318a5c110a86569bd4e4b8fd7263c684245e6049 lrnassar Thu Oct 10 10:54:48 2019 -0700 Changing JSON API to REST API and adding new entry to API help page refs #24282 diff --git src/hg/htdocs/FAQ/FAQdownloads.html src/hg/htdocs/FAQ/FAQdownloads.html index e6f82b8..0badfb4 100755 --- src/hg/htdocs/FAQ/FAQdownloads.html +++ src/hg/htdocs/FAQ/FAQdownloads.html @@ -68,31 +68,31 @@ after a failure, when run again. Please see the previous link for examples.</p> <p> You can also download data from our <a href="http://hgdownload.soe.ucsc.edu/downloads.html">Downloads</a> page or our <a href="../cgi-bin/das/dsn" target="_blank">DAS server</a>. To download a specific subset of the data or to configure the output format of the data, use the <a href="../cgi-bin/hgTables">Table Browser</a>. For information on extracting a large set of sequences from an assembly, see <a href="#download32">Extracting sequence in batch from an assembly</a>.</p> <p> For more information on using the UCSC DAS server, see <a href="#download23">Downloading data from the UCSC DAS server</a>.</p> <p> <p> Another option for querying sequence and annotation data is the <a href='../goldenPath/help/api.html' -target=_blank>JSON API</a>. This interface allows for extraction of sequence and annotations from +target=_blank>REST API</a>. This interface allows for extraction of sequence and annotations from both UCSC assemblies and from hubs.</p> <p> <strong>To quickly download large volumes of data you can use UDR (UDT Enabled Rysnc):</strong> UDR provides users much faster download rates. Here is an example using UDR, once installed, to download all the mouse mm9 ENCODE information that amounts to several terabytes:</p> <pre><code>$ udr rsync -avP hgdownload.soe.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> <pre><code>$ udr rsync -avP hgdownload-euro.soe.ucsc.edu::goldenPath/mm9/encodeDCC/ /my/local/mm9/</code></pre> <p> Please read more about the new UDR method <a href="../../goldenPath/newsarch.html#030315" target="_blank">here</a>.</p> <a name="download35"></a> <h2>Metadata tables for GenBank and RefSeq moved to hgFixed database</h2> <h6>I can no longer find metadata tables like gbCdnaInfo for an assembly.</h6> <p> @@ -203,31 +203,31 @@ for an assembly with requests of the form:</p> <pre><code>http://genome.ucsc.edu/cgi-bin/das/[db_name]/entry_points http://genome.ucsc.edu/cgi-bin/das/[db_name]/types </code></pre> <p> where [db_name] is the UCSC name for the assembly, e.g. hg16, mm4.</p> <p> For example, here is a query that returns all the records in the refGene table for the chromosome position chr1:1-100000 on the hg16 assembly: <pre><a href="../cgi-bin/das/hg16/features?segment=1:1,100000;type=refGene">http://genome.ucsc.edu/cgi-bin/das/hg16/features?segment=1:1,100000;type=refGene</a></pre> <p> For more information on DAS, see the <a href="http://www.biodas.org" target="_blank">Biodas website</a> and the <a href="http://www.biodas.org/documents/spec.html" target="_blank">DAS specification</a>.</p> <p> A more recent alternative to the DAS server is the <a href='../goldenPath/help/api.html' -target=_blank>JSON API</a>.</p> +target=_blank>REST API</a>.</p> <a name="download27"></a> <h2>Downloading the UCSC Genome Browser source</h2> <h6>Where can I download the Genome Browser source code and executables?</h6> <p> The Genome Browser source code and executables are freely available for academic, nonprofit, and personal use (see <a href="FAQlicense.html#license2">Licensing the Genome Browser or Blat</a> for commercial licensing requirements). The latest version of the source code may be downloaded <a href="http://genome-store.ucsc.edu">here</a>.</p> <p> See <a href="FAQblat.html#blat3">Downloading Blat source and documentation</a> for information on Blat downloads.</p> <a name="download2"></a> <h2>Download restrictions</h2> @@ -870,31 +870,31 @@ feature starts on as displayed in the browser.</li> <li> Strand: forward(f) or reverse(-) strand.</li> </ul> <a name="download36"></a> <h2>Track Data Access</h2> <h6>How do I access the data underlying a track?</h6> <p> The raw data underlying a track can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a>, <a href="../cgi-bin/hgIntegrator">Data Integrator</a>, or <a href="../cgi-bin/hgVai">Variant Annotation Integrator</a>. For automated analysis, the genome annotation can be downloaded from the <a href="http://hgdownload.soe.ucsc.edu/">downloads server</a>, one of our two <a href="http://genome.ucsc.edu/goldenPath/help/mysql.html">public MariaDB servers</a>, or -using our <a href='../goldenPath/help/api.html' target=_blank>JSON API</a>.</p> +using our <a href='../goldenPath/help/api.html' target=_blank>REST API</a>.</p> <p> <strong>bigBed data:</strong> For <a href="FAQformat.html#format1.5">bigBed</a> files, individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range using one of the hgdownload servers, example:</p> <ul> <li> North American server: <pre><code>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/path/to/file/bigBedfile.bb -chrom=chr21 -start=0 -end=1000000 stdout </code></pre> </li> <li> European server: