利用者:Was a bee/Infobox gene/doc
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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
[編集]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
[編集]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
[編集]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
[編集]"An Error has occurred retrieving Wikidata item for infobox" Indicates a non gene/protein Wikidata item or an incomplete Wikidata item.
Categories
[編集]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
[編集]![](http://upload.wikimedia.org/wikipedia/commons/thumb/9/9d/ProteinBoxBot_Network_Diagram_Oct_2016.png/220px-ProteinBoxBot_Network_Diagram_Oct_2016.png)
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
[編集]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
[編集]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
[編集]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}} }} | ソニック・ヘッジホッグ | ● | ● | |||
Aliases | Aliases | {{wikidata|aliases|{{User:Was a bee/Infobox gene/sub|getPageQID|Human|Gene}} }} | ● | ● | ||||
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/>}} | • 金属イオン結合 • ペプチダーゼ活性 • 加水分解酵素活性 • 血漿タンパク結合 |
● | ● | |||
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}} | 7番染色体 (ヒト)[1] | ● | ● | |||
Chromosome number | P1813 | {{wikidata|property| {{wikidata|property|raw|{{Infobox gene/sub|getPageQID|Human|Gene}}|P1057}} |P1813}} | ● | |||||
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}} | Lua エラー モジュール:Wd 内、2009 行目: attempt to concatenate a nil value | ● | ● | |||
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}} | ● | ● | ||||
NCBI Locus tag | P2393 | {{wikidata|properties|{{Infobox gene/sub|getPageQID|Human|Gene}}|P2393}} |
Installation
[編集]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**
" withCTRL+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.
Similar templates
[編集]- Template:Infobox protein
- Template:Infobox enzyme
- Template:Infobox protein family
- Template:Infobox nonhuman protein
- Template:GNF Protein box - historical?
See also
[編集]- d:User:ProteinBoxBot - Enormous bio/med data in Wikidata are mostly posted and maintained by this team
- Template:Wikidata - Most data retrievals are done through this template (and User:Was a bee/Infobox gene/sub)
- mw:Help:Extension:ParserFunctions
- 個人設定 → ガジェット → Editing →
- ^ アンサンブル・リリース106, アンサンブル 遺伝子ID ENSG00000164690, Wikidata Q111699881