From 024da2ed7f7d0a37f44a3ed99114a992f7ad2064 Mon Sep 17 00:00:00 2001 From: jamie-m-a Date: Wed, 1 Apr 2026 15:10:01 +0100 Subject: [PATCH 1/2] more updated pages --- .../phenotype/phenotype_annotation.html | 20 +- .../genome/variation/species/populations.html | 179 ++++++++++++++++++ .../species/sources_documentation.html | 112 +++++------ 3 files changed, 245 insertions(+), 66 deletions(-) diff --git a/ensembl/htdocs/info/genome/variation/phenotype/phenotype_annotation.html b/ensembl/htdocs/info/genome/variation/phenotype/phenotype_annotation.html index daffed2883..333c9655a1 100644 --- a/ensembl/htdocs/info/genome/variation/phenotype/phenotype_annotation.html +++ b/ensembl/htdocs/info/genome/variation/phenotype/phenotype_annotation.html @@ -76,16 +76,16 @@

Phenotype classes

- - + + - - + + - +
Classes Example phenotypes Example variants
trait'Inborn genetic diseases' from ClinVarrs376574181'OSTEOGENESIS IMPERFECTA' from ClinVarrs193922173
tumour'Lung tumour' from COSMICCOSV67207411'Central nervous system tumour' from COSMICCOSV99527653
non_specified 'not specified' from ClinVarrs751840065rs1414372233
@@ -107,27 +107,27 @@

Phenotype/disease ontologies

CMO Clinical Measurement Ontology - + 2.252 EFO Experimental Factor Ontology - 3.76.0 + 3.80.0 HPO Human Phenotype Ontology - 2025-01-16 + 2025-05-06 MP Mammalian Phenotype Ontology - 2025-01-30 + 2025-07-29 VT Vertebrate Trait Ontology - 2024-05-15 + 2025-07-15 diff --git a/ensembl/htdocs/info/genome/variation/species/populations.html b/ensembl/htdocs/info/genome/variation/species/populations.html index 2a3be99c4a..1fb049126b 100644 --- a/ensembl/htdocs/info/genome/variation/species/populations.html +++ b/ensembl/htdocs/info/genome/variation/species/populations.html @@ -1966,7 +1966,186 @@

Populations from the + Sus_scrofa +

Sus scrofa (Pig)

+ +
+ +

Populations from the EVA study PRJEB93975

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameSizeDescription
PRJEB93975:ALL127ALL populations from EVA study PRJEB93975
  • PRJEB93975:SWC
57South Western China super-population from EVA study PRJEB93975
  • PRJEB93975:Tibetan
29Tibetan population from EVA study PRJEB93975
  • PRJEB93975:Wujin
3Wujin population from EVA study PRJEB93975
  • PRJEB93975:Yanan
3Yanan population from EVA study PRJEB93975
  • PRJEB93975:Neijiang
3Neijiang population from EVA study PRJEB93975
  • PRJEB93975:Xiaoer
7Xiaoer population from EVA study PRJEB93975
  • PRJEB93975:Hechuan
7Hechuan population from EVA study PRJEB93975
  • PRJEB93975:cwb1
3cwb1 population from EVA study PRJEB93975
  • PRJEB93975:Bamei
1Bamei population from EVA study PRJEB93975
  • PRJEB93975:Rongchang
1Rongchang population from EVA study PRJEB93975
  • PRJEB93975:SCC
57South Central China super-population from EVA study PRJEB93975
  • PRJEB93975:Penzhou
2Penzhou population from EVA study PRJEB93975
  • PRJEB93975:Ningxiang
17Ningxiang population from EVA study PRJEB93975
  • PRJEB93975:Debao
7Debao population from EVA study PRJEB93975
  • PRJEB93975:Qinshaohua
7Qinshaohua population from EVA study PRJEB93975
  • PRJEB93975:Daweizi
7Daweizi population from EVA study PRJEB93975
  • PRJEB93975:Shaziling
7Shaziling population from EVA study PRJEB93975
  • PRJEB93975:Bama-miniature
1Bama-miniature population from EVA study PRJEB93975
  • PRJEB93975:EC
12Eastern China super-population from EVA study PRJEB93975
  • PRJEB93975:Jinhua
4Jinhua population from EVA study PRJEB93975
  • PRJEB93975:Tiegu
7Tiegu population from EVA study PRJEB93975
  • PRJEB93975:Meishan
1Meishan population from EVA study PRJEB93975
  • PRJEB93975:WE
12Western Europe super-population from EVA study PRJEB93975
  • PRJEB93975:Hampshire
1Hampshire population from EVA study PRJEB93975
  • PRJEB93975:Berkshire
1Berkshire population from EVA study PRJEB93975
  • PRJEB93975:Landrace
1Landrace population from EVA study PRJEB93975
  • PRJEB93975:Pietrain
1Pietrain population from EVA study PRJEB93975
  • PRJEB93975:LargeWhite
1LargeWhite population from EVA study PRJEB93975
  • PRJEB93975:Others
5Others super-population from EVA study PRJEB93975
  • PRJEB93975:USMARC
1USMARC population from EVA study PRJEB93975
  • PRJEB93975:Duroc
1Duroc population from EVA study PRJEB93975
  • PRJEB93975:PK-15_cell_line
3PK-15_cell_line population from EVA study PRJEB93975
diff --git a/ensembl/htdocs/info/genome/variation/species/sources_documentation.html b/ensembl/htdocs/info/genome/variation/species/sources_documentation.html index 6ac6840e69..d99eb21290 100644 --- a/ensembl/htdocs/info/genome/variation/species/sources_documentation.html +++ b/ensembl/htdocs/info/genome/variation/species/sources_documentation.html @@ -1751,8 +1751,8 @@

American bison EVA - - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -1807,8 +1807,8 @@

American mink EVA - - - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -1847,7 +1847,7 @@

Arabian camel EVA 8 - Variants imported from EVA + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -1886,7 +1886,7 @@

Atlantic herring EVA 8 - Variants imported from EVA + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -1941,8 +1941,8 @@

Atlantic salmon EVA - - - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2420,8 +2420,8 @@

Chimpanzee EVA - 16/12/2025 - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2459,8 +2459,8 @@

Collared flycatch EVA - 16/12/2025 - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2498,8 +2498,8 @@

Crab-eating macaq EVA - 16/12/2025 - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2747,8 +2747,8 @@

Domestic yak EVA - 16/12/2025 - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2787,7 +2787,7 @@

Duck EVA 8 - Variants imported from EVA + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2826,7 +2826,7 @@

European seabass EVA 8 - + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2865,7 +2865,7 @@

Fruit fly EVA 8 - + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -2904,7 +2904,7 @@

Gibbon EVA 8 - + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3034,8 +3034,8 @@

Golden-collared ma EVA - 08/01/2026 - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3073,8 +3073,8 @@

Great Tit EVA - 08/01/2026 - + 8 + Short variant data feteched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3129,8 +3129,8 @@

Greater amberjack EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3168,8 +3168,8 @@

Guinea Pig EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3335,8 +3335,8 @@

Japanese quail EVA - 16/12/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3374,8 +3374,8 @@

Macaque EVA - 16/12/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3413,8 +3413,8 @@

Mallard EVA - 16/12/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3548,8 +3548,8 @@

Mouse Lemur EVA - 23/04/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3587,8 +3587,8 @@

Nile tilapia EVA - 23/04/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -3643,8 +3643,8 @@

Northe EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4054,8 +4054,8 @@

Pike-perch EVA - 16/10/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4155,8 +4155,8 @@

Prairie vole EVA - 149 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4211,8 +4211,8 @@

Rabbit EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4250,8 +4250,8 @@

Rainbow trout EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4615,8 +4615,8 @@

Sumatran orangutan EVA - 29/04/2025 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4714,8 +4714,8 @@

Turkey EVA - 132 - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4770,8 +4770,8 @@

Vervet-AGM EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
@@ -4809,8 +4809,8 @@

White-tufted-ear m EVA - - - + 8 + Short variant data fetched on the fly from the European Variation Archive
Variant (from VCF)
From 1950a14c24f78e1063de36b1ac23943a0fd1f450 Mon Sep 17 00:00:00 2001 From: jamie-m-a Date: Wed, 1 Apr 2026 15:15:42 +0100 Subject: [PATCH 2/2] text tweak --- .../species/sources_documentation.html | 62 +++++++++---------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/ensembl/htdocs/info/genome/variation/species/sources_documentation.html b/ensembl/htdocs/info/genome/variation/species/sources_documentation.html index d99eb21290..10092351d3 100644 --- a/ensembl/htdocs/info/genome/variation/species/sources_documentation.html +++ b/ensembl/htdocs/info/genome/variation/species/sources_documentation.html @@ -1752,7 +1752,7 @@

American bison EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -1808,7 +1808,7 @@

American mink EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -1847,7 +1847,7 @@

Arabian camel EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -1886,7 +1886,7 @@

Atlantic herring EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -1942,7 +1942,7 @@

Atlantic salmon EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2421,7 +2421,7 @@

Chimpanzee EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2460,7 +2460,7 @@

Collared flycatch EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2499,7 +2499,7 @@

Crab-eating macaq EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2748,7 +2748,7 @@

Domestic yak EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2787,7 +2787,7 @@

Duck EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2826,7 +2826,7 @@

European seabass EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2865,7 +2865,7 @@

Fruit fly EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -2904,7 +2904,7 @@

Gibbon EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3035,7 +3035,7 @@

Golden-collared ma EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3074,7 +3074,7 @@

Great Tit EVA 8 - Short variant data feteched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3130,7 +3130,7 @@

Greater amberjack EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3169,7 +3169,7 @@

Guinea Pig EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3336,7 +3336,7 @@

Japanese quail EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3375,7 +3375,7 @@

Macaque EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3414,7 +3414,7 @@

Mallard EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3549,7 +3549,7 @@

Mouse Lemur EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3588,7 +3588,7 @@

Nile tilapia EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -3644,7 +3644,7 @@

Northe EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4055,7 +4055,7 @@

Pike-perch EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4156,7 +4156,7 @@

Prairie vole EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4212,7 +4212,7 @@

Rabbit EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4251,7 +4251,7 @@

Rainbow trout EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4616,7 +4616,7 @@

Sumatran orangutan EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4715,7 +4715,7 @@

Turkey EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4771,7 +4771,7 @@

Vervet-AGM EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)
@@ -4810,7 +4810,7 @@

White-tufted-ear m EVA 8 - Short variant data fetched on the fly from the European Variation Archive + Short variant data streamed live from the European Variation Archive
Variant (from VCF)