{"lab": {"display_title": "4DN DCIC, HMS", "@id": "/labs/4dn-dcic-lab/", "title": "4DN DCIC, HMS", "@type": ["Lab", "Item"], "uuid": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989", "status": "current", "correspondence": [{"contact_email": "cGV0ZXJfcGFya0BobXMuaGFydmFyZC5lZHU=", "@id": "/users/fb287a31-e765-41c5-8c1d-665f8e9f025b/", "display_title": "Peter Park"}], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.828cd4fe-ebb0-4b36-a94a-d2e3a36cc989"]}}, "body": "The data portal has an implementation of the `Data Repository Service v1.0 API <https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.0.0/docs/>`_.\n\nThis standard has been developed and adopted as part of the `Global Alliance for Genomics and Health (GA4GH) <https://www.ga4gh.org/>`_ and implementation has been encouraged by the `Common Fund Data Ecosystem <https://www.nih-cfde.org/>`_.\n\nIn brief from the specification, the Data Repository Service (DRS) API provides a generic interface to data repositories so data consumers, including workflow systems, can access data in a single, standard way regardless of where it\u2019s stored and how it\u2019s managed.\n\nA DRS request uses 4DN file accessions as unique identifiers and can be made with the following uri formats:\n\n`drs://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs <https://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs>`_\n\n`drs://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL <https://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL>`_\n\nand will return a json that follows the API specification: ::\n\n    {\n        \"id\": \"/files-processed/4DNFIIA7E3HL/\",\n        \"created_time\": \"2022-02-25T20:40:38.976850+00:00\",\n        \"drs_id\": \"4DNFIIA7E3HL\",\n        \"self_uri\": \"drs://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs\",\n        \"access_methods\": [\n          {\n              \"access_url\": {\n                 \"url\": \"https://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n              },\n              \"type\": \"https\"\n          },\n          {\n              \"access_url\": {\n                 \"url\": \"http://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n              },\n              \"type\": \"http\"\n          }\n       ],\n       \"description\": \"ATAC-seq signal fold change\",\n       \"size\": 2345462672,\n       \"aliases\": [\n           \"4692b7c1-addf-47aa-b4cb-e30dc65a38f6\"\n       ],\n       \"checksums\": [\n          {\n             \"checksum\": \"73a2635fe8382a28339370a22b84de48\",\n             \"type\": \"md5\"\n          }\n       ],\n       \"version\": \"73a2635fe8382a28339370a22b84de48\",\n       \"updated_time\": \"2022-05-03T21:45:53.756034+00:00\"\n    }\n\nA request that specifies the access method will return a uri that can be used for data download e.g.\n\n``https://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL/access/https``\n\nReturns: ::\n\n    {\n        \"url\": \"https://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n    }\n\nAccess to the data via the ``access_url`` respects the authentication and authorization for that data and therefore, attempts to download data to which you do not have access will fail.\n", "name": "help.user-guide.data-access.drsapi", "award": {"project": "4DN", "name": "2U01CA200059-06", "uuid": "71171a4e-dca1-44cb-8375-fafd896c6923", "status": "current", "description": "DCIC: The goals of the 4D Nucleome (4DN) Data Coordination and Integration Center (DCIC) are to collect, store, curate, display, and analyze data generated in the 4DN Network. We have assembled a team of investigators, staff scientists, and developers with a strong track record in analysis of chromatin interaction data, image processing, data visualization, integrative analysis of genomic and epigenomic data, data portal development, large-scale computing, and development of secure and \ufb02exible cloud technologies. In the \ufb01rst phase of the 4DN Project, we have developed the 4DN Data Portal as a central resource with tools for data submission, curation, analysis and quality control, visualization, exploration, and download. The portal provides an easy-to-navigate interface for accessing raw and intermediate data \ufb01les, allows for programmatic access via APIs, and incorporates novel analysis and visualization tools developed by DCIC as well as other Network members. In the second phase of the 4DN Project, we will continue to support the research activities by the 4DN Network, and to lead the creation of a well curated 4DN data resource for the scienti\ufb01c community. At the same time, we propose to enhance the utility of the 4DN Scienti\ufb01c Data and the Data Portal in multiple ways: i. We will create a platform to integrate imaging and sequencing data and support the creating of reference nuclear maps in a common coordinate system; ii. We will provide support for 4DN Projects on Human Health and Disease with customized ontology applications and protected data management; iii. We will develop new cloud platform capabilities to bring user analyses to the 4DN Data Portal, and apply cost-ef\ufb01ciency improvements to support increasing data volumes; iv. We will perform regular outreach activities to raise awareness about the data and tools generated by the Network and DCIC. Overall, we will ensure that the data generated in 4DN will have maximal impact for the scienti\ufb01c community.", "center_title": "DCIC - Park", "display_title": "4D NUCLEOME NETWORK DATA COORDINATION AND INTEGRATION CENTER - PHASE II", "@id": "/awards/2U01CA200059-06/", "@type": ["Award", "Item"], "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "title": "DRS API", "status": "released", "aliases": ["4dn-dcic-lab:drs_api_doc"], "options": {"filetype": "rst", "collapsible": false, "default_open": true, "convert_ext_links": true}, "date_created": "2023-09-11T16:05:13.797299+00:00", "section_type": "Page Section", "submitted_by": {"error": "no view permissions"}, "last_modified": {"modified_by": {"error": "no view permissions"}, "date_modified": "2024-08-19T22:15:20.158532+00:00"}, "schema_version": "2", "@id": "/static-sections/997569ea-34bc-4bc1-9483-0240e5c09624/", "@type": ["StaticSection", "UserContent", "Item"], "uuid": "997569ea-34bc-4bc1-9483-0240e5c09624", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.owner", "userid.986b362f-4eb6-4a9c-8173-3ab267227777"]}, "display_title": "DRS API", "external_references": [], "content": "The data portal has an implementation of the `Data Repository Service v1.0 API <https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.0.0/docs/>`_.