{"id":974,"date":"2024-07-10T08:00:00","date_gmt":"2024-07-10T08:00:00","guid":{"rendered":"https:\/\/terrabioappdev.wpenginepowered.com\/?p=974"},"modified":"2024-07-11T16:43:38","modified_gmt":"2024-07-11T16:43:38","slug":"accessing-cancer-research-data-commons-resources-in-terra","status":"publish","type":"post","link":"https:\/\/terra.bio\/accessing-cancer-research-data-commons-resources-in-terra\/","title":{"rendered":"Accessing Cancer Research Data Commons resources in Terra"},"content":{"rendered":"\n<p>For researchers trying to understand and treat cancer, searching for useful datasets consumes valuable time. Even after accessing a dataset, researchers must figure out how\u2014and where\u2014to analyze it. After all, it is no mean task to wrangle petabytes of data.&nbsp;<\/p>\n\n\n\n<p>Luckily, the Cancer Research Data Commons (CRDC) addresses many of these challenges. A <a href=\"https:\/\/aacrjournals.org\/cancerres\/article\/84\/9\/1396\/745074\/NCI-Cancer-Research-Data-Commons-Cloud-Based\" target=\"_blank\" rel=\"noreferrer noopener\">recent paper<\/a> in <em>Cancer Research <\/em>outlines how the CRDC accelerates researchers\u2019 work by hosting large, cancer-related datasets on the cloud. Terra is proud to support this effort: an NCI-branded version of Terra (Firecloud) is one of three platforms that both host the CRDC\u2019s datasets and provide cloud-based analysis tools to uncover the insights in that data.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">How to access CRDC data in Terra<\/h3>\n\n\n\n<p>Through Terra, researchers can access several of the CRDC\u2019s open- and controlled-access cancer datasets. These include reference genomes and files (such as those from the <a href=\"https:\/\/www.internationalgenome.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">1,000 Genomes Project<\/a>), as well as data from <a href=\"https:\/\/www.cancer.gov\/ccg\/research\/genome-sequencing\/tcga\" target=\"_blank\" rel=\"noreferrer noopener\">The Cancer Genome Atlas<\/a> (TGCA), <a href=\"https:\/\/www.cancer.gov\/ccg\/research\/genome-sequencing\/target\" target=\"_blank\" rel=\"noreferrer noopener\">Therapeutically Applicable Research to Generate Effective Treatments<\/a> (TARGET), and the <a href=\"https:\/\/sites.broadinstitute.org\/ccle\/\" target=\"_blank\" rel=\"noreferrer noopener\">Cancer Cell Line Encyclopedia<\/a> (CCLE). These datasets are multimodal: they include genomics, proteomics, and imaging data.<\/p>\n\n\n\n<p>Rather than analyzing each dataset in isolation, researchers can combine and subset the data to build a cohort that is appropriate for a specific project. In addition, researchers can combine the CRDC\u2019s cancer datasets with other data that are accessible through Terra\u2014for example, from the Analysis, Visualization, and Informatics Lab-space (AnVIL)\u2014or with data from researchers\u2019 own labs.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">How to analyze cancer data in Terra<\/h3>\n\n\n\n<p>Once researchers have collected the right data for their scientific questions, Terra provides easy access to several analysis tools to begin answering those questions. These include a library of existing workflows (automated pipelines for high-throughput analyses) and interactive analysis notebooks, with tools for long- and short-read variant calling, Genome-Wide Association Studies, epigenomic and RNAseq data processing, and fusion transcript detection.&nbsp;<\/p>\n\n\n\n<p>In addition to leveraging pre-existing tools from the research community, analyzing CRDC data in the cloud is much more lightweight than on a personal or high-performance computer (HPC). Large datasets require a specialized computational infrastructure, but there\u2019s no need to set up or maintain this infrastructure when working in the cloud. There\u2019s also no need to set up a data security system, because data analyzed in Terra remains safely in a FedRAMP- and FISMA-certified environment.