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feat: update resource files
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@mkarmona
mkarmona committed Feb 27, 2020
1 parent b6c6933 commit ea2b9cd
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Showing 3 changed files with 24 additions and 2 deletions.
2 changes: 1 addition & 1 deletion build.sbt
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Expand Up @@ -61,7 +61,7 @@ libraryDependencies += "com.typesafe.play" %% "play" % "2.6.23"
libraryDependencies += "com.typesafe.play" %% "play-logback" % "2.6.23"
libraryDependencies += "com.typesafe.play" %% "play-json" % "2.6.13"
libraryDependencies += "com.typesafe.play" %% "play-slick" % "3.0.3"
libraryDependencies += "ru.yandex.clickhouse" % "clickhouse-jdbc" % "0.2.3"
libraryDependencies += "ru.yandex.clickhouse" % "clickhouse-jdbc" % "0.2.4"
libraryDependencies += "org.sangria-graphql" %% "sangria" % "1.4.2"
libraryDependencies += "org.sangria-graphql" %% "sangria-play-json" % "1.0.5"
libraryDependencies += "com.nrinaudo" %% "kantan.csv" % "0.4.0"
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22 changes: 22 additions & 0 deletions resources/v2g_biofeature_labels.json
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Expand Up @@ -47,6 +47,28 @@
{"original_source": "GTEXv7", "biofeature_string": "Vagina", "label": "Vagina", "biofeature_code": "UBERON_0000996"}
{"original_source": "GTEXv7", "biofeature_string": "Whole_Blood", "label": "Whole blood", "biofeature_code": "UBERON_0000178"}
{"original_source": "GTEXv7", "biofeature_string": "blood_plasma", "label": "Blood plasma", "biofeature_code": "UBERON_0001969"}
{"original_source": "jung2019", "biofeature_string": "Trophoblast", "label": "Trophoblast", "biofeature_code": "UBERON_0000088"}
{"original_source": "jung2019", "biofeature_string": "Left Ventricle", "label": "Heart left ventricle", "biofeature_code": "UBERON_0002084"}
{"original_source": "jung2019", "biofeature_string": "Adrenal Gland", "label": "Adrenal gland", "biofeature_code": "UBERON_0002369"}
{"original_source": "jung2019", "biofeature_string": "Human ES cells", "label": "Embryonic stem cells", "biofeature_code": "ES_CELLS"}
{"original_source": "jung2019", "biofeature_string": "Neural Progenitor Cell", "label": "Neural Progenitor Cell", "biofeature_code": "NEURAL_PROGENITOR_CELL"}
{"original_source": "jung2019", "biofeature_string": "Small Bowel", "label": "Small intestine", "biofeature_code": "UBERON_0002108"}
{"original_source": "jung2019", "biofeature_string": "Right Ventricle", "label": "Right Ventricle", "biofeature_code": "UBERON_0002080"}
{"original_source": "jung2019", "biofeature_string": "Mesendoderm", "label": "Mesendoderm", "biofeature_code": "MESENDODERM"}
{"original_source": "jung2019", "biofeature_string": "Mesenchymal Stem Cell", "label": "Mesenchymal Stem Cell", "biofeature_code": "MESENCHYMAL_STEM_CELL"}
{"original_source": "jung2019", "biofeature_string": "Sigmoid Colon", "label": "Colon sigmoid", "biofeature_code": "UBERON_0001159"}
{"original_source": "jung2019", "biofeature_string": "Fibroblast", "label": "Fibroblast", "biofeature_code": "FIBROBLAST"}
{"original_source": "jung2019", "biofeature_string": "Hippocampus", "label": "Brain hippocampus", "biofeature_code": "UBERON_0002421"}
{"original_source": "jung2019", "biofeature_string": "Esophagus", "label": "Esophagus", "biofeature_code": "UBERON_0001043"}
{"original_source": "jung2019", "biofeature_string": "Dorsolateral Prefrontal Cortex", "label": "Dorsolateral Prefrontal Cortex", "biofeature_code": "UBERON_0009834"}
{"original_source": "jung2019", "biofeature_string": "Fat", "label": "Fat", "biofeature_code": "FAT"}
{"original_source": "jung2019", "biofeature_string": "Bladder", "label": "Bladder", "biofeature_code": "UBERON_0001255"}
{"original_source": "jung2019", "biofeature_string": "Thymus", "label": "Thymus", "biofeature_code": "UBERON_0002370"}
{"original_source": "jung2019", "biofeature_string": "Psoas", "label": "Psoas", "biofeature_code": "UBERON_0008450"}
{"original_source": "jung2019", "biofeature_string": "Lymphoblastoid cell lines", "label": "Lymphoblastoid cell lines", "biofeature_code": "LYMPHOBLASTOID_CELL"}
{"original_source": "jung2019", "biofeature_string": "Aorta", "label": "Artery aorta", "biofeature_code": "UBERON_0000947"}
{"original_source": "jung2019", "biofeature_string": "Gastric", "label": "Gastric", "biofeature_code": "GASTRIC"}
{"original_source": "jung2019", "biofeature_string": "Right Atrium", "label": "Right Atrium", "biofeature_code": "UBERON_0002078"}
{"original_source": "javierre2016", "biofeature_string": "Endothelial_precursors", "label": "Endothelial precursors", "biofeature_code": "ENDOTHELIAL_PRECURSORS"}
{"original_source": "javierre2016", "biofeature_string": "Erythroblasts", "label": "Erythroblasts", "biofeature_code": "ERYTHROBLASTS"}
{"original_source": "javierre2016", "biofeature_string": "Foetal_thymus", "label": "Foetal thymus", "biofeature_code": "FOETAL_THYMUS"}
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2 changes: 1 addition & 1 deletion resources/v2g_display_labels.json
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Expand Up @@ -3,7 +3,7 @@
{"key":"thurman2012","value":{"display_label":"DHS-promoter corr (Thurman, 2012)","overview_tooltip":"Summary of evidence linking this variant to genes using correlation of DNase I hypersensitive site and gene promoters across 125 cell and tissue types from ENCODE","tab_subtitle":"Evidence linking this variant to genes using correlation of DNase I hypersensitive site and gene promoters across 125 cell and tissue types from ENCODE","pmid":"PMID:22955617"}}
{"key":"andersson2014","value":{"display_label":"Enhancer-TSS corr (FANTOM5)","overview_tooltip":"Summary of evidence linking this variant to genes using correlation between the transcriptional activity of enhancers and transcription start sites using the FANTOM5 CAGE expression atlas","tab_subtitle":"Evidence linking this variant to genes using correlation between the transcriptional activity of enhancers and transcription start sites using the FANTOM5 CAGE expression atlas","pmid":"PMID:24670763"}}
{"key":"javierre2016","value":{"display_label":"PCHi-C (Javierre, 2016)","overview_tooltip":"Summary of evidence linking this variant to genes using Promoter Capture Hi-C in *any* of the 17 human primary hematopoietic cell types","tab_subtitle":"Evidence linking this variant to genes using Promoter Capture Hi-C in each of the 17 human primary hematopoietic cell types","pmid":"PMID:27863249"}}
{"key":"jung2019","value":{"display_label":"PCHi-C (Jung, 2019)","overview_tooltip":"Summary of evidence linking this variant to genes using Promoter Capture Hi-C in *any* of the 27 human cell/tissue types","tab_subtitle":"Evidence linking this variant to genes using Promoter Capture Hi-C in each of the 27 human cell/tissue types","pmid":"PMID:31501517"}}
{"key":"vep","value":{"display_label":"VEP (Ensembl)","overview_tooltip":"Most severe coding-sequence consequence(s) from Ensembl's Variant Effect Predictor","tab_subtitle":"Most severe coding-sequence consequence(s) from Ensembl's Variant Effect Predictor","pmid":"PMID:27268795"}}
{"key":"eqtl","value":{"display_label":"eQTL","overview_tooltip":"Summary of evidence linking this variant to changes in gene expression","tab_subtitle":"Evidence linking this variant to changes gene expression across tissues/cell types","pmid":null}}
{"key":"pqtl","value":{"display_label":"pQTL (Sun, 2018)","overview_tooltip":"Summary of evidence linking this variant to protein abundance in blood plasma","tab_subtitle":"Evidence linking this variant to protein abundance in Sun *et al.* (2018) pQTL data","pmid":"PMID:29875488"}}
{"key":"canonical_tss","value":{"display_label":"Distance (Canonical TSS)","overview_tooltip":"Distance from the variant to the transcription start site (TSS) of each gene within ±500Kb","tab_subtitle":"Distance from the variant to the transcription start site (TSS) of each gene within ±500Kb","pmid":null}}

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