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This is a newer version where each record is a unique combination of subjectID-predicate- objectID and contains a count of the unique pmids and predications supporting it.","termsOfService":"https://biothings.io/about","title":"BioThings SEMMEDDB API","version":"43_2024R","x-translator":{"biolink-version":"4.2.6","component":"KP","infores":"infores:biothings-semmeddb","team":["Service Provider"]}},"openapi":"3.0.3","paths":{"/association/{id}":{"get":{"description":"Retrieve one association record from the SEMMEDDB dataset by its identifier. Covers disease, phenotype, gene, chemical data. Source: SEMMEDDB data (download data here).\nBy default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. 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A <a href=\"#projects\">**Project**</a> may specify the default policy for objects belonging to that <a href=\"#projects\">**Project**</a>\n\nThe **Policy** specifies the visibility of the object to non-registered people or <a href=\"#people\">**People**</a> not allowed special access.\n\nThe access may be one of (in order of increasing \"power\"):\n\n* no_access\n* view\n* download\n* edit\n* manage\n\nIn addition a **Policy** may give special access to specific <a href=\"#people\">**People**</a>, People working at an <a href=\"#institutions\">**Institution**</a> or working on a <a href=\"#projects\">**Project**</a>.\n\n===\n\n## License\n<a name=\"License\"></a>\nThe license specifies the license that will apply to any <a href=\"#dataFiles\">**DataFiles**</a>, <a href=\"#models\">**Models**</a>, <a href=\"#sops\">**SOPs**</a>, <a href=\"#documents\">**Documents**</a> and <a href=\"#presentations\">**Presentations**</a> associated with a <a href=\"#projects\">**Project**</a>.\n\nThe license can currently be:\n\n* [CC0-1.0](https://creativecommons.org/publicdomain/zero/1.0/) - CC0 1.0\n* [CC-BY-4.0](https://creativecommons.org/licenses/by/4.0/) - Creative Commons Attribution 4.0\n* [CC-BY-SA-4.0](https://creativecommons.org/licenses/by-sa/4.0/) - Creative Commons Attribution Share-Alike 4.0\n* [ODC-BY-1.0](http://www.opendefinition.org/licenses/odc-by) - Open Data Commons Attribution License 1.0\n* [ODbL-1.0](http://www.opendefinition.org/licenses/odc-odbl) - Open Data Commons Open Database License 1.0\n* [ODC-PDDL-1.0](http://www.opendefinition.org/licenses/odc-pddl) - Open Data Commons Public Domain Dedication and Licence 1.0\n* notspecified - License Not Specified\n* other-at - Other (Attribution)\n* other-open - Other (Open)\n* other-pd - Other (Public Domain)\n* [AFL-3.0](http://www.opensource.org/licenses/AFL-3.0) - Academic Free License 3.0\n* [Against-DRM](http://www.opendefinition.org/licenses/against-drm) - Against DRM\n* [CC-BY-NC-4.0](https://creativecommons.org/licenses/by-nc/4.0/) - Creative Commons Attribution-NonCommercial 4.0\n* [DSL](http://www.opendefinition.org/licenses/dsl) - Design Science License\n* [FAL-1.3](http://www.opendefinition.org/licenses/fal) - Free Art License 1.3\n* [GFDL-1.3-no-cover-texts-no-invariant-sections](http://www.opendefinition.org/licenses/gfdl) - GNU Free Documentation License 1.3 with no cover texts and no invariant sections\n* [geogratis](http://geogratis.gc.ca/geogratis/licenceGG) - Geogratis\n* [hesa-withrights](http://www.hesa.ac.uk/index.php?option=com_content&amp;task=view&amp;id=2619&amp;Itemid=209) - Higher Education Statistics Agency Copyright with data.gov.uk rights\n* localauth-withrights - Local Authority Copyright with data.gov.uk rights\n* [MirOS](http://www.opensource.org/licenses/MirOS) - MirOS Licence\n* [NPOSL-3.0](http://www.opensource.org/licenses/NPOSL-3.0) - Non-Profit Open Software License 3.0\n* [OGL-UK-1.0](http://reference.data.gov.uk/id/open-government-licence) - Open Government Licence 1.0 (United Kingdom)\n* [OGL-UK-2.0](https://www.nationalarchives.gov.uk/doc/open-government-licence/version/2/) - Open Government Licence 2.0 (United Kingdom)\n* [OGL-UK-3.0](https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/) - Open Government Licence 3.0 (United Kingdom)\n* [OGL-Canada-2.0](http://data.gc.ca/eng/open-government-licence-canada) - Open Government License 2.0 (Canada)\n* [OSL-3.0](http://www.opensource.org/licenses/OSL-3.0) - Open Software License 3.0\n* [dli-model-use](http://data.library.ubc.ca/datalib/geographic/DMTI/license.html) - Statistics Canada: Data Liberation Initiative (DLI) - Model Data Use Licence\n* [Talis](http://www.opendefinition.org/licenses/tcl) - Talis Community License\n* ukclickusepsi - UK Click Use PSI\n* ukcrown-withrights - UK Crown Copyright with data.gov.uk rights\n* [ukpsi](http://www.opendefinition.org/licenses/ukpsi) - UK PSI Public Sector Information\n\n===\n\n## ContentBlob\n<a name=\"ContentBlob\"></a>\n<a name=\"contentBlobs\"></a>\nThe content of a <a href=\"#dataFiles\">**DataFile**</a>, <a href=\"#documents\">**Document**</a>, <a href=\"#models\">**Model**</a>, <a href=\"#sops\">**SOP**</a> or <a href=\"#presentations\">**Presentation**</a> is specified as a set of **ContentBlobs**.\n\nWhen a resource with content is created, it is possible to specify a ContentBlob either as:\n\n* A remote ContentBlob with:\n  * **URI to the content's location**\n  * The original filename for the content\n  * The content type of the remote content as a [MIME media type](https://en.wikipedia.org/wiki/Media_type)\n* A placeholder that will be filled with uploaded content\n  * **The original filename for the content**\n  * **The content type of the content as a [MIME media type](https://en.wikipedia.org/wiki/Media_type)**\n\nThe creation of the resource will return a JSON document containing ContentBlobs corresponding to the remote ContentBlob and to the ContentBlob placeholder. The blobs contain a URI to their location.\n\nA placeholder can then be satisfied by uploading a file to the location URI. For example by a placeholder such as \n\n```\n\"content_blobs\": [\n  {\n    \"original_filename\": \"a_pdf_file.pdf\",\n    \"content_type\": \"application/pdf\",\n    \"link\": \"http://fairdomhub.org/data_files/57/content_blobs/313\"\n  }\n],\n```\n\nmay be satisfied by uploading a file to http://fairdomhub.org/data_files/57/content_blobs/313 using the <a href=\"#uploadDataFileContent\">uploadDataFileContent</a> operation\n\nThe content of a resource may be downloaded by first *reading* the resource and then *downloading* the ContentBlobs from their URI.\n\n===\n","license":{"name":"The 3-Clause BSD License","url":"https://opensource.org/licenses/BSD-3-Clause"},"title":"JSON API to FAIRDOM SEEK","version":"0.1","x-logo":{"backgroundColor":"#FFFFFF","url":"./definitions/seek.png"}},"paths":{"/search":{"get":{"description":"<a name=\"searchOperation\"></a>**search** returns a list of references to resources\n\n* of the specified type\n* that are visible to the authenticated user, and\n* contain the specified test\n","operationId":"search","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Lactate flux inhibition data"},"id":"1213","links":{"self":"/data_files/1213"},"type":"data_files"},{"attributes":{"title":"Characterization of kinetics of the lactate dehydrogenase of S. pyogenes"},"id":"70","links":{"self":"/data_files/70"},"type":"data_files"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/searchResponse"}}},"tags":["search"]},"parameters":[{"default":"lactate inhibition","description":"The text to search for\n","in":"query","name":"q","required":true,"type":"string"},{"default":"data_files","description":"The type of resource to return","enum":["assays","data_files","events","institutions","investigations","models","people","presentations","programmes","projects","publications","sample_types","sops","studies"],"in":"query","name":"search_type","required":false,"type":"string"}]},"/assays":{"get":{"description":"<a name=\"listAssays\"></a>The **listAssays** operation returns a JSON object containing a list of all the <a href=\"#assays\">**Assays**</a> to which the authenticated user has accesss.\n","operationId":"listAssays","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Standard-based Excel template for metabolomics data"},"id":"1","links":{"self":"/assays/1"},"type":"assays"},{"attributes":{"title":"Gene expression(Transcriptome)"},"id":"2","links":{"self":"/assays/2"},"type":"assays"},{"attributes":{"title":"metabolome-LCMS"},"id":"3","links":{"self":"/assays/3"},"type":"assays"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/assaysResponse"}},"501":{"description":"Not implemented"}},"tags":["list","assays"]},"post":{"description":"<a name=\"createAssay\"></a>A **createAssay** operation creates a new instance of a <a href=\"#assays\">**Assay**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createAssay** operation returns a JSON object representing the newly created <a href=\"#assays\">**Assay**</a> and redirects to its URL.\n","operationId":"createAssay","parameters":[{"description":"The assay to create.","in":"body","name":"assay","schema":{"$ref":"#/definitions/assayPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"assay_class":{"description":"An experimental assay class description","key":"EXP","title":"Experimental assay"},"assay_type":{"label":null,"uri":"http://jermontology.org/ontology/JERMOntology#Transcriptomics"},"description":"A Western Blot Assay","other_creators":"Anonymous creator","policy":{"access":"download","permissions":[{"access":"manage","resource":{"id":"442","type":"projects"}}]},"technology_type":{"label":null,"uri":"http://jermontology.org/ontology/JERMOntology#RNA-Seq"},"title":"A Maximal experimental Assay"},"id":"54","links":{"self":"/assays/54"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:27:53.800Z","modified":"2018-04-27T14:27:54.372Z","uuid":"18867f90-2c55-0136-ec2f-08002734982f"},"relationships":{"creators":{"data":[{"id":"287","type":"people"}]},"data_files":{"data":[{"id":"16","type":"data_files"}]},"documents":{"data":[{"id":"32","type":"documents"}]},"investigation":{"data":{"id":"66","type":"investigations"}},"models":{"data":[{"id":"5","type":"models"}]},"organisms":{"data":[{"id":"3","type":"organisms"}]},"people":{"data":[{"id":"287","type":"people"}]},"projects":{"data":[{"id":"436","type":"projects"}]},"publications":{"data":[{"id":"16","type":"publications"}]},"sops":{"data":[{"id":"4","type":"sops"}]},"study":{"data":{"id":"66","type":"studies"}},"submitter":{"data":[{"id":"287","type":"people"}]}},"type":"assays"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/assayResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","assays"]}},"/assays/{id}":{"delete":{"description":"<a name=\"deleteAssay\"></a>A **deleteAssay** operation will delete the specified <a href=\"#assays\">**Assay**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteAssay","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","assays"]},"get":{"description":"<a name=\"readAssay\"></a>A **readAssay** operation will return information about the <a href=\"#assays\">Assay</a> identified, provided the authenticated user has access to it.\n\nThe **readAssay** operation returns a JSON object representing the <a href=\"#assays\">**Assay**</a>.\n","operationId":"readAssay","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"assay_class":{"description":null,"key":"EXP","title":"Experimental Assay"},"assay_type":{"label":"Experimental Assay Type","uri":"http://jermontology.org/ontology/JERMOntology#Experimental_assay_type"},"description":null,"technology_type":{"label":"Technology Type","uri":"http://jermontology.org/ontology/JERMOntology#Technology_type"},"title":"Culturing and synchronisation of P. falciparum"},"id":"267","links":{"self":"/assays/267"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org","created":"2014-08-15T13:01:52.000Z","modified":"2017-11-08T14:21:08.000Z","uuid":"510b329d-1628-4e19-9ecb-4efd8966baa6"},"relationships":{"creators":{"data":[]},"data_files":{"data":[]},"documents":{"data":[]},"investigation":{"data":{"id":"56","type":"investigations"}},"models":{"data":[]},"organisms":{"data":[]},"people":{"data":[{"id":"411","type":"people"}]},"projects":{"data":[{"id":"17","type":"projects"}]},"publications":{"data":[]},"sops":{"data":[]},"study":{"data":{"id":"118","type":"studies"}},"submitter":{"data":[{"id":"411","type":"people"}]}},"type":"assays"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/assayResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","assays"]},"parameters":[{"default":267,"description":"The assay to be fetched, updated or deleted","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateAssay\"></a>An **updateAssay** operation will modify the information held about the specified <a href=\"#assays\">**Assay**</a>. This operation is only available if the authenticated user has access to the <a href=\"#assays\">**Assay**</a>.\n\nThe **updateAssay** operation returns a JSON object representing the modified <a href=\"#assays\">**Assay**</a>.