Template:Infobox gene: Difference between revisions
adding human protein category to match pbb template approach (should update this to a gene category instead at some point) |
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<includeonly>{{#invoke: |
<includeonly>{{#invoke:Infobox gene|getTemplateData}}</includeonly><noinclude> |
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[[Category:Human proteins]]</includeonly> |
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<noinclude> |
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{{Documentation|heading=Infobox Gene documentation}} |
{{Documentation|heading=Infobox Gene documentation}} |
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Latest revision as of 01:05, 25 February 2021
 | 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: |
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
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) ↑ ↓ |
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| Mouse | Mouse gene data page Reln (d:Q14331135) |
→encodes (d:P:P688)→ ←encoded by (d:P:P702)← |
Mouse protein data page Reelin (d:Q14331165) |
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| ↑ ↓ ortholog (d:P:P684) ↑ ↓ |
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| ⋮ | ⋮ | ⋮ |
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 | 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 | 
|
● | ||||
| 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
- 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.