8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/human/dbSnp155Composite.html src/hg/makeDb/trackDb/human/dbSnp155Composite.html index a622dfe..376e91b 100644 --- src/hg/makeDb/trackDb/human/dbSnp155Composite.html +++ src/hg/makeDb/trackDb/human/dbSnp155Composite.html @@ -167,31 +167,31 @@ whole-genome sequencing of 71,702 samples mapped to the GRCh38 build of the human reference genome. </li> <li> <a href="https://www.rug.nl/research/genetics/databases/genomeofthenetherlands/" target=_blank>GoNL</a>: The Genome of the Netherlands (GoNL) Project characterizes DNA sequence variation, common and rare, for SNVs and short insertions and deletions (indels) and large deletions in 769 individuals of Dutch ancestry selected from five biobanks under the auspices of the Dutch hub of the Biobanking and Biomolecular Research Infrastructure (BBMRI-NL). </li> <li> <a href="https://www.geenivaramu.ee/en" target=_blank>Estonian</a>: The dataset contains genetic variation in the Estonian population: pharmacogenomics study of adverse drug effects using electronic health records. </li> <li> -<a href="http://genomes.vn/" target=_blank>Vietnamese</a>: +<a href="https://genomes.vn/" target=_blank>Vietnamese</a>: The Kinh Vietnamese database contains 24.81 million variants (22.47 million single nucleotide polymorphisms (SNPs) and 2.34 million indels), of which 0.71 million variants are novel. </li> <li> <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA609628" target=_blank>Korea1K</a>: The dataset contains 1,094 Korean personal genomes with clinical information. </li> <li> <a href="https://hapmap.ncbi.nlm.nih.gov/" target=_blank>HapMap</a>: (HapMap is being retired.) The International HapMap Project contains samples from African, Asian, or European populations. </li> <li> <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB36033" target=_blank>PRJEB36033</a>: The dataset contains ancient Sardinia genome-wide 1240k capture data from 70 ancient Sardinians. @@ -494,32 +494,32 @@ dbSNP has collected genetic variant reports from researchers worldwide for <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2019/10/07/dbsnp-celebrates-20-years/" target=_blank>more than 20 years</a>. Since the advent of next-generation sequencing methods and the population sequencing efforts that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes <em>et al.</em>) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, because most submissions have been genomic variant calls in VCF format as opposed to independent sequences. </p> <p> We downloaded JSON files available from dbSNP at -<a href="http://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/" -target=_blank>http://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/</a>, +<a href="https://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/" +target=_blank>https://ftp.ncbi.nlm.nih.gov/snp/archive/b155/JSON/</a>, extracted a subset of the information about each variant, and collated it into a bigBed file using the <a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/bigDbSnp.as" target=_blank>bigDbSnp.as</a> schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (<a href="https://genome-source.gi.ucsc.edu/gitlist/kent.git/blob/master/src/hg/lib/dbSnpDetails.as" target=_blank>dbSnpDetails.as</a> schema). <h2>Data Access</h2> <p> <b>Note:</b> It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following <a href="/FAQ/FAQreleases.html#snpConversion">FAQ entry</a>.</p> @@ -671,31 +671,31 @@ <a href="https://www.bristol.ac.uk/alspac/" target=_blank>ALSPAC</a> </li> <li> <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB19794" target=_blank>GENOME_DK</a> </li> <li> <a href="https://gnomad.broadinstitute.org/" target=_blank>GnomAD</a> </li> <li> <a href="https://www.rug.nl/research/genetics/databases/genomeofthenetherlands/" target=_blank>GoNL</a> </li> <li> <a href="https://www.geenivaramu.ee/en" target=_blank>Estonian</a> </li> <li> -<a href="http://genomes.vn/" target=_blank>Vietnamese</a> +<a href="https://genomes.vn/" target=_blank>Vietnamese</a> </li> <li> <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA609628" target=_blank>Korea1K</a> </li> <li> <a href="https://hapmap.ncbi.nlm.nih.gov/" target=_blank>HapMap</a> </li> <li> <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB36033" target=_blank>PRJEB36033</a> </li> <li> <a href="https://www.hagsc.org/hgdp/" target=_blank>HGDP_Stanford</a> </li> <li> <a href="https://www.ncbi.nlm.nih.gov/bioproject/576826" target=_blank>Daghestan</a>