\n","operationId":"updateAssay","parameters":[{"description":"The assay to patch","in":"body","name":"assay","schema":{"$ref":"#/definitions/assayPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"assay_class":{"description":"An experimental assay class description","key":"EXP","title":"Experimental assay"},"assay_type":{"label":null,"uri":"http://jermontology.org/ontology/JERMOntology#Transcriptomics"},"description":"A Western Blot Assay","other_creators":"Anonymous creator","policy":{"access":"download","permissions":[{"access":"manage","resource":{"id":"585","type":"projects"}}]},"technology_type":{"label":null,"uri":"http://jermontology.org/ontology/JERMOntology#RNA-Seq"},"title":"A Maximal Assay"},"id":"72","links":{"self":"/assays/72"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:28:46.000Z","modified":"2018-04-27T14:28:51.457Z","uuid":"37b79600-2c55-0136-ec2f-08002734982f"},"relationships":{"creators":{"data":[{"id":"391","type":"people"}]},"data_files":{"data":[{"id":"18","type":"data_files"}]},"documents":{"data":[{"id":"34","type":"documents"}]},"investigation":{"data":{"id":"94","type":"investigations"}},"models":{"data":[{"id":"8","type":"models"}]},"organisms":{"data":[{"id":"4","type":"organisms"}]},"people":{"data":[{"id":"391","type":"people"}]},"projects":{"data":[{"id":"583","type":"projects"}]},"publications":{"data":[{"id":"18","type":"publications"}]},"sops":{"data":[{"id":"6","type":"sops"}]},"study":{"data":{"id":"94","type":"studies"}},"submitter":{"data":[{"id":"391","type":"people"}]}},"type":"assays"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/assayResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","assays"]}},"/data_files":{"get":{"description":"<a name=\"listDataFiles\"></a>The **listDataFiles** operation returns a JSON object containing a list of all the <a href=\"#dataFiles\">**DataFiles**</a> to which the authenticated user has accesss.\n","operationId":"listDataFiles","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Growth-rate dependent catabolic flux disitribution"},"id":"1","links":{"self":"/data_files/1"},"type":"data_files"},{"attributes":{"title":"Excel sheet template : concentrations of intracellular metabolites"},"id":"2","links":{"self":"/data_files/2"},"type":"data_files"},{"attributes":{"title":"0804_shake-flask-sigB-starvation"},"id":"6","links":{"self":"/data_files/6"},"type":"data_files"},{"attributes":{"title":"Transcriptomics Template (ArrayExpress Format)"},"id":"8","links":{"self":"/data_files/8"},"type":"data_files"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/dataFilesResponse"}},"501":{"description":"Not implemented"}},"tags":["list","dataFiles"]},"post":{"description":"<a name=\"createDataFile\"></a>A **createDataFile** operation creates a new instance of a <a href=\"#dataFiles\">**DataFile**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createDataFile** operation returns a JSON object representing the newly created <a href=\"#dataFiles\">**DataFile**</a> and redirects to its URL.\n","operationId":"createDataFile","parameters":[{"description":"The dataFile to create.","in":"body","name":"dataFile","schema":{"$ref":"#/definitions/dataFilePost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/data_files/57/content_blobs/313","md5sum":null,"original_filename":"a_pdf_file.pdf","sha1sum":null,"size":null,"url":null}],"created_at":"2018-04-27T14:43:12.000Z","description":"This is the description","latest_version":1,"license":"CC-BY-4.0","other_creators":"John Smith, Jane Smith","policy":{"access":"download","permissions":[{"access":"edit","resource":{"id":"2058","type":"projects"}}]},"revision_comments":null,"tags":["tag1","tag2"],"title":"A Maximal Data File","updated_at":"2018-04-27T14:43:12.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/data_files/57?version=1","version":1}]},"id":"57","links":{"self":"/data_files/57?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:43:12.273Z","modified":"2018-04-27T14:43:13.177Z","uuid":"3bf3e270-2c57-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[{"id":"186","type":"assays"}]},"creators":{"data":[{"id":"1369","type":"people"}]},"events":{"data":[{"id":"70","type":"events"}]},"investigations":{"data":[{"id":"298","type":"investigations"}]},"people":{"data":[{"id":"1368","type":"people"},{"id":"1369","type":"people"}]},"projects":{"data":[{"id":"2058","type":"projects"}]},"publications":{"data":[{"id":"87","type":"publications"}]},"studies":{"data":[{"id":"250","type":"studies"}]},"submitter":{"data":[{"id":"1368","type":"people"}]}},"type":"data_files"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/dataFileResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","dataFiles"]}},"/data_files/{id}":{"delete":{"description":"<a name=\"deleteDataFile\"></a>A **deleteDataFile** operation will delete the specified <a href=\"#dataFiles\">**DataFile**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteDataFile","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","dataFiles"]},"get":{"description":"<a name=\"readDataFile\"></a>A **readDataFile** operation will return information about the <a href=\"#dataFiles\">DataFile</a> identified, provided the authenticated user has access to it.\n\nThe **readDataFile** operation returns a JSON object representing the <a href=\"#dataFiles\">**DataFile**</a>.\n","operationId":"readDataFile","parameters":[{"default":2,"description":"The version of the data file to get","in":"query","name":"version","required":true,"type":"integer"}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/vnd.ms-excel","link":"https://fairdomhub.org/data_files/1152/content_blobs/1831","md5sum":"54470f803b4e5348096c63bdda458ae6","original_filename":"G3PDH_kinetics-SEEK.xls","sha1sum":"9a88d3c402fe060453001ac3d82974ee91f4095f","size":100864,"url":null}],"created_at":"2014-12-08T17:25:32.000Z","description":"Experimental data set for the kinetic characterisation of G3PDH","latest_version":2,"license":null,"revision_comments":null,"tags":null,"title":"G3PDH Kinetic data","updated_at":"2015-05-07T12:16:24.000Z","version":2,"versions":[{"revision_comments":null,"url":"https://fairdomhub.org/data_files/1152?version=1","version":1},{"revision_comments":null,"url":"https://fairdomhub.org/data_files/1152?version=2","version":2}]},"id":"1152","links":{"self":"/data_files/1152?version=2"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org","created":"2014-08-11T06:32:28.000Z","modified":"2015-03-03T09:54:27.000Z","uuid":"d6a8a3a9-44da-46c9-a36e-f6fad19de5f7"},"relationships":{"assays":{"data":[{"id":"253","type":"assays"}]},"creators":{"data":[{"id":"411","type":"people"},{"id":"49","type":"people"}]},"events":{"data":[]},"investigations":{"data":[{"id":"56","type":"investigations"}]},"people":{"data":[{"id":"49","type":"people"},{"id":"411","type":"people"}]},"projects":{"data":[{"id":"17","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[{"id":"118","type":"studies"}]},"submitter":{"data":[{"id":"411","type":"people"}]}},"type":"data_files"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/dataFileResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","dataFiles"]},"parameters":[{"default":1152,"description":"The data file to fetch","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateDataFile\"></a>An **updateDataFile** operation will modify the information held about the specified <a href=\"#dataFiles\">**DataFile**</a>. This operation is only available if the authenticated user has access to the <a href=\"#dataFiles\">**DataFile**</a>.\n\nThe **updateDataFile** operation returns a JSON object representing the modified <a href=\"#dataFiles\">**DataFile**</a>.\n","operationId":"updateDataFile","parameters":[{"description":"The data file to patch","in":"body","name":"data file","schema":{"$ref":"#/definitions/dataFilePatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/data_files/68/content_blobs/324","md5sum":"565ae8a7a743c3bfd9f15c69647f5b8b","original_filename":"a_pdf_file.pdf","sha1sum":"b9d2148740050b7f37975edd0fb97faa508ff767","size":8827,"url":null}],"created_at":"2018-04-27T14:43:48.000Z","description":"Study of the Human Genome","latest_version":1,"license":null,"other_creators":null,"policy":{"access":"manage","permissions":[]},"revision_comments":null,"tags":null,"title":"A Data File_62","updated_at":"2018-04-27T14:43:52.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/data_files/68?version=1","version":1}]},"id":"68","links":{"self":"/data_files/68?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:43:48.000Z","modified":"2018-04-27T14:43:49.000Z","uuid":"51b0b600-2c57-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"1413","type":"people"}]},"events":{"data":[]},"investigations":{"data":[]},"people":{"data":[{"id":"1412","type":"people"},{"id":"1413","type":"people"}]},"projects":{"data":[{"id":"2117","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[]},"submitter":{"data":[{"id":"1412","type":"people"}]}},"type":"data_files"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/dataFileResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","dataFiles"]}},"/{asset_types}/{id}/content_blobs/{blob_id}":{"get":{"description":"<a name=\"readContentBlob\"></a>A **readContentBlob** operation will return information about the <a href=\"#contentBlobs\">ContentBlob</a> identified, provided the authenticated user has access to it.\n\nThe **readContentBlob** operation may return\n* a JSON object representing the <a href=\"#contentBlobs\">**ContentBlob**</a>.\n* a csv file, if **text/csv** is specified in the **Accept** header and if the content blob can be converted into a csv or is already a csv\n","operationId":"readContentBlob","produces":["application/json","text/csv"],"responses":{"200":{"description":"Success","schema":{"$ref":"#/definitions/contentBlobResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","contentBlobs"]},"parameters":[{"default":"data_files","description":"The typs of asset being fetched, uploaded or downloaded","in":"path","name":"asset_types","required":true,"type":"string"},{"default":1152,"description":"The asset content to fetch, upload or download","in":"path","name":"id","required":true,"type":"integer"},{"default":1831,"description":"The asset identifier to fetch, upload or download","in":"path","name":"blob_id","required":true,"type":"integer"}],"put":{"consumes":["application/octet-stream"],"description":"<a name=\"uploadAssetContent\"></a>Upload the message body into the blob of the identified asset","operationId":"uploadAssetContent","parameters":[{"description":"The blob content to fetch, upload or download","in":"body","name":"blobContent","schema":{"format":"binary","type":"string"}}],"produces":["*/*"],"responses":{"200":{"description":"Success"}},"tags":["upload","contentBlobs"]}},"/{asset_types}/{id}/content_blobs/{blob_id}/download":{"get":{"description":"<a name=\"downloadAssetContent\"></a>Return the identified content of the identified asset","operationId":"downloadAssetContent","produces":["*/*"],"responses":{"200":{"description":"Success"},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["download","contentBlobs"]},"parameters":[{"default":"data_files","description":"The typs of asset being downloaded","in":"path","name":"asset_types","required":true,"type":"string"},{"default":1152,"description":"The asset to fetch","in":"path","name":"id","required":true,"type":"integer"},{"default":1831,"description":"The blob to download","in":"path","name":"blob_id","required":true,"type":"integer"}]},"/documents":{"get":{"description":"<a name=\"listDocuments\"></a>The **listDocuments** operation returns a JSON object containing a list of all the <a href=\"#documents\">**Documents**</a> to which the authenticated user has accesss.\n","operationId":"listDocuments","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"OpenAPI Specification | Swagger"},"id":"1","links":{"self":"/documents/1"},"type":"documents"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://testing.sysmo-db.org"}}},"schema":{"$ref":"#/definitions/documentsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","documents"]},"post":{"description":"<a name=\"createDocument\"></a>A **createDocument** operation creates a new instance of a <a href=\"#documents\">**Document**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createDocument** operation returns a JSON object representing the newly created <a href=\"#documents\">**Document**</a> and redirects to its URL.\n","operationId":"createDocument","parameters":[{"description":"The document to create.","in":"body","name":"document","schema":{"$ref":"#/definitions/documentPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/documents/14/content_blobs/48","md5sum":null,"original_filename":"a_pdf_file.pdf","sha1sum":null,"size":null,"url":null}],"created_at":"2018-04-27T14:26:09.000Z","description":"This is the description","latest_version":1,"license":"CC-BY-4.0","other_creators":"John Smith, Jane Smith","policy":{"access":"download","permissions":[{"access":"edit","resource":{"id":"359","type":"projects"}}]},"revision_comments":null,"tags":["tag1","tag2"],"title":"A Maximal Document","updated_at":"2018-04-27T14:26:09.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/documents/14?version=1","version":1}]},"id":"14","links":{"self":"/documents/14?