ea458a5d4f7e2dd216b35aeabd648030197f4be9 max Thu Jan 2 10:20:44 2025 -0800 clarifying decipher ddgp downloads after question from decipher Julia Foreman diff --git src/hg/makeDb/trackDb/human/decipherContainer.html src/hg/makeDb/trackDb/human/decipherContainer.html index 1cc2ec8..a70db06 100644 --- src/hg/makeDb/trackDb/human/decipherContainer.html +++ src/hg/makeDb/trackDb/human/decipherContainer.html @@ -4,31 +4,31 @@ <P><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> While the DECIPHER database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions. </P> <P>Because the UCSC Genes mappings for CNVs are based on associations from RefSeq and UniProt, they are dependent on any interpretations from those sources. Furthermore, because many DECIPHER records refer to multiple gene names, or syndromes not tightly mapped to individual genes, the associations in this track should be treated with skepticism and any conclusions based on them should be carefully scrutinized using independent resources. </P> <p><b>Data Display Agreement Notice</b><br> - These data are only available for display in the Browser, and not for bulk + The CNV/SNV data are only available for display in the Browser, and not for bulk download. Access to bulk data may be obtained directly from DECIPHER (<a href='https://www.deciphergenomics.org/about/data-sharing' target='_blank' >https://www.deciphergenomics.org/about/data-sharing</a>) and is subject to a Data Access Agreement, in which the user certifies that no attempt to identify individual patients will be undertaken. The same restrictions apply to the public data displayed at UCSC in the UCSC Genome Browser; no one is authorized to attempt to identify patients by any means. </p> <p>These data are made available as soon as possible and may be a pre-publication release. For information on the proper use of DECIPHER data, please see <a href='https://www.deciphergenomics.org/about/data-sharing' target='_blank'>https://www.deciphergenomics.org/about/data-sharing</a>. </p> <p>The DECIPHER consortium provides these data in good faith as a research tool, but without verifying the accuracy, clinical validity, or utility of @@ -46,30 +46,31 @@ microdeletions/duplications/insertions, translocations and inversions, and displays this information on the human genome map. <p> The <b>CNVs and SNVs</b> tracks show genomic regions of reported cases and their associated phenotype information. All data have passed the strict consent requirements of the DECIPHER project and are approved for unrestricted public release. Clicking the Patient View ID link brings up a more detailed informational page on the patient at the DECIPHER web site.</p> <p> The <b>DDG2P (Developmental Disorders Genotype-to-Phenotype)</b> track represents a curated collection of genomic variants associated with developmental disorders. Each entry in the DDG2P track corresponds to specific genomic regions linked to developmental disorders, annotated with relevant phenotypic descriptions. +This dataset can be downloaded without restrictions from the DECIPHER website, see data access below. </p> <H2>Display Conventions and Configuration</H2> <P> The genomic locations of DECIPHER variants are labeled with the DECIPHER variant descriptions. <b>Mouseover</b> on items shows variant details, clinical interpretation, and associated conditions. Further information on each variant is displayed on the details page by a click onto any variant. </p> <P> For the <b>CNVs track</b>, the entries are colored by the <b>type of variant</b>: <ul> <li><b><font color="red">red</font></b> for loss</li> <li><b><font color="blue">blue</font></b> for gain</li> <li><b><font color="grey">grey</font></b> for amplification</li> @@ -125,32 +126,34 @@ with individual patients. </P> <H2>Contact</H2> <P> For more information on DECIPHER, please contact <A HREF="mailto:contact@deciphergenomics. org"> contact@deciphergenomics. org</A> </P> <h2>Data Access</h2> <p> -The DECIPHER project data access and documentation can be found at +The DECIPHER CNV/SNV data access and documentation can be found at <a href="https://www.deciphergenomics.org/about/downloads" target="_blank">DECIPHER Downloads</a>. +The DECIPHER DDGP table can be downloaded from the <a href="https://www.deciphergenomics.org/ddd/ddgenes">Decipher DDGP page</a>. + </p> <p> The raw data can be explored interactively with the <a target="_blank" href="/cgi-bin/hgTables">Table Browser</a> or the <a target="_blank" href="/cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a target="_blank" href="/goldenPath/help/api.html">REST API</a> or downloaded from our <a target="_blank" href="https://hgdownload.soe.ucsc.edu/gbdb/$db/decipher/"> Downloads site</a>. Please refer to our <a target="_blank" href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome"> mailing list archives</a> for questions, or our <a target="_blank" href="/FAQ/FAQdownloads.html#downloads36"> Data Access FAQ</a> for more information. </p>