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Template:Infobox gene

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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

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

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

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

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 SHH
Aliases Aliases HHG1, HLP3, HPE3, MCOPCB5, SMMCI, TPT, TPTPS, sonic hedgehog, Sonic hedgehog, ShhNC
HGNC gene symbol P353 SHH
Entrez Gene ID P351 6469
Image P18 Shh structure.png
Ensembl Gene ID P594 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 PBB GE SHH 207586 at fs.png
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
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 Category:Genes on human chromosome 7
Cytogenetic location P4196 7q36.3
Genomic start P644 155799986
Genomic end P645 155812273
Strand orientation P2548 Reverse Strand

Similar templates

See also

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