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:26:09.713Z","modified":"2018-04-27T14:26:10.078Z","uuid":"da7cb1a0-2c54-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[{"id":"38","type":"assays"}]},"creators":{"data":[{"id":"234","type":"people"}]},"investigations":{"data":[{"id":"51","type":"investigations"}]},"people":{"data":[{"id":"233","type":"people"},{"id":"234","type":"people"}]},"projects":{"data":[{"id":"359","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[{"id":"51","type":"studies"}]},"submitter":{"data":[{"id":"233","type":"people"}]}},"type":"documents"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/documentResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","documents"]}},"/documents/{id}":{"delete":{"description":"<a name=\"deleteDocument\"></a>A **deleteDocument** operation will delete the specified <a href=\"#documents\">**Document**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteDocument","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","documents"]},"get":{"description":"<a name=\"readDocument\"></a>A **readDocument** operation will return information about the <a href=\"#documents\">Document</a> identified, provided the authenticated user has access to it.\n\nThe **readDocument** operation returns a JSON object representing the <a href=\"#documents\">**Document**</a>.\n","operationId":"readDocument","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/documents/14/content_blobs/48","md5sum":null,"original_filename":"a_pdf_file.pdf","sha1sum":null,"size":null,"url":null}],"created_at":"2018-04-27T14:26:09.000Z","description":"This is the description","latest_version":1,"license":"CC-BY-4.0","other_creators":"John Smith, Jane Smith","policy":{"access":"download","permissions":[{"access":"edit","resource_id":"359","resource_type":"projects"}]},"revision_comments":null,"tags":["tag1","tag2"],"title":"A Maximal Document","updated_at":"2018-04-27T14:26:09.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/documents/14?version=1","version":1}]},"id":"14","links":{"self":"/documents/14?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:26:09.713Z","modified":"2018-04-27T14:26:10.078Z","uuid":"da7cb1a0-2c54-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[{"id":"38","type":"assays"}]},"creators":{"data":[{"id":"234","type":"people"}]},"investigations":{"data":[{"id":"51","type":"investigations"}]},"people":{"data":[{"id":"233","type":"people"},{"id":"234","type":"people"}]},"projects":{"data":[{"id":"359","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[{"id":"51","type":"studies"}]},"submitter":{"data":[{"id":"233","type":"people"}]}},"type":"documents"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/documentResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","documents"]},"parameters":[{"default":1152,"description":"The document to fetch","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateDocument\"></a>An **updateDocument** operation will modify the information held about the specified <a href=\"#documents\">**Document**</a>. This operation is only available if the authenticated user has access to the <a href=\"#documents\">**Document**</a>.\n\nThe **updateDocument** operation returns a JSON object representing the modified <a href=\"#documents\">**Document**</a>.\n","operationId":"updateDocument","parameters":[{"description":"The document to patch.","in":"body","name":"document","schema":{"$ref":"#/definitions/documentPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/documents/25/content_blobs/59","md5sum":"443130e29a37e34e439a5b391efd1d42","original_filename":"file-17","sha1sum":"3da9d44ef741dda15ef1194e949f6c3b02c597bd","size":9,"url":null}],"created_at":"2018-04-27T14:27:09.000Z","description":"A report about the thing that happened","latest_version":1,"license":null,"other_creators":null,"policy":{"access":"manage","permissions":[]},"revision_comments":null,"tags":null,"title":"This Document","updated_at":"2018-04-27T14:27:15.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/documents/25?version=1","version":1}]},"id":"25","links":{"self":"/documents/25?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:27:09.000Z","modified":"2018-04-27T14:27:12.000Z","uuid":"fde626a0-2c54-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"262","type":"people"}]},"investigations":{"data":[]},"people":{"data":[{"id":"261","type":"people"},{"id":"262","type":"people"}]},"projects":{"data":[{"id":"400","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[]},"submitter":{"data":[{"id":"261","type":"people"}]}},"type":"documents"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/documentResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","documents"]}},"/events":{"get":{"description":"<a name=\"listEvents\"></a>The **listEvents** operation returns a JSON object containing a list of all the <a href=\"#events\">**Events**</a> to which the authenticated user has accesss.\n","operationId":"listEvents","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"SysMO Conference 2011"},"id":"1","links":{"self":"/events/1"},"type":"events"},{"attributes":{"title":"All Hands SySMO PALs  meeting "},"id":"2","links":{"self":"/events/2"},"type":"events"},{"attributes":{"title":"SilicoTryp student & post-doc meeting"},"id":"4","links":{"self":"/events/4"},"type":"events"},{"attributes":{"title":"Bacell-meeting 1109-Groningen"},"id":"5","links":{"self":"/events/5"},"type":"events"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/eventsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","events"]},"post":{"description":"<a name=\"createEvent\"></a>A **createEvent** operation creates a new instance of a <a href=\"#events\">**Event**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createEvent** operation returns a JSON object representing the newly created <a href=\"#events\">**Event**</a> and redirects to its URL.\n","operationId":"createEvent","parameters":[{"description":"The event to create.","in":"body","name":"sop","schema":{"$ref":"#/definitions/eventPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"address":"Sofienstr 2","city":"Heidelberg","country":"Germany","description":"This is the description","end_date":"2017-01-01T00:22:00.000Z","policy":{"access":"view","permissions":[{"access":"edit","resource":{"id":"242","type":"projects"}}]},"start_date":"2017-01-01T00:20:00.000Z","title":"A Maximal Event","url":"http://www.example.com/events/123"},"id":"3","links":{"self":"/events/3"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:25:05.300Z","modified":"2018-04-27T14:25:05.300Z","uuid":"b410eb70-2c54-0136-ec2f-08002734982f"},"relationships":{"data_files":{"data":[{"id":"4","type":"data_files"}]},"presentations":{"data":[{"id":"1","type":"presentations"}]},"projects":{"data":[{"id":"242","type":"projects"}]},"publications":{"data":[{"id":"4","type":"publications"}]},"submitter":{"data":[{"id":"177","type":"people"}]}},"type":"events"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/eventResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","events"]}},"/events/{id}":{"delete":{"description":"<a name=\"deleteEvent\"></a>A **deleteEvent** operation will delete the specified <a href=\"#events\">**Event**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteEvent","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","events"]},"get":{"description":"<a name=\"readEvent\"></a>A **readEvent** operation will return information about the <a href=\"#events\">Event</a> identified, provided the authenticated user has access to it.\n\nThe **readEvent** operation returns a JSON object representing the <a href=\"#events\">**Event**</a>.\n","operationId":"readEvent","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"address":null,"city":"Kologne","country":"Germany","description":"The kickoff meeting of CropClock team took place in November 12, 2014 at the Max Plank Institute (MPIPZ, http://www.mpipz.mpg.de/en), Kologne, Germany. The goal for this meeting was for the members of the various teams to get acquainted with each other’s expertise and to discuss the following items: 1) Logistics about the project start,  2) Data that need to be shared,  3) Matlab code that needs to shared among the teams. \r\nThe initial plan of action for data sharing was also laid out.","end_date":"2014-11-12T00:00:00.000Z","start_date":"2014-11-12T00:00:00.000Z","title":"CropClock Kick-off Meeting, November 2014","url":"http://www.mpipz.mpg.de/en"},"id":"75","links":{"self":"/events/75"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org","created":"2017-04-24T09:49:00.000Z","modified":"2017-04-26T07:43:42.000Z","uuid":"2adac480-0b01-0135-8501-549f350973c0"},"relationships":{"data_files":{"data":[]},"presentations":{"data":[]},"projects":{"data":[{"id":"26","type":"projects"}]},"publications":{"data":[]}},"type":"events"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/eventResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","events"]},"parameters":[{"default":75,"description":"The event to fetch","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateEvent\"></a>An **updateEvent** operation will modify the information held about the specified <a href=\"#events\">**Event**</a>. This operation is only available if the authenticated user has access to the <a href=\"#events\">**Event**</a>.\n\nThe **updateEvent** operation returns a JSON object representing the modified <a href=\"#events\">**Event**</a>.\n","operationId":"updateEvent","parameters":[{"description":"The event to update.","in":"body","name":"sop","schema":{"$ref":"#/definitions/eventPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"address":null,"city":null,"country":null,"description":"A thing that will happen","end_date":"2018-04-28T14:24:49.000Z","policy":{"access":"manage","permissions":[]},"start_date":"2018-04-27T14:24:49.000Z","title":"An Event","url":null},"id":"14","links":{"self":"/events/14"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:25:29.000Z","modified":"2018-04-27T14:25:30.000Z","uuid":"c2d344b0-2c54-0136-ec2f-08002734982f"},"relationships":{"data_files":{"data":[]},"presentations":{"data":[]},"projects":{"data":[{"id":"310","type":"projects"}]},"publications":{"data":[]},"submitter":{"data":[{"id":"205","type":"people"}]}},"type":"events"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/eventResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","events"]}},"/institutions":{"get":{"description":"<a name=\"listInstitutions\"></a>The **listInstitutions** operation returns a JSON object containing a list of all the <a href=\"#institutions\">**Institutions**</a> to which the authenticated user has accesss.\n","operationId":"listInstitutions","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Institute of Physiology Academy of Sciences"},"id":"1","links":{"self":"/institutions/1"},"type":"institutions"},{"attributes":{"title":"Autonomous University of Barcelona"},"id":"2","links":{"self":"/institutions/2"},"type":"institutions"},{"attributes":{"title":"CSIC Granada"},"id":"3","links":{"self":"/institutions/3"},"type":"institutions"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/institutionsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","institutions"]},"post":{"description":"<a name=\"createInstitution\"></a>A **createInstitution** operation creates a new instance of a <a href=\"#institutions\">**Institution**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createInstitution** operation returns a JSON object representing the newly created <a href=\"#institutions\">**Institution**</a> and redirects to its URL.\n","operationId":"createInstitution","parameters":[{"description":"The institution to create.","in":"body","name":"institution","schema":{"$ref":"#/definitions/institutionPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"address":"Manchester Centre for Integrative Systems Biology, MIB/CEAS, The University of Manchester Faraday Building, Sackville Street, Manchester M60 1QD United Kingdom","avatar":null,"city":"Manchester","country":"Brazil","country_code":"br","title":"Post An Institution: 886 Max","web_page":"http://www.mib.ac.uk/"},"id":"1063","links":{"self":"/institutions/1063"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:38:14.497Z","modified":"2018-04-27T14:38:14.497Z","uuid":"8a81b740-2c56-0136-ec2f-08002734982f"},"relationships":{"people":{"data":[]},"projects":{"data":[]}},"type":"institutions"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/institutionResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","institutions"]}},"/institutions/{id}":{"delete":{"description":"<a name=\"deleteInstitution\"></a>A **deleteInstitution** operation will delete the specified <a href=\"#institutions\">**Institution**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteInstitution","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","institutions"]},"get":{"description":"<a name=\"readInstitution\"></a>A **readInstitution** operation will return information about the <a href=\"#institutions\">Institution</a> identified, provided the authenticated user has access to it.\n\nThe **readInstitution** operation returns a JSON object representing the <a href=\"#institutions\">**Institution**</a>.