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">CRDC data in action: the Proteomic Data Commons<\/h3>\n\n\n\n<p>Researchers have already leveraged Terra\u2019s CRDC resources to push the cancer field forward. For example, the Broad Institute\u2019s Proteomics Platform integrated data from the <a href=\"https:\/\/pdc.cancer.gov\/pdc\/cloud-data-analysis\" target=\"_blank\" rel=\"noreferrer noopener\">Proteomic Data Commons<\/a> (PDC) into Terra to make it easier for researchers to uncover cancer mechanisms and biomarkers.<\/p>\n\n\n\n<p>The PDC is an important resource for cancer researchers because it hosts data generated by several large cancer programs\u2014these include TCGA, TARGET, the <a href=\"https:\/\/proteomics.cancer.gov\/programs\/cptac\" target=\"_blank\" rel=\"noreferrer noopener\">Clinical Proteomic Tumor Analysis Consortium<\/a> (CPTAC), and the <a href=\"https:\/\/proteomics.cancer.gov\/programs\/apollo-network\" target=\"_blank\" rel=\"noreferrer noopener\">Applied Proteogenomics Organizational Learning and Outcomes<\/a> (APOLLO) Network. D.R. Mani\u2019s team at the Proteomics Platform worked with the Terra team to build a way for researchers to export data from the PDC into a Terra workspace with the click of a button.<\/p>\n\n\n\n<p>Once the data is in Terra, it\u2019s ready to be analyzed with a common proteomics analysis toolkit: <a href=\"https:\/\/fragpipe.nesvilab.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">FragPipe<\/a>. To make this process even more seamless, the group set up a <a href=\"https:\/\/app.terra.bio\/#workspaces\/broad-firecloud-cptac\/PDC_Direct_Data_Import\" target=\"_blank\" rel=\"noreferrer noopener\">template workspace<\/a> with step-by-step instructions for selecting PDC data and importing it into Terra. The workspace also includes a FragPipe workflow and an interactive notebook that walks researchers through how to analyze PDC data with an example FragPipe tool.<\/p>\n\n\n\n<p>With cloud-based integrations like this uniting CRDC data and analysis tools, researchers can focus on understanding and treating cancer, rather than accessing and wrangling data.&nbsp;<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Use Terra\u2019s CRDC resources in your own work<\/h3>\n\n\n\n<p>To explore Terra\u2019s CRDC resources further, <a href=\"https:\/\/terra.bio\/terra-plans\/\" target=\"_blank\" rel=\"noreferrer noopener\">register for an account<\/a> and explore Terra\u2019s <a href=\"https:\/\/app.terra.bio\/#library\/showcase?selectedSections%5B0%5D%5Bheader%5D=Projects&amp;selectedSections%5B0%5D%5Bvalues%5D%5B0%5D=NCI\" target=\"_blank\" rel=\"noreferrer noopener\">NCI featured workspaces<\/a>. These workspaces provide further instructions to access connected datasets and suggest tools to analyze the data. Note that you will need an <a href=\"https:\/\/www.era.nih.gov\/register-accounts\/understanding-era-commons-accounts.htm\" target=\"_blank\" rel=\"noreferrer noopener\">eRA Commons account<\/a> to access CRDC data on Terra.&nbsp;<\/p>\n\n\n\n<p><em>Thank you to Alex Baumann, Emily LaPlante, and Katherine Thayer for their help preparing this post.<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>For researchers trying to understand and treat cancer, searching for useful datasets consumes valuable time. Even after accessing a dataset, researchers must figure out how\u2014and where\u2014to analyze it. After all, it is no mean task to wrangle petabytes of data.\u00a0<\/p>\n","protected":false},"author":58,"featured_media":975,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[68,18,1],"tags":[],"class_list":["post-974","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-cancer","category-data","category-uncategorized"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.0 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Accessing Cancer Research Data Commons resources in Terra - Terra<\/title>\n<meta name=\"description\" content=\"For researchers trying to understand and treat cancer, searching for useful datasets consumes valuable time.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/terra.bio\/accessing-cancer-research-data-commons-resources-in-terra\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Accessing Cancer Research Data Commons resources in Terra - 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