[ensembl-dev] phenotype description for SNPs

[Helen Schuilenburg]

Hi

For  http://feb2014.archive.ensembl.org, variants with phenotypes with 
non-significant associations, are not shown on the website.

The non-significant phenotype associations are available through the 
Ensembl BioMart for this release.

In BioMart you can filter and display Phenotype significance [0 non 
significant, 1 significant]

For later releases we stopped using this filtering.

If possible, using more recent data from a later release would be 
beneficial.

Regards
Helen


On 02/11/2020 13:05, Türküler Özgümüş wrote:
> Hi,
>
> I am using the below code to map some SNP IDs to the following 
> attributes. I have a problem with phenotype_description. Some of the 
> SNPs match phenotypes such as BMI, fasting plasma glucose and fasting 
> insulin whereas there is no such information on the webpage for the 
> same SNPs on ensembl or gwas catalog (For example, rs546206 and 
> rs11877729). Is this a problem with the database? If it is not where 
> is this information coming from?
>
> Thank you for your help.
>
> Best,
> Turkuler
>
> -------------------------------------------------------------------------------------------------------------------
> *code:*
> snp_mart <- useMart("ENSEMBL_MART_SNP", dataset="hsapiens_snp", host = 
> "http://feb2014.archive.ensembl.org <http://feb2014.archive.ensembl.org>")
> snp_ids <- df_FDR005$SNP
> snp_attributes <- c("refsnp_id", "chr_name", "chrom_start", 
> "clinical_significance",
>                     "associated_gene", "phenotype_description", 
> "ensembl_gene_stable_id",
>                     "ensembl_transcript_stable_id", "consequence_type_tv",
>                     "polyphen_prediction", "polyphen_score", 
> "sift_prediction", "sift_score",
>                     "consequence_types_20126")
> snp_locations <- getBM(attributes=snp_attributes, filters="snp_filter",
>                       values=snp_ids, mart=snp_mart)
>
> *sessionInfo()*
> R version 4.0.3 (2020-10-10)
> Platform: x86_64-apple-darwin17.0 (64-bit)
> Running under: macOS Catalina 10.15.7
>
> Matrix products: default
> BLAS: 
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK: 
> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] biomaRt_2.44.1  forcats_0.5.0   stringr_1.4.0 dplyr_1.0.1     
> purrr_0.3.4     readr_1.3.1     tidyr_1.1.1
>  [8] tibble_3.0.3    ggplot2_3.3.2   tidyverse_1.3.0
>
> loaded via a namespace (and not attached):
>  [1] Biobase_2.48.0       httr_1.4.2           bit64_4.0.2     
>  jsonlite_1.7.0       modelr_0.1.8
>  [6] assertthat_0.2.1     askpass_1.1          stats4_4.0.3       
> BiocFileCache_1.12.1 blob_1.2.1
> [11] cellranger_1.1.0     yaml_2.2.1           progress_1.2.2       
> pillar_1.4.6         RSQLite_2.2.0
> [16] backports_1.1.8      glue_1.4.1           digest_0.6.25     
>  rvest_0.3.6          snakecase_0.11.0
> [21] colorspace_1.4-1     htmltools_0.5.0      XML_3.99-0.5       
> pkgconfig_2.0.3      broom_0.7.0
> [26] haven_2.3.1          scales_1.1.1         openssl_1.4.2     
>  generics_0.0.2       IRanges_2.22.2
> [31] ellipsis_0.3.1       withr_2.2.0          janitor_2.0.1     
>  BiocGenerics_0.34.0  cli_2.0.2
> [36] magrittr_1.5         crayon_1.3.4         readxl_1.3.1       
> memoise_1.1.0        evaluate_0.14
> [41] fs_1.5.0             fansi_0.4.1          xml2_1.3.2       
> tools_4.0.3          prettyunits_1.1.1
> [46] hms_0.5.3            lifecycle_0.2.0  S4Vectors_0.26.1     
> munsell_0.5.0        reprex_0.3.0
> [51] AnnotationDbi_1.50.3 compiler_4.0.3       rlang_0.4.7     
>  grid_4.0.3           rstudioapi_0.11
> [56] rappdirs_0.3.1       rmarkdown_2.3        gtable_0.3.0       
> DBI_1.1.0            curl_4.3
> [61] R6_2.4.1             lubridate_1.7.9      knitr_1.29       
> bit_4.0.4            utf8_1.1.4
> [66] stringi_1.4.6        parallel_4.0.3       Rcpp_1.0.5       
> vctrs_0.3.2          dbplyr_1.4.4
> [71] tidyselect_1.1.0     xfun_0.16
> -----------------------------------------------------------------------------------------------------------
>
> Turkuler Ozgumus
> Postdoctoral researcher
> Department of Clinical Science (K2)
> University of Bergen
> Bergen, Norway
>
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