\n","operationId":"readInstitution","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"address":null,"avatar":null,"city":null,"country":"FR","title":"Some university","web_page":null},"id":"70","links":{"self":"/institutions/70"},"meta":{"api_version":"0.1","base_url":"https://testing.sysmo-db.org","created":"2018-04-12T09:46:10.695Z","modified":"2018-04-12T09:46:10.695Z","uuid":"414f8a70-2064-0136-17ed-54bed9b4c528"},"relationships":{"people":{"data":[]},"projects":{"data":[]}},"type":"institutions"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/institutionResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","institutions"]},"parameters":[{"default":142,"description":"The institution to fetch, patch or delete","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateInstitution\"></a>An **updateInstitution** operation will modify the information held about the specified <a href=\"#institutions\">**Institution**</a>. This operation is only available if the authenticated user has access to the <a href=\"#institutions\">**Institution**</a>.\n\nThe **updateInstitution** operation returns a JSON object representing the modified <a href=\"#institutions\">**Institution**</a>.\n","operationId":"updateInstitution","parameters":[{"description":"The data with which to update the institution.","in":"body","name":"institution","schema":{"$ref":"#/definitions/institutionPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"address":"NoName street 23","avatar":null,"city":"Heidelberg","country":"Germany","country_code":"de","title":"Patched institution","web_page":"http://my.Institution.com"},"id":"1094","links":{"self":"/institutions/1094"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:38:21.000Z","modified":"2018-04-27T14:38:23.245Z","uuid":"8e95da20-2c56-0136-ec2f-08002734982f"},"relationships":{"people":{"data":[]},"projects":{"data":[]}},"type":"institutions"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/institutionResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","institutions"]}},"/investigations":{"get":{"description":"<a name=\"listInvestigations\"></a>The **listInvestigations** operation returns a JSON object containing a list of all the <a href=\"#investigations\">**Investigations**</a> to which the authenticated user has accesss.\n","operationId":"listInvestigations","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Creating data sheet template for 'omics data"},"id":"1","links":{"self":"/investigations/1"},"type":"investigations"},{"attributes":{"title":"The transition from growing to non-growing Bacillus subtilis cells"},"id":"2","links":{"self":"/investigations/2"},"type":"investigations"},{"attributes":{"title":"Systems Biology of Clostridium acetobutylicum - a possible answer to dwindling crude oil reserves"},"id":"3","links":{"self":"/investigations/3"},"type":"investigations"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/investigationsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","investigations"]},"post":{"description":"<a name=\"createInvestigation\"></a>A **createInvestigation** operation creates a new instance of a <a href=\"#investigations\">**Investigation**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createInvestigation** operation returns a JSON object representing the newly created <a href=\"#investigations\">**Investigation**</a> and redirects to its URL.\n","operationId":"createInvestigation","parameters":[{"description":"The investigation to create.","in":"body","name":"investigation","schema":{"$ref":"#/definitions/investigationPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"description":"This is a more complex investigation","other_creators":"Max Blumenthal, Ed Snowden","policy":{"access":"download","permissions":[{"access":"manage","resource":{"id":"809","type":"projects"}},{"access":"manage","resource":{"id":"859","type":"projects"}}]},"title":"A Maximal Investigation"},"id":"122","links":{"self":"/investigations/122"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:31:15.345Z","modified":"2018-04-27T14:31:15.859Z","uuid":"90a27200-2c55-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"555","type":"people"}]},"data_files":{"data":[]},"documents":{"data":[]},"models":{"data":[]},"people":{"data":[{"id":"555","type":"people"}]},"projects":{"data":[{"id":"809","type":"projects"},{"id":"859","type":"projects"}]},"publications":{"data":[{"id":"23","type":"publications"}]},"sops":{"data":[]},"studies":{"data":[]},"submitter":{"data":[{"id":"555","type":"people"}]}},"type":"investigations"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/investigationResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","investigations"]}},"/investigations/{id}":{"delete":{"description":"<a name=\"deleteInvestigation\"></a>A **deleteInvestigation** operation will delete the specified <a href=\"#investigations\">**Investigation**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteInvestigation","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","investigations"]},"get":{"description":"<a name=\"readInvestigation\"></a>A **readInvestigation** operation will return information about the <a 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This operation is only available if the authenticated user has access to the <a href=\"#investigations\">**Investigation**</a>.\n\nThe **updateInvestigation** operation returns a JSON object representing the modified <a href=\"#investigations\">**Investigation**</a>.\n","operationId":"updateInvestigation","parameters":[{"description":"The investigation to patch.","in":"body","name":"investigation","schema":{"$ref":"#/definitions/investigationPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"description":"This is a more complex investigation","other_creators":"Max Blumenthal, Ed Snowden","policy":{"access":"download","permissions":[{"access":"manage","resource":{"id":"1293","type":"projects"}},{"access":"manage","resource":{"id":"1343","type":"projects"}}]},"title":"A Maximal Investigation"},"id":"196","links":{"self":"/investigations/196"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:35:11.000Z","modified":"2018-04-27T14:35:19.217Z","uuid":"1d766430-2c56-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"838","type":"people"}]},"data_files":{"data":[]},"documents":{"data":[]},"models":{"data":[]},"people":{"data":[{"id":"838","type":"people"}]},"projects":{"data":[{"id":"1293","type":"projects"},{"id":"1343","type":"projects"}]},"publications":{"data":[{"id":"41","type":"publications"}]},"sops":{"data":[]},"studies":{"data":[]},"submitter":{"data":[{"id":"838","type":"people"}]}},"type":"investigations"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/investigationResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","investigations"]}},"/models":{"get":{"description":"<a name=\"listModels\"></a>The **listModels** operation returns a JSON object containing a list of all the <a href=\"#models\">**Models**</a> to which the authenticated user has accesss.\n","operationId":"listModels","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Basic kinetic model of Escherichia coli's electron transport chain (ETC)"},"id":"16","links":{"self":"/models/16"},"type":"models"},{"attributes":{"title":"Development of agent-based models describing the response of Escherichia coli to changes in oxygen availability"},"id":"18","links":{"self":"/models/18"},"type":"models"},{"attributes":{"title":"sigB-response_starvation_shakeflask"},"id":"20","links":{"self":"/models/20"},"type":"models"},{"attributes":{"title":"Model for ED pathway in Sulfolobus solfataricus"},"id":"21","links":{"self":"/models/21"},"type":"models"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/modelsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","models"]},"post":{"description":"<a name=\"createModel\"></a>A **createModel** operation creates a new instance of a <a href=\"#models\">**Model**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createModel** operation returns a JSON object representing the newly created <a href=\"#models\">**Model**</a> and redirects to its URL.\n","operationId":"createModel","parameters":[{"description":"The model to create.","in":"body","name":"model","schema":{"$ref":"#/definitions/modelPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/models/60/content_blobs/230","md5sum":null,"original_filename":"docs.pdf","sha1sum":null,"size":null,"url":null},{"content_type":"application/xml","link":"http://localhost:3000/models/60/content_blobs/231","md5sum":null,"original_filename":"the_model.xml","sha1sum":null,"size":null,"url":null}],"created_at":"2018-04-27T14:37:09.000Z","description":"This is the description","environment":"JWS 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This operation is only available if the authenticated user has access to the <a href=\"#models\">**Model**</a>.\n\nThe **updateModel** operation returns a JSON object representing the modified <a href=\"#models\">**Model**</a>.\n","operationId":"updateModel","parameters":[{"description":"The model to patch.","in":"body","name":"model","schema":{"$ref":"#/definitions/modelPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"text/xml","link":"http://localhost:3000/models/71/content_blobs/242","md5sum":"6b9283ed4ca52a081398b715aaeb8113","original_filename":"cronwright.xml","sha1sum":"454e4b6067f577b680bb8538772b12ebcdb6c4a4","size":5933,"url":null}],"created_at":"2018-04-27T14:38:03.000Z","description":"A simulation of a 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The instance is populated with the content of the body of the API call.\n\nThe **createPerson** operation returns a JSON object representing the newly created <a href=\"#people\">**Person**</a> and redirects to its URL.\n","operationId":"createPerson","parameters":[{"description":"The person to create.","in":"body","name":"person","schema":{"$ref":"#/definitions/personPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"avatar":null,"description":"A person with all possible details","expertise":["modeling","programming"],"first_name":"Post","last_name":"Last","mbox_sha1sum":"d6b1a16fb3c8678069841a2e47f0f5bdd5103a6e","orcid":"http://orcid.org/0000-0001-9842-9718","project_positions":null,"title":"Post Last","tools":["CeriusII","Gromacs","Python"]},"id":"441","links":{"self":"/people/441"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:29:10.153Z","modified":"2018-04-27T14:29:10.153Z","uuid":"460c1550-2c55-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"data_files":{"data":[]},"documents":{"data":[]},"events":{"data":[]},"institutions":{"data":[]},"investigations":{"data":[]},"models":{"data":[]},"presentations":{"data":[]},"projects":{"data":[]},"publications":{"data":[]},"sops":{"data":[]},"studies":{"data":[]}},"type":"people"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/personResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","people"]}},"/people/{id}":{"delete":{"description":"<a name=\"deletePerson\"></a>A **deletePerson** operation will delete the specified <a href=\"#people\">**Person**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deletePerson","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","people"]},"get":{"description":"<a name=\"readPerson\"></a>A **readPerson** operation will return information about the <a href=\"#people\">Person</a> identified, provided the authenticated user has access to it.\n\nThe **readPerson** operation returns a JSON object representing the <a href=\"#people\">**Person**</a>.\n","operationId":"readPerson","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"avatar":"/people/132/avatars/4","description":"I am a Research Fellow at the University of Manchester, working in Bioinformatics and Computer Science. 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This operation is only available if the authenticated user has access to the <a href=\"#people\">**Person**</a>.\n\nThe **updatePerson** operation returns a JSON object representing the modified <a href=\"#people\">**Person**</a>.\n","operationId":"updatePerson","parameters":[{"description":"The data with which to update the person.","in":"body","name":"person","schema":{"$ref":"#/definitions/personPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"avatar":null,"description":"A person with all possible details","expertise":["modeling","programming"],"first_name":"Patched","last_name":"Name","mbox_sha1sum":"5f9cd9691c643af7e4506ff02cdb6629b9bb880f","orcid":"http://orcid.org/0000-0001-9842-9718","project_positions":[{"position_id":"1","position_name":"A Role","project_id":"676"}],"title":"Patched Name","tools":["CeriusII","Gromacs","Python"]},"id":"472","links":{"self":"/people/472"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:29:35.000Z","modified":"2018-04-27T14:29:39.205Z","uuid":"552d8ab0-2c55-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"data_files":{"data":[]},"documents":{"data":[]},"events":{"data":[]},"institutions":{"data":[{"id":"473","type":"institutions"}]},"investigations":{"data":[]},"models":{"data":[]},"presentations":{"data":[]},"projects":{"data":[{"id":"676","type":"projects"}]},"publications":{"data":[]},"sops":{"data":[]},"studies":{"data":[]}},"type":"people"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/personResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","people"]}},"/presentations":{"get":{"description":"<a name=\"listPresentations\"></a>The **listPresentations** operation returns a JSON object containing a list of all the <a href=\"#presentations\">**Presentations**</a> to which the authenticated user has accesss.