644}}	155592680	●		●
Genomic end	P645	{{wikidata\|property\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P645}}	155604967	●		●
Strand orientation	P2548	{{wikidata\|property\|references\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P2548}}	reverse strand^[1]	●		●
NCBI Locus tag	P2393	{{wikidata\|properties\|{{Infobox gene/sub\|getPageQID\|Human\|Gene}}\|P2393}}

Installation[edit]

This section explains how to install this template into your language edition.

Copy Template:infobox gene to your language project.
Then localize texts into your language (you can find corresponding texts easily by searching "**lclz**" with CTRL+F)
Copy Template:infobox gene/sub to sub page of copied template. No localization needed on this page.

If this works properly, that's all.

If you got error(s), checking following points.

Check whether Template:Wikidata and Module:wd are installed in your wiki. If not, copy-and-paste that to your wiki.
If installed, check the version of the module. Older version (before Sep. 2017) doesn't have some functionalities used in this template. If version is old, copy-and-paste the latest version to your wiki.
Many other templates and modules are used.

On categories (under development)

If you make categories like Category:Genes on human chromosome 1 in your language edition
and create d:Help:Sitelinks,
this template detect that and automatically categorize each pages into corresponding categories.