\n\nThis standard has been developed and adopted as part of the `Global Alliance for Genomics and Health (GA4GH) <https://www.ga4gh.org/>`_ and implementation has been encouraged by the `Common Fund Data Ecosystem <https://www.nih-cfde.org/>`_.\n\nIn brief from the specification, the Data Repository Service (DRS) API provides a generic interface to data repositories so data consumers, including workflow systems, can access data in a single, standard way regardless of where it\u2019s stored and how it\u2019s managed.\n\nA DRS request uses 4DN file accessions as unique identifiers and can be made with the following uri formats:\n\n`drs://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs <https://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs>`_\n\n`drs://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL <https://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL>`_\n\nand will return a json that follows the API specification: ::\n\n    {\n        \"id\": \"/files-processed/4DNFIIA7E3HL/\",\n        \"created_time\": \"2022-02-25T20:40:38.976850+00:00\",\n        \"drs_id\": \"4DNFIIA7E3HL\",\n        \"self_uri\": \"drs://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs\",\n        \"access_methods\": [\n          {\n              \"access_url\": {\n                 \"url\": \"https://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n              },\n              \"type\": \"https\"\n          },\n          {\n              \"access_url\": {\n                 \"url\": \"http://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n              },\n              \"type\": \"http\"\n          }\n       ],\n       \"description\": \"ATAC-seq signal fold change\",\n       \"size\": 2345462672,\n       \"aliases\": [\n           \"4692b7c1-addf-47aa-b4cb-e30dc65a38f6\"\n       ],\n       \"checksums\": [\n          {\n             \"checksum\": \"73a2635fe8382a28339370a22b84de48\",\n             \"type\": \"md5\"\n          }\n       ],\n       \"version\": \"73a2635fe8382a28339370a22b84de48\",\n       \"updated_time\": \"2022-05-03T21:45:53.756034+00:00\"\n    }\n\nA request that specifies the access method will return a uri that can be used for data download e.g.\n\n``https://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL/access/https``\n\nReturns: ::\n\n    {\n        \"url\": \"https://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n    }\n\nAccess to the data via the ``access_url`` respects the authentication and authorization for that data and therefore, attempts to download data to which you do not have access will fail.\n", "filetype": "rst", "content_as_html": "<div class=\"rst-container\"><p>The data portal has an implementation of the <a class=\"reference external\" href=\"https://ga4gh.github.io/data-repository-service-schemas/preview/release/drs-1.0.0/docs/\" rel=\"noopener noreferrer\" target=\"_blank\">Data Repository Service v1.0 API</a>.</p><p>This standard has been developed and adopted as part of the <a class=\"reference external\" href=\"https://www.ga4gh.org/\" rel=\"noopener noreferrer\" target=\"_blank\">Global Alliance for Genomics and Health (GA4GH)</a> and implementation has been encouraged by the <a class=\"reference external\" href=\"https://www.nih-cfde.org/\" rel=\"noopener noreferrer\" target=\"_blank\">Common Fund Data Ecosystem</a>.</p><p>In brief from the specification, the Data Repository Service (DRS) API provides a generic interface to data repositories so data consumers, including workflow systems, can access data in a single, standard way regardless of where it\u2019s stored and how it\u2019s managed.</p><p>A DRS request uses 4DN file accessions as unique identifiers and can be made with the following uri formats:</p><p><a class=\"reference external\" href=\"https://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs\" rel=\"noopener noreferrer\" target=\"_blank\">drs://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs</a></p><p><a class=\"reference external\" href=\"https://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL\" rel=\"noopener noreferrer\" target=\"_blank\">drs://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL</a></p><p>and will return a json that follows the API specification:</p><pre class=\"literal-block\">\n{\n    \"id\": \"/files-processed/4DNFIIA7E3HL/\",\n    \"created_time\": \"2022-02-25T20:40:38.976850+00:00\",\n    \"drs_id\": \"4DNFIIA7E3HL\",\n    \"self_uri\": \"drs://data.4dnucleome.org/files-processed/4DNFIIA7E3HL/@@drs\",\n    \"access_methods\": [\n      {\n          \"access_url\": {\n             \"url\": \"https://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n          },\n          \"type\": \"https\"\n      },\n      {\n          \"access_url\": {\n             \"url\": \"http://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n          },\n          \"type\": \"http\"\n      }\n   ],\n   \"description\": \"ATAC-seq signal fold change\",\n   \"size\": 2345462672,\n   \"aliases\": [\n       \"4692b7c1-addf-47aa-b4cb-e30dc65a38f6\"\n   ],\n   \"checksums\": [\n      {\n         \"checksum\": \"73a2635fe8382a28339370a22b84de48\",\n         \"type\": \"md5\"\n      }\n   ],\n   \"version\": \"73a2635fe8382a28339370a22b84de48\",\n   \"updated_time\": \"2022-05-03T21:45:53.756034+00:00\"\n}\n</pre><p>A request that specifies the access method will return a uri that can be used for data download e.g.</p><p><code>https://data.4dnucleome.org/ga4gh/drs/v1/objects/4DNFIIA7E3HL/access/https</code></p><p>Returns:</p><pre class=\"literal-block\">\n{\n    \"url\": \"https://data.4dnucleome.org/4DNFIIA7E3HL/@@download\"\n}\n</pre><p>Access to the data via the <code>access_url</code> respects the authentication and authorization for that data and therefore, attempts to download data to which you do not have access will fail.</p></div>", "@context": "/terms/", "aggregated-items": {}, "validation-errors": []}