\n","operationId":"listPresentations","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Feed-back regulation of the anabolic (ProB) and osmoadaptive (ProJ) glutamate kinases: predicted role of a flexible protein loop."},"id":"2","links":{"self":"/presentations/2"},"type":"presentations"},{"attributes":{"title":"Balancing the osmotic gradient: adaptation of the cytoplasmic solute pool via de novo synthesis and compatible solute uptake in response to hyper-osmolarity."},"id":"3","links":{"self":"/presentations/3"},"type":"presentations"},{"attributes":{"title":"Towards system understanding of B. subtilis - integrating fluxes and cellular components under salt stress"},"id":"4","links":{"self":"/presentations/4"},"type":"presentations"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/presentationsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","presentations"]},"post":{"description":"<a name=\"createPresentation\"></a>A **createPresentation** operation creates a new instance of a <a href=\"#presentations\">**Presentation**</a>. 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This operation is only available if the authenticated user has access to the <a href=\"#presentations\">**Presentation**</a>.\n\nThe **updatePresentation** operation returns a JSON object representing the modified <a href=\"#presentations\">**Presentation**</a>.\n","operationId":"updatePresentation","parameters":[{"description":"The presentation to update.","in":"body","name":"presentation","schema":{"$ref":"#/definitions/presentationPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/presentations/47/content_blobs/275","md5sum":"5b153092cb9837ee9dc6665518e68047","original_filename":"test.pdf","sha1sum":"da439390f7d1cd5e459c008103c4f1582658888a","size":10,"url":null}],"created_at":"2018-04-27T14:40:42.000Z","description":"A report about the thing that happened","latest_version":1,"license":null,"other_creators":null,"policy":{"access":"manage","permissions":[]},"revision_comments":null,"tags":null,"title":"A Presentation 44","updated_at":"2018-04-27T14:40:47.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/presentations/47?version=1","version":1}]},"id":"47","links":{"self":"/presentations/47?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:40:42.000Z","modified":"2018-04-27T14:40:43.000Z","uuid":"e27753f0-2c56-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"1250","type":"people"}]},"events":{"data":[]},"investigations":{"data":[]},"people":{"data":[{"id":"1249","type":"people"},{"id":"1250","type":"people"}]},"projects":{"data":[{"id":"1895","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[]},"submitter":{"data":[{"id":"1249","type":"people"}]}},"type":"presentations"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/presentationResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","presentations"]}},"/programmes":{"get":{"description":"<a name=\"listProgrammes\"></a>The **listProgrammes** operation returns a JSON object containing a list of all the <a href=\"#programmes\">**Programmes**</a> to which the authenticated user has accesss.\n","operationId":"listProgrammes","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"SysMO"},"id":"1","links":{"self":"/programmes/1"},"type":"programmes"},{"attributes":{"title":"e:Bio"},"id":"2","links":{"self":"/programmes/2"},"type":"programmes"},{"attributes":{"title":"SARCHI: Mechanistic modelling of health and epidemiology"},"id":"3","links":{"self":"/programmes/3"},"type":"programmes"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/programmesResponse"}},"501":{"description":"Not implemented"}},"tags":["list","programmes"]},"post":{"description":"<a name=\"createProgramme\"></a>A **createProgramme** operation creates a new instance of a <a href=\"#programmes\">**Programme**</a>. 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This operation is only available if the authenticated user has access to the <a href=\"#programmes\">**Programme**</a>.\n\nThe **updateProgramme** operation returns a JSON object representing the modified <a href=\"#programmes\">**Programme**</a>.\n","operationId":"updateProgramme","parameters":[{"description":"The data with which to update the programme.","in":"body","name":"programme","schema":{"$ref":"#/definitions/programmePatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"avatar":null,"description":"A very exciting programme patched!","funding_codes":["AVH"],"funding_details":"Someone ELSE is funding this for me","title":"Changed title","web_page":"http://www.synbiochem.co.uk"},"id":"18","links":{"self":"/programmes/18"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:30:16.000Z","modified":"2018-04-27T14:30:19.653Z","uuid":"6d7b2ed0-2c55-0136-ec2f-08002734982f"},"relationships":{"administrators":{"data":[{"id":"510","type":"people"}]},"assays":{"data":[]},"data_files":{"data":[]},"documents":{"data":[]},"events":{"data":[]},"institutions":{"data":[]},"investigations":{"data":[]},"models":{"data":[]},"people":{"data":[]},"presentations":{"data":[]},"projects":{"data":[{"id":"731","type":"projects"}]},"publications":{"data":[]},"sops":{"data":[]},"studies":{"data":[]}},"type":"programmes"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/programmeResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","programmes"]}},"/projects":{"get":{"description":"<a name=\"listProjects\"></a>The **listProjects** operation returns a JSON object containing a list of all the <a href=\"#projects\">**Projects**</a> to which the authenticated user has accesss.\n","operationId":"listProjects","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"BaCell-SysMO"},"id":"1","links":{"self":"/projects/1"},"type":"projects"},{"attributes":{"title":"COSMIC"},"id":"2","links":{"self":"/projects/2"},"type":"projects"},{"attributes":{"title":"SUMO"},"id":"3","links":{"self":"/projects/3"},"type":"projects"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/projectsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","projects"]},"post":{"description":"<a name=\"createProject\"></a>A **createProject** operation creates a new instance of a <a href=\"#projects\">**Project**</a>. 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This operation is only available if the authenticated user has access to the <a href=\"#projects\">**Project**</a>.\n\nThe **updateProject** operation returns a JSON object representing the modified <a href=\"#projects\">**Project**</a>.\n","operationId":"updateProject","parameters":[{"description":"The data with which to update the project.","in":"body","name":"project","schema":{"$ref":"#/definitions/projectPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"avatar":null,"default_license":"Other (Open)","default_policy":{"access":"no_access","permissions":[{"access":"manage","resource":{"id":"1296","type":"people"}},{"access":"download","resource":{"id":"1956","type":"projects"}},{"access":"view","resource":{"id":"1321","type":"institutions"}}]},"description":"with a new description!","title":"Updated Project","web_page":"http://www.taverna.org.uk","wiki_page":"http://www.mygrid.org.uk"},"id":"1953","links":{"self":"/projects/1953"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:41:23.000Z","modified":"2018-04-27T14:41:26.457Z","uuid":"fadec2a0-2c56-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"data_files":{"data":[]},"documents":{"data":[]},"events":{"data":[]},"institutions":{"data":[]},"investigations":{"data":[]},"models":{"data":[]},"organisms":{"data":[{"id":"6","type":"organisms"}]},"people":{"data":[]},"presentations":{"data":[]},"programmes":{"data":[{"id":"28","type":"programmes"}]},"publications":{"data":[]},"sops":{"data":[]},"studies":{"data":[]}},"type":"projects"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/projectResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","projects"]}},"/publications":{"get":{"description":"<a name=\"listPublications\"></a>The **listPublications** operation returns a JSON object containing a list of all the <a href=\"#publications\">**Publications**</a> to which the authenticated user has accesss.\n","operationId":"listPublications","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Quantitative proteomic analysis of Sulfolobus solfataricus membrane proteins"},"id":"1","links":{"self":"/publications/1"},"type":"publications"},{"attributes":{"title":"Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology"},"id":"2","links":{"self":"/publications/2"},"type":"publications"},{"attributes":{"title":"Functional analysis of new transporters involved in stress tolerance inPseudomonas putidaDOT-T1E"},"id":"4","links":{"self":"/publications/4"},"type":"publications"},{"attributes":{"title":"Identification and characterization of the PhhR regulon inPseudomonas putida"},"id":"5","links":{"self":"/publications/5"},"type":"publications"},{"attributes":{"title":"Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor"},"id":"7","links":{"self":"/publications/7"},"type":"publications"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/publicationsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","publications"]}},"/publications/{id}":{"get":{"description":"<a name=\"readPublication\"></a>A **readPublication** operation will return information about the <a href=\"#publications\">Publication</a> identified, provided the authenticated user has access to it.\n\nThe **readPublication** operation returns a JSON object representing the <a href=\"#publications\">**Publication**</a>.\n","operationId":"readPublication","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"abstract":"The enzymes in the Embden–Meyerhof–Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation of the model, we compared model predictions for steady-state fluxes and metabolite concentrations of the hexose phosphates with experimental values for intact parasites. The model, which is completely based on kinetic parameters that were measured for the individual enzymes, gives an accurate prediction of the steady-state fluxes and intermediate concentrations. This is the first detailed kinetic model for glucose metabolism in P. falciparum, one of the most prolific malaria-causing protozoa, and the high predictive power of the model makes it a strong tool for future drug target identification studies. The modelling workflow is transparent and reproducible, and completely documented in the SEEK platform, where all experimental data and model files are available for download.","authors":["Gerald Penkler","Francois du Toit","Waldo Adams","Marina Rautenbach","Daniel C. Palm","Dawie Van Niekerk","Jacky Snoep"],"citation":"FEBS J 282(8) : 1481","doi":"10.1111/febs.13237","journal":"FEBS J","link_to_pub":"https://www.ncbi.nlm.nih.gov/pubmed/","published_date":"2015-04-01","pubmed_id":null,"title":"Construction and validation of a detailed kinetic model of glycolysis in\n              Plasmodium falciparum"},"id":"240","links":{"self":"/publications/240"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org","created":"2015-07-09T15:30:55.000Z","modified":"2016-09-19T13:34:11.000Z","uuid":"69bebf90-087d-0133-36e3-549f350973c0"},"relationships":{"assays":{"data":[]},"data_files":{"data":[]},"events":{"data":[]},"investigations":{"data":[{"id":"56","type":"investigations"}]},"models":{"data":[]},"people":{"data":[{"id":"49","type":"people"},{"id":"411","type":"people"}]},"presentations":{"data":[]},"projects":{"data":[{"id":"17","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[{"id":"118","type":"studies"},{"id":"119","type":"studies"},{"id":"138","type":"studies"}]}},"type":"publications"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/publicationResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","publications"]},"parameters":[{"default":240,"description":"The publication to fetch, patch or delete","in":"path","name":"id","required":true,"type":"integer"}]},"/sample_types":{"get":{"description":"<a name=\"listSampleTypes\"></a>The **listSampleTypes** operation returns a JSON object containing a list of all the <a href=\"#sampleTypes\">**SampleTypes**</a> to which the authenticated user has accesss.\n","operationId":"listSampleTypes","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"SysMO Biosample"},"id":"1","links":{"self":"/sample_types/1"},"type":"sample_types"},{"attributes":{"title":"YEAST_chemostat_steady_state_culture"},"id":"2","links":{"self":"/sample_types/2"},"type":"sample_types"},{"attributes":{"title":"chemostat_yeast_anaerobic"},"id":"3","links":{"self":"/sample_types/3"},"type":"sample_types"},{"attributes":{"title":"test for SysMetEx1"},"id":"4","links":{"self":"/sample_types/4"},"type":"sample_types"},{"attributes":{"title":"SysMetEx_Cell_Culture"},"id":"8","links":{"self":"/sample_types/8"},"type":"sample_types"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/sampleTypesResponse"}},"501":{"description":"Not implemented"}},"tags":["list","sampleTypes"]}},"/sops":{"get":{"description":"<a name=\"listSops\"></a>The **listSops** operation returns a JSON object containing a list of all the <a href=\"#sops\">**Sops**</a> to which the authenticated user has accesss.