e1ba1311138c92cc9c93e2bb5f08c303e79e1eeb gperez2 Tue Jan 4 09:12:50 2022 -0800 Updated the wording of my previous query entries, refs #28588 diff --git src/hg/htdocs/goldenPath/help/query.html src/hg/htdocs/goldenPath/help/query.html index b01957f..9d56e6e 100755 --- src/hg/htdocs/goldenPath/help/query.html +++ src/hg/htdocs/goldenPath/help/query.html @@ -133,49 +133,51 @@ chrX:g.31500000_31600000del<br> NR_111987:n.-1 <br> NM_015102.5:n.3038-2<br> NM_001372044:c.1528_1530del</td> <td>Displays the region that matches the <a href="http://varnomen.hgvs.org/" target="_blank">HGVS</a> expression, usually in the format <tt><transcript or protein>:<position> <amino acid or nucleotide change></tt><br>If a gene symbol is used, HGVS search will try all RefSeq transcripts to find the nucleotide or amino acid at the position indicated in the expression. If there are multiple matches, a disambiguation page will be shown. If the RefSeq sequence differs from the genome sequence, then currently the search will use the genome, not the transcript, for codon counting and amino acid / nucleotide comparison. Please contact us if this is inconvenient.</td></tr> <!-- commented out -- not working <tr> <td>15q11;15q13</td> <td>bands 15q11 to 15q13, or SNPs rs1042522 and rs1800370. This syntax may also be used for other range queries</td></tr> <tr> <td>rs1042522;rs1800370</td> <td>such as between uniquely determined ESTs, mRNAs, refSeqs, etc.</td></tr> --> <tr> <td>essv8694097</td> - <td>Displays the region containing Database of Genomic Variants (DGV)</td></tr> + <td>Displays the region covering the copy number variant with the accession essv8694097 in the + Database of Genomic Variants (DGV)</td></tr> <tr> <td>nssv3446126</td> - <td>Displays the region containing copy number variation from cases of developmental delay</td></tr> + <td>Displays the region covering the copy number variant with the accession nssv3446126 in the cases of developmental delay</td></tr> <tr> <td>CTD-3071L10</td> - <td>Displays the region containing NCBI clone end mappings from the NCBI Clone DB database</td></tr> + <td>Displays the region covering the CTD-3071L10 NCBI clone end mapping in the NCBI Clone DB database</td></tr> <tr> <td>nssv16167444</td> - <td>Displays the region containing common copy number genomic variations from nstd186 (NCBI Curated Common Structural Variants)</td></tr> + <td>Displays the region covering the common copy number genomic variant with the accession nssv16167444 in the + nstd186 (NCBI Curated Common Structural Variants) dataset</td></tr> <tr> <td>COSM6161404</td> - <td>Displays the region containing Catalogue Of Somatic Mutations In Cancer (COSMIC)</td></tr> + <td>Displays the region covering COSM6161404 in the Catalogue Of Somatic Mutations In Cancer (COSMIC) database</td></tr> <tr> <td>nssv3395351</td> - <td>Displays the region containing ClinVar Copy Number Variants in the ClinVar database</td></tr> + <td>Displays the region covering ClinVar Copy Number Variant with the accession nssv3395351 in the ClinVar database</td></tr> <tr> <td>BRCT_assoc</td> - <td>Displays the region containing manually-curated Pfam-A domains found in the GENCODE Genes</td></tr> + <td>Displays the region covering the manually-curated Pfam-A domain BRCT_assoc found in GENCODE Genes</td></tr> <tr> <td>U133A:219211_at</td> <td>Displays the region containing the consensus and exemplar sequences used for the selection of probes on the Affymetrix HG-U133A chips</td></tr> <tr> <td>chr1 0 1000</td> <td>When entered without ":" and "-", uses 0-based, half-open coordinates (like custom tracks and internal table coordinates), so displays chr1:1-1000</td> </tr> <tr> <td>pseudogene mRNA</td> <td>Lists transcribed pseudogenes, but not cDNAs</td></tr> <tr> <td>p53</td> <td>Lists mRNAs related to the p53 tumor suppressor</td></tr> <tr> <td>T-cell receptor</td>