\n","operationId":"listSops","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Fluorescent probe labeling for microarrays"},"id":"4","links":{"self":"/sops/4"},"type":"sops"},{"attributes":{"title":"Guidelines for Writing Standard Operating Procedures (SOP)"},"id":"5","links":{"self":"/sops/5"},"type":"sops"},{"attributes":{"title":"Flash-labeling of tetra-cyc-modified proteins in E.coli"},"id":"16","links":{"self":"/sops/16"},"type":"sops"},{"attributes":{"title":"Measuring the mobility of soluble and aggergating protein using fluorescence recovery after photobleaching (FRAP) in normal and osmotically stressed cells."},"id":"17","links":{"self":"/sops/17"},"type":"sops"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/sopsResponse"}},"501":{"description":"Not implemented"}},"tags":["list","sops"]},"post":{"description":"<a name=\"createSop\"></a>A **createSop** operation creates a new instance of a <a href=\"#sops\">**Sop**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createSop** operation returns a JSON object representing the newly created <a href=\"#sops\">**Sop**</a> and redirects to its URL.\n","operationId":"createSop","parameters":[{"description":"The sop to create.","in":"body","name":"sop","schema":{"$ref":"#/definitions/sopPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/sops/39/content_blobs/286","md5sum":null,"original_filename":"a_pdf_file.pdf","sha1sum":null,"size":null,"url":null}],"created_at":"2018-04-27T14:41:44.000Z","description":"This is the description","latest_version":1,"license":"CC-BY-4.0","other_creators":"John Smith, Jane Smith","policy":{"access":"download","permissions":[{"access":"edit","resource":{"id":"1973","type":"projects"}}]},"revision_comments":null,"tags":["tag1","tag2"],"title":"A Maximal 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experiments","updated_at":"2015-04-17T10:27:22.000Z","version":1,"versions":[{"revision_comments":null,"url":"https://fairdomhub.org/sops/203?version=1","version":1}]},"id":"203","links":{"self":"/sops/203?version=1"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org","created":"2014-08-15T13:00:40.000Z","modified":"2015-04-17T10:27:22.000Z","uuid":"90825ba2-b548-49e0-9215-a8c3ba19ee4b"},"relationships":{"assays":{"data":[{"id":"260","type":"assays"},{"id":"266","type":"assays"}]},"creators":{"data":[{"id":"411","type":"people"},{"id":"49","type":"people"}]},"investigations":{"data":[{"id":"56","type":"investigations"}]},"people":{"data":[{"id":"49","type":"people"},{"id":"411","type":"people"}]},"projects":{"data":[{"id":"17","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[{"id":"119","type":"studies"}]},"submitter":{"data":[{"id":"411","type":"people"}]}},"type":"sops"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/sopResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","sops"]},"parameters":[{"default":203,"description":"The SOP to fetch, patch or delete","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateSop\"></a>An **updateSop** operation will modify the information held about the specified <a href=\"#sops\">**Sop**</a>. This operation is only available if the authenticated user has access to the <a href=\"#sops\">**Sop**</a>.\n\nThe **updateSop** operation returns a JSON object representing the modified <a href=\"#sops\">**Sop**</a>.\n","operationId":"updateSop","parameters":[{"description":"The sop to update.","in":"body","name":"sop","schema":{"$ref":"#/definitions/sopPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"content_blobs":[{"content_type":"application/pdf","link":"http://localhost:3000/sops/49/content_blobs/296","md5sum":"479e5c9c6807e8de11ab91b273c0eae7","original_filename":"file-97","sha1sum":"2977f9e45eb27e83c8389ea18e663ab7d840b19c","size":10,"url":null}],"created_at":"2018-04-27T14:42:16.000Z","description":"Protocol","latest_version":1,"license":null,"other_creators":null,"policy":{"access":"manage","permissions":[]},"revision_comments":null,"tags":null,"title":"This Sop","updated_at":"2018-04-27T14:42:21.000Z","version":1,"versions":[{"revision_comments":null,"url":"http://localhost:3000/sops/49?version=1","version":1}]},"id":"49","links":{"self":"/sops/49?version=1"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:42:15.000Z","modified":"2018-04-27T14:42:17.000Z","uuid":"1a593b30-2c57-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"1333","type":"people"}]},"investigations":{"data":[]},"people":{"data":[{"id":"1332","type":"people"},{"id":"1333","type":"people"}]},"projects":{"data":[{"id":"2010","type":"projects"}]},"publications":{"data":[]},"studies":{"data":[]},"submitter":{"data":[{"id":"1332","type":"people"}]}},"type":"sops"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/sopResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","sops"]}},"/studies":{"get":{"description":"<a name=\"listStudies\"></a>The **listStudys** operation returns a JSON object containing a list of all the Studys to which the authenticated user has accesss.\n","operationId":"listStudies","responses":{"200":{"description":"OK","examples":{"application/json":{"data":[{"attributes":{"title":"Creating template for metabolomics data"},"id":"1","links":{"self":"/studies/1"},"type":"studies"},{"attributes":{"title":"Biphase Batch Fermentation(2009/02/04)"},"id":"2","links":{"self":"/studies/2"},"type":"studies"},{"attributes":{"title":"Investigation of different pH values for metabolic shift"},"id":"3","links":{"self":"/studies/3"},"type":"studies"}],"jsonapi":{"version":"1.0"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org"}}},"schema":{"$ref":"#/definitions/studiesResponse"}},"501":{"description":"Not implemented"}},"tags":["list","studies"]},"post":{"description":"<a name=\"createStudy\"></a>A **createStudy** operation creates a new instance of a <a href=\"#studies\">**Study**</a>. The instance is populated with the content of the body of the API call.\n\nThe **createStudy** operation returns a JSON object representing the newly created <a href=\"#studies\">**Study**</a> and redirects to its URL.\n","operationId":"createStudy","parameters":[{"description":"The study to create.","in":"body","name":"study","schema":{"$ref":"#/definitions/studyPost"}}],"responses":{"201":{"description":"Created","examples":{"application/json":{"data":{"attributes":{"description":"The Study of many things","experimentalists":"Wet lab people","other_creators":"Marie Curie","person_responsible_id":"1092","policy":{"access":"download","permissions":[{"access":"view","resource":{"id":"1672","type":"projects"}}]},"title":"A Maximal Study"},"id":"208","links":{"self":"/studies/208"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:38:32.768Z","modified":"2018-04-27T14:38:33.012Z","uuid":"956368a0-2c56-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"1092","type":"people"}]},"data_files":{"data":[]},"documents":{"data":[]},"investigation":{"data":{"id":"243","type":"investigations"}},"models":{"data":[]},"people":{"data":[{"id":"1092","type":"people"}]},"projects":{"data":[{"id":"1672","type":"projects"}]},"publications":{"data":[{"id":"64","type":"publications"}]},"sops":{"data":[]},"submitter":{"data":[{"id":"1092","type":"people"}]}},"type":"studies"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/studyResponse"}},"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["create","studies"]}},"/studies/{id}":{"delete":{"description":"<a name=\"deleteStudy\"></a>A **deleteStudy** operation will delete the specified <a href=\"#studies\">**Study**</a>, if the authenticated user has sufficient access to it.\n","operationId":"deleteStudy","responses":{"200":{"description":"OK","schema":{"$ref":"#/definitions/ok"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["delete","studies"]},"get":{"description":"<a name=\"readStudy\"></a>A **readStudy** operation will return information about the <a href=\"#studies\">Study</a> identified, provided the authenticated user has access to it.\n\nThe **readStudy** operation returns a JSON object representing the <a href=\"#studies\">**Study**</a>.\n","operationId":"readStudy","responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"description":null,"experimentalists":null,"person_responsible_id":"411","title":"Model analysis"},"id":"138","links":{"self":"/studies/138"},"meta":{"api_version":"0.1","base_url":"https://fairdomhub.org","created":"2015-07-01T08:14:11.000Z","modified":"2015-07-01T08:14:11.000Z","uuid":"29af988a-9b3b-4ce3-a42d-1bebf0c4cbe1"},"relationships":{"assays":{"data":[{"id":"294","type":"assays"},{"id":"295","type":"assays"},{"id":"296","type":"assays"}]},"creators":{"data":[]},"data_files":{"data":[{"id":"1213","type":"data_files"},{"id":"1214","type":"data_files"}]},"documents":{"data":[]},"investigation":{"data":{"id":"56","type":"investigations"}},"models":{"data":[{"id":"144","type":"models"},{"id":"175","type":"models"},{"id":"176","type":"models"},{"id":"177","type":"models"},{"id":"179","type":"models"}]},"people":{"data":[{"id":"411","type":"people"}]},"projects":{"data":[{"id":"17","type":"projects"}]},"publications":{"data":[{"id":"240","type":"publications"},{"id":"268","type":"publications"}]},"sops":{"data":[]},"submitter":{"data":[{"id":"411","type":"people"}]}},"type":"studies"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/studyResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"tags":["read","studies"]},"parameters":[{"default":138,"description":"The study to fetch, patch or delete","in":"path","name":"id","required":true,"type":"integer"}],"patch":{"description":"<a name=\"updateStudy\"></a>An **updateStudy** operation will modify the information held about the specified <a href=\"#studies\">**Study**</a>. This operation is only available if the authenticated user has access to the <a href=\"#studies\">**Study**</a>.\n\nThe **updateStudy** operation returns a JSON object representing the modified <a href=\"#studies\">**Study**</a>.\n","operationId":"updateStudy","parameters":[{"description":"The study to update.","in":"body","name":"study","schema":{"$ref":"#/definitions/studyPatch"}}],"responses":{"200":{"description":"OK","examples":{"application/json":{"data":{"attributes":{"description":"The Study of many things","experimentalists":"Wet lab people","other_creators":"Marie Curie","person_responsible_id":"1161","policy":{"access":"download","permissions":[{"access":"view","resource":{"id":"1777","type":"projects"}}]},"title":"A Maximal Study"},"id":"227","links":{"self":"/studies/227"},"meta":{"api_version":"0.1","base_url":"http://localhost:3000","created":"2018-04-27T14:39:15.000Z","modified":"2018-04-27T14:39:20.814Z","uuid":"aedad830-2c56-0136-ec2f-08002734982f"},"relationships":{"assays":{"data":[]},"creators":{"data":[{"id":"1161","type":"people"}]},"data_files":{"data":[]},"documents":{"data":[]},"investigation":{"data":{"id":"272","type":"investigations"}},"models":{"data":[]},"people":{"data":[{"id":"1161","type":"people"}]},"projects":{"data":[{"id":"1777","type":"projects"}]},"publications":{"data":[{"id":"66","type":"publications"}]},"sops":{"data":[]},"submitter":{"data":[{"id":"1161","type":"people"}]}},"type":"studies"},"jsonapi":{"version":"1.0"}}},"schema":{"$ref":"#/definitions/studyResponse"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"tags":["update","studies"]}}},"produces":["application/json"],"schemes":["https"],"security":[{"basicAuth":[]}],"securityDefinitions":{"basicAuth":{"description":"<a name=\"authentication\"></a>The JSON API uses [Basic access\nauthentication](https://en.wikipedia.org/wiki/Basic_access_authentication)\nwhere the *username* and *password* correspond to a registered user on\nthe SEEK that is being accessed.\n\nThe **List** and **Read** API calls may be used without authentication. In\nthat case, they will only list, or allow reading of, publicly viewable\nobjects.","type":"basic"}},"swagger":"2.0","tags":[{"description":"<a name=\"list\"></a>**List** operations return a JSON object containing a list of all the objects of the specified class to which the authenticated user has access.\n\nSuccess response codes:\n* 200 OK\n\nError response codes:","name":"list","x-traitTag":true},{"description":"<a name=\"create\"></a>A **Create** operation creates a new instance of the specified class. The instance is populated with the content of the body of the API call.\n\nThe **Create** call returns a JSON object representing the newly created instance.\n\nSuccess response codes:\n* 201 Created\n\nError response codes:\n* 400 Bad request\n* 403 Forbidden\n* 422 Unprocessable entity\n","name":"create","x-traitTag":true},{"description":"<a name=\"read\"></a>A **Read** operation will return information about the instance identified, provided the authenticated user has access to it.\n\nThe **Read** operation returns a JSON object representing the instance.\n\nSuccess response codes:\n\n* 200 OK\n\nError response codes:\n* 403 Forbidden\n* 404 Not found\n","name":"read","x-traitTag":true},{"description":"<a name=\"update\"></a>An **Update** operation will modify the information held about the specified instance. This operation is only available if the authenticated user has access to the object.\n\nSuccess response codes:\n* 200 OK\n\nError response codes:\n* 403 Forbidden\n* 404 Not found\n* 422 Unprocessable entity\n","name":"update","x-traitTag":true},{"description":"<a name=\"delete\"></a>A **Delete** operation will delete the specified instance, if the authenticated user has sufficient access to it.\n\nSuccess response codes:\n* 200 OK\n\nError response codes:\n* 403 Forbidden\n* 404 Not found\n","name":"delete","x-traitTag":true},{"description":"<a name=\"upload\"></a>**Upload** operations are used to satisfy the required content of previously created resources such as <a href=\"#dataFiles\">**DataFile**</a>, <a href=\"#documents\">**Document**</a>, <a href=\"#models\">**Model**</a>, <a href=\"#sops\">**SOP**</a> or <a href=\"#presentations\">**Presentation**</a>. See <a href=\"#ContentBlob\">**ContentBlob**</a> for more details.\n","name":"upload","x-traitTag":true},{"description":"<a name=\"download\"></a>**Download** operations are used to retrieve the content of resources such as <a href=\"#dataFiles\">**DataFile**</a>, <a href=\"#documents\">**Document**</a>, <a href=\"#models\">**Model**</a>, <a href=\"#sops\">**SOP**</a> or <a href=\"#presentations\">**Presentation**</a>. See <a href=\"#ContentBlob\">**ContentBlob**</a> for more details.\n","name":"download","x-traitTag":true},{"description":"<a name=\"search\"></a>","name":"search"},{"description":"<a name=\"institutions\"></a>An **Institition** in SEEK is where someone is employed or works. It is normal for an **Institution** to have a physical location - a set of buildings in which <a href=\"#people\">**People**</a> work.\n\nSEEK does not impose any constraints on the granularity of the **Institution** so it may represent a whole university or company, or be limited to a specific site.\n\nAn **Institution** has the following associated information:\n\n* **The title of the Institution**\n* A reference to an avatar / logo for the **Institution**\n* The two letter country code\n* The name of the city where the **Institution** has its headquarters\n* The address of the **Institution** within the city\n* A URI to the webpage for the **Institution**\n\nA response for an **Institution** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* References to registered <a href=\"#people\">**People**</a> who work at the **Institution**\n* References to the <a href=\"#projects\">**Projects**</a> in which the **Institution** is a partner.\n","name":"institutions"},{"description":"<a name=\"people\"></a>A **Person** in SEEK is someone who participates directly or indirectly in the scientific research described within SEEK. A person may:\n\n* work at one or more <a href=\"#institutions\">**Institutions**</a>\n* work on one or more <a href=\"#projects\">**Projects**</a>\n\nA **Person** can have helped to carry out <a href=\"#investigations\">**Investigations**</a>, <a href=\"#studies\">**Studies**</a> and <a href=\"#assays\">**Assays**</a>, and to have been involved in the creation of resources such as <a href=\"#dataFiles\">**DataFles**</a>.\n\nA **Person** has the following associated information:\n\n* **The person's first name**\n* **The person's last name**\n* A personal description\n* An email address for the **Person**\n* A URI to a webpage about the **Person**\n* The [ORCID](https://orcid.org/) for the **Person**\n* A list of strings describing the expertise of the **Person**\n* A list of strings describing the tools that the **Person** uses\n* The telephone number of the **Person**, including country code\n* The [Skype](https://www.skype.com) name of the **Person**\n\nA response for a **Person** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* A URI to an image used as the **Person's** avatar\n* The **Person's** title, made from their first and last name\n* A list of the <a href=\"#projects\">**Project**</a> positions held by the **Person**\n\n* References to the <a href=\"#projects\">**Projects**</a> in which the **Person** is involved\n* References to the <a href=\"#institutions\">**Institutions**</a> where the **Person** works\n* References to the <a href=\"#investigations\">**Investigations**</a> in which the **Person** is involved\n* References to the <a href=\"#studies\">**Studies**</a> in which the **Person** is involved\n* References to the <a href=\"#assays\">**Assays**</a> in which the **Person** is involved\n* References to the <a href=\"#dataFiles\">**DataFiles**</a> associated with the **Person**\n* References to the <a href=\"#documents\">**Documents**</a> associated with the **Person**\n* References to the <a href=\"#models\">**Models**</a> associated with the **Person**\n* References to the <a href=\"#sops\">**SOPs**</a> associated with the **Person**\n* References to the <a href=\"#publications\">**Publications**</a> associated with the **Person**\n* References to the <a href=\"#presentations\">**Presentations**</a> associated with the **Person**\n* References to the <a href=\"#events\">**Events**</a> associated with the **Person**\n\n**Note that in the Person response the email address is encoded in mbox_sha1sum**","name":"people"},{"description":"<a name=\"programmes\"></a>**Programmes** are an umbrella group for one or more <a href=\"#projects\">**Projects**</a>. They are usually, but not always, associated with a particular funded piece of research.\n\nA **Programme** has the following associated information:\n\n* ** The title of the Programme **\n* A description of the **Programme**\n* A URI to a webpage about the **Programme**\n* A string containing details about the funding of the **Programme**\n* A list of the funding codes for the **Programme**\n\n* References to the <a href=\"#people\">**People**</a> who are administrators for the **Programme**\n* References to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n\nA response for a **Programme** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* References to <a href=\"#people\">**People**</a> who work on the **Programme** and are not administrators\n* References to <a href=\"#institutions\">**Institutions**</a> that are involved in the **Programme**\n* References to <a href=\"#investigations\">**Investigations**</a> that are part of the **Programme**\n* References to <a href=\"#studies\">**Studies**</a> that are part of the **Programme**\n* References to <a href=\"#assays\">**Assays**</a> that are part of the **Programme**\n* References to <a href=\"#dataFiles\">**DataFiles**</a> that belong to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n* References to <a href=\"#documents\">**Documents**</a> that belong to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n* References to <a href=\"#models\">**Models**</a> that belong to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n* References to <a href=\"#sops\">**Sops**</a> that belong to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n* References to <a href=\"#publications\">**Publications**</a> that belong to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n* References to <a href=\"#presentations\">**Presentations**</a> that belong to <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n* References to <a href=\"#events\">**Events**</a> that are held by or attended by <a href=\"#projects\">**Projects**</a> that are part of the **Programme**\n","name":"programmes"},{"description":"<a name=\"projects\"></a>A **Project** is an area of research carried out as part of a <a href=\"#programmes\">**Programme**</a> and consisting of one or more <a href=\"#investigations\">**Investigations**</a>.\n\n**In the current version of the API, the <a href=\"#Policy\">Policy</a> and the description of Project members and administrative roles does not work correctly.  This will be improved in future versions of the API.**\n\nA **Project** has the following associated information:\n\n* **The title of the Project**\n* A reference to an avatar / logo for the **Project**\n* A description of the **Project**\n* A URI to a webpage about the **Project**\n* A URI to the wiki of the **Project**\n* The default <a href=\"#Policy\">**Policy**</a> applied to objects belonging to the **Project**\n* The default <a href=\"#License\">**License**</a> applied to objects belonging to the **Project**\n\n* References to the <a href=\"#programmes\">**Programmes**</a> that the **Project** is part of\n* References to the <a href=\"#organisms\">**Organisms**</a> studied by the **Project**\n\nA response for a **Project** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* References to <a href=\"#people\">**People**</a> who work on the **Project**\n* References to <a href=\"#institutions\">**Institutions**</a> that are involved in the **Project**\n* References to <a href=\"#investigations\">**Investigations**</a> that are part of the **Project**\n* References to <a href=\"#studies\">**Studies**</a> that are part of the **Project**\n* References to <a href=\"#assays\">**Assays**</a> that are part of the **Project**\n* References to <a href=\"#dataFiles\">**DataFiles**</a> that belong to the <a href=\"#projects\">**Project**</a>\n* References to <a href=\"#documents\">**Documents**</a> that belong to the <a href=\"#projects\">**Project**</a>\n* References to <a href=\"#models\">**Models**</a> that belong to the <a href=\"#projects\">**Project**</a>\n* References to <a href=\"#sops\">**Sops**</a> that belong to the <a href=\"#projects\">**Project**</a>\n* References to <a href=\"#publications\">**Publications**</a> that belong to the <a href=\"#projects\">**Project**</a>\n* References to <a href=\"#presentations\">**Presentations**</a> that belong to the <a href=\"#projects\">**Project**</a>\n* References to <a href=\"#events\">**Events**</a> that are held by or attended by the <a href=\"#projects\">**Project**</a>\n","name":"projects"},{"description":"<a name=\"investigations\"></a>**Investigations** are high level descriptions of the research carried out by a particular <a href=\"#projects\">**Project**</a>. They typically reflect the general aims of the <a href=\"#projects\">**Project**</a>, for example, carbon metabolism or anaerobic/aerobic transitions.\n\nAn **Investigation** has the following associated information:\n\n* **The title of the Investigation**\n* A description of the **Investigation**\n* A string listing other creators of the **Investigation**\n* The sharing <a href=\"#Policy\">**Policy**</a> of the **Investigation**\n* References to the <a href=\"#people\">**People**</a> who created the **Investigation**\n* References to the <a href=\"#projects\">**Projects**</a> which the **Investigation** is part of\n* References to <a href=\"#publications\">**Publications**</a> about the **Investigation**\n\nA response for an **Investigation** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* A reference to the <a href=\"#people\">**Person**</a> who registered (submitted) the **Investigation** into SEEK\n* References to <a href=\"#studies\">**Studies**</a> that are part of the **Investigation**\n* References to <a href=\"#assays\">**Assays**</a> that are part of the **Investigation**\n* References to <a href=\"#dataFiles\">**DataFiles**</a> that belong to the **Investigation**\n* References to <a href=\"#documents\">**Documents**</a> that belong to the **Investigation**\n* References to <a href=\"#models\">**Models**</a> that belong to the **Investigation**\n* References to <a href=\"#sops\">**Sops**</a> that belong to the **Investigation**\n* References to <a href=\"#publications\">**Publications**</a> that belong to the **Investigation**\n","name":"investigations"},{"description":"<a name=\"studies\"></a>A **Study** is a series of experiments (or <a href=\"#assays\">**Assays**</a> ) which can be combined to answer a particular biological question. These experiments might be a series of the same type of <a href=\"#assays\">**Assay**</a> (for example, microarrays for different conditions), or they may be a collection of different types of <a href=\"#assays\">**Assay**</a> (e.g. a combination of array and mass spec measurements).\n\nA **Study** has the following associated information:\n\n* **The title of the Study**\n* A description of the **Study**\n* A string listing experimentalists of the **Study**\n* A string listing other creators of the **Study**\n* A string containing the id of the <a href=\"#people\">**Person**</a> responsible for the **Study**\n* The sharing <a href=\"#Policy\">**Policy**</a> of the **Study**\n* References to the <a href=\"#people\">**People**</a> who created the **Study**\n** A reference to the <a href=\"#investigations\">Investigation</a> containing the Study**\n* References to <a href=\"#publications\">**Publications**</a> about the **Study**\n\nA response for a **Study** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* A reference to the <a href=\"#people\">**Person**</a> who registered (submitted) the **Study** into SEEK\n* References to the <a href=\"#projects\">**Projects**</a> that indirectly contain the **Study**\n* References to the <a href=\"#assays\">**Assays**</a> that belong to the **Stuady**\n* References to <a href=\"#dataFiles\">**DataFiles**</a> that belong to the **Study**\n* References to <a href=\"#documents\">**Documents**</a> that belong to the **Study**\n* References to <a href=\"#models\">**Models**</a> that belong to the **Study**\n* References to <a href=\"#sops\">**Sops**</a> that belong to the **Study**\n* References to <a href=\"#publications\">**Publications**</a> that belong to the **Study**\n","name":"studies"},{"description":"<a name=\"assays\"></a>An **Assay** describes a particular experiment. It allows you to associate <a href=\"#dataFiles\">**DataFiles**</a>, <a href=\"#sops\">**SOPs**</a> and <a href=\"#models\">**Models**</a> together as well as describing the type of **Assay** and any technology required to perform the experiment.\n\nAn **Assay** has the following associated information:\n\n* **The title of the Assay**\n* A description of the **Assay**\n* A string listing other creators of the **Assay**\n* A string containing the abbreviated form of the kind of **Assay** - normally *EXP* for experimental or *MOD* for modelling\n* A URI to the type of **Assay** resolving to an entry in the [JERM ontology](http://jermontology.org/ontology/JERMOntology)\n* A URI to the technology used in the **Assay** resolving to an entry in the [JERM ontology](http://jermontology.org/ontology/JERMOntology)\n* The sharing <a href=\"#Policy\">**Policy**</a> of the **Assay**\n* References to the <a href=\"#people\">**People**</a> who created the **Assay**\n* A singleton reference to the <a href=\"#studies\">**Study**</a> which the **Assay** is part of\n* References to <a href=\"#publications\">**Publications**</a> about the **Assay**\n* References to <a href=\"#dataFiles\">**DataFiles**</a> that belong to the **Assay**\n* References to <a href=\"#documents\">**Documents**</a> that belong to the **Assay**\n* References to <a href=\"#models\">**Models**</a> that belong to the **Assay**\n* References to <a href=\"#sops\">**Sops**</a> that belong to the **Assay**\n* References to the <a href=\"#organisms\">**Organisms**</a> studied in the **Assay**\n\nA response for an **Assay** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* A singleton reference to the <a href=\"#investigations\">**Investigation**</a> which the **Assay** is part of\n* References to the <a href=\"#projects\">**Projects**</a> that indirectly contain the **Assay**\n","name":"assays"},{"description":"","name":"contentBlobs"},{"description":"<a name=\"dataFiles\"></a>A **dataFile** can be any file containing data relevant to the <a href=\"#assays\">**Assay**</a> (raw data, processed data, calibration information etc). They can be in any format (word files, e-lab notebooks, code, annotated spreadsheets etc).\n\n**Although dataFiles are versioned, this is out of scope for the current release of the API.**\n\nA **DataFile** has the following associated information:\n\n* **The title of the DataFile**\n* **The specification for the <a href=\"#ContentBlob\">ContentBlobs</a> in the DataFile**\n* **References to the <a href=\"#projects\">Projects</a> documented**\n* A string containing a list of tags for the **DataFile**\n* A description of the **DataFile**\n* The <a href=\"#License\">**License**</a> applied to the **DataFile**\n* The sharing <a href=\"#Policy\">**Policy**</a> applied to the **DataFile**\n* A string listing other creators of the **DataFile**\n* References to the <a href=\"#people\">**People**</a> who wrote the **DataFile**\n* References to the <a href=\"#assays\">**Assays**</a> associated with the **DataFile**\n* References to the <a href=\"#publications\">**Publications**</a> associated with the **DataFile**\n* References to the <a href=\"#events\">**Events**</a> associated with the **DataFile**\n\nA response for a **DataFile** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* ** An array of the versions of the DataFile**\n* ** A number indicating the latest version**\n* ** The time when the DataFile was created**\n* ** The last time the DataFile was updated**\n* A reference to the <a href=\"#people\">**Person**</a> who submitted the **DataFile**\n* References to the <a href=\"#investigations\">**Investigations**</a> associated with the **DataFile**\n* References to the <a href=\"#studies\">**Studies**</a> associated with the **DataFile**\n","name":"dataFiles"},{"description":"<a name=\"documents\"></a>A **Document** is any documentation that describes an <a href=\"#investigations\">**Investigation**</a>, <a href=\"#studies\">**Study**</a> or <a href=\"#assays\">**Assay**</a>. The content of a **Document** is descriptive and it must not contain any data that is consumed or produced by an <a href=\"#assays\">**Assay**</a>.\n\n**Although documents are versioned, this is out of scope for the current release of the API.**\n\nA **Document** has the following associated information:\n\n* **The title of the Document**\n* **The specification for the <a href=\"#ContentBlob\">ContentBlobs</a> in the Document**\n* **References to the <a href=\"#projects\">Projects</a> documented**\n* A string containing a list of tags for the **Document**\n* A description of the **Document**\n* The <a href=\"#License\">**License**</a> applied to the **Document**\n* The sharing <a href=\"#Policy\">**Policy**</a> applied to the **Document**\n* A string listing other creators of the **Document**\n* References to the <a href=\"#people\">**People**</a> who wrote the **Document**\n* References to the <a href=\"#assays\">**Assays**</a> documented\n\nA response for a **Document** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* ** An array of the versions of the Document**\n* ** A number indicating the latest version**\n* ** The time when the Document was created**\n* ** The last time the Document was updated**\n* A reference to the <a href=\"#people\">**Person**</a> who submitted the **Document**\n* References to the <a href=\"#investigations\">**Investigations**</a> associated with the **Document**\n* References to the <a href=\"#studies\">**Studies**</a> associated with the **Document**\n* References to the <a href=\"#publications\">**Publications**</a> associated with the **Document**\n","name":"documents"},{"description":"<a name=\"models\"></a>A **Model** is a computer model of a biological or biochemical network or process.Some **Models** may be simulated using the JWSOnline system.\n\n**Although models are versioned, this is out of scope for the current release of the API.**\n\nA **Model** has the following associated information:\n\n* **The title of the Model**\n* **The specification for the <a href=\"#ContentBlob\">ContentBlobs</a> in the Model**\n* **References to the <a href=\"#projects\">Projects</a> documented**\n* A string containing a list of tags for the **Model**\n* A description of the **Model**\n* The <a href=\"#License\">**License**</a> applied to the **Model**\n* The sharing <a href=\"#Policy\">**Policy**</a> applied to the **Model**\n* A string listing other creators of the **Model**\n* A string specifying the **Model** type\n* A string specifying the **Model** format\n* A string specifying the execution environment of the **Model**\n* References to the <a href=\"#people\">**People**</a> who wrote the **Model**\n* References to the <a href=\"#assays\">**Assays**</a> associated with the **Model**\n* References to the <a href=\"#publications\">**Publications**</a> associated with the **Model**\n\nA response for a **Model** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* ** An array of the versions of the Model**\n* ** A number indicating the latest version**\n* ** The time when the Model was created**\n* ** The last time the Model was updated**\n* A reference to the <a href=\"#people\">**Person**</a> who submitted the **Model**\n* References to the <a href=\"#investigations\">**Investigations**</a> associated with the **Model**\n* References to the <a href=\"#studies\">**Studies**</a> associated with the **Model**\n","name":"models"},{"description":"<a name=\"publications\"></a>A **Publication** is a publication about a <a href=\"#projects\">**Project**</a>, It normally has a [DOI](http://www.doi.org/) or [PubMed ID](https://en.wikipedia.org/wiki/Wikipedia:PMID).\n\nThe response to a read of a **Publication** includes the following information:\n\n* **The title of the Publication**\n* **The journal in which the Publication is published**\n* **A string containing the date of publication**\n* **The PubMed ID**\n* **The preferred string for citing the Publication**\n* **A link to the Publication**\n* The DOI of the **Publication**\n* A list of strings for the authors\n* The sharing <a href=\"#Policy\">**Policy**</a> for the **Publication**\n* References to the <a href=\"#people\">**People**</a> who wrote the **Publication**\n* References to the <a href=\"#projects\">**Projects**</a> described in the **Publication**\n* References to the <a href=\"#investigations\">**Investigations**</a> described in the **Publication**\n* References to the <a href=\"#studies\">**Studies**</a> described in the **Publication**\n* References to the <a href=\"#assays\">**Assays**</a> described in the **Publication**\n* References to <a href=\"#dataFiles\">**DataFiles**</a> that were used in the work described in the **Publication**\n* References to <a href=\"#models\">**Models**</a> that were used in the work described in the **Publication**\n* References to related **Publications**\n* References to <a href=\"#presentations\">**Presentations**</a> associated with the **Publication**\n* References to <a href=\"#events\">**Events**</a> associated with the **Publication**\n","name":"publications"},{"description":"<a name=\"sops\"></a>**SOPs** are standard operating procedures which describe the protocol required to reproduce an <a href=\"#assays\">**Assay**</a>. They can be in any format (word files, e-lab notebooks, code, annotated spreadsheets etc). Relevant **SOPs** can be linked directly to the <a href=\"#assays\">**Assay**</a>.\n\n**Although SOPs are versioned, this is out of scope for the current release of the API.**\n\nA **SOP** has the following associated information:\n\n* **The title of the SOP**\n* **The specification for the <a href=\"#ContentBlob\">ContentBlobs</a> in the SOP**\n* **References to the <a href=\"#projects\">Projects</a> relevant to the SOP**\n* A string containing a list of tags for the **SOP**\n* A description of the **SOP**\n* The <a href=\"#License\">**License**</a> applied to the **SOP**\n* The sharing <a href=\"#Policy\">**Policy**</a> applied to the **SOP**\n* A string listing other creators of the **SOP**\n* References to the <a href=\"#people\">**People**</a> who wrote the **SOP**\n* References to the <a href=\"#assays\">**Assays**</a> relevant to the SOP\n\nA response for a **SOP** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* ** An array of the versions of the SOP**\n* ** A number indicating the latest version**\n* ** The time when the SOP was created**\n* ** The last time the SOP was updated**\n* A reference to the <a href=\"#people\">**Person**</a> who submitted the **SOP**\n* References to the <a href=\"#investigations\">**Investigations**</a> associated with the **SOP**\n* References to the <a href=\"#studies\">**Studies**</a> associated with the **SOP**\n* References to the <a href=\"#publications\">**Publications**</a> associated with the **SOP**\n","name":"sops"},{"description":"<a name=\"events\"></a>An **Event** is an event that is associated with one or more <a href=\"#projects\">**Projects**</a>, happening on specified dates and at a specific, actual or virtual, location.\n\nAn **Event** has the following associated information:\n\n* **The title of the Event**\n* **The start date of the Event**\n* A description of the **Event**\n* A URI to a webpage about the **Event**\n* The two letter country code for where the **Event** is\n* The name of the city where the **Event** takes place\n* The address within the city where the **Event** takes place\n* The end date of the **Event**\n* The sharing <a href=\"#Policy\">**Policy**</a> for the **Event**\n* **References to the <a href=\"#projects\">Projects</a> associated with the Event**\n* References to any <a href=\"#dataFiles\">**DataFiles**</a>  associated with the **Event**\n* References to any <a href=\"#publications\">**Publications**</a>  associated with the **Event**\n* References to any <a href=\"#presentations\">**Presentations**</a>  associated with the **Event**\n\nA response for an **Event** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* Reference to the <a href=\"#people\">**Person**</a> who submitted the **Event**","name":"events"},{"description":"<a name=\"presentations\"></a>A **Presentation** is a presentation about one or more <a href=\"#projects\">**Projects**</a>.\n\n**Although presentations are versioned, this is out of scope for the current release of the API.**\n\nA **Presentation** has the following associated information:\n\n* **The title of the Presentation**\n* **The specification for the <a href=\"#ContentBlob\">ContentBlobs</a> in the Presentation**\n* **References to the <a href=\"#projects\">Projects</a> documented**\n* A string containing a list of tags for the **Presentation**\n* A description of the **Presentation**\n* The <a href=\"#License\">**License**</a> applied to the **Presentation**\n* The sharing <a href=\"#Policy\">**Policy**</a> applied to the **Presentation**\n* A string listing other creators of the **Presentation**\n* References to the <a href=\"#people\">**People**</a> who wrote the **Presentation**\n* References to the <a href=\"#assays\">**Assays**</a> associated with the **Presentation**\n* References to the <a href=\"#publications\">**Publications**</a> associated with the **Presentation**\n* References to the <a href=\"#events\">**Events**</a> associated with the **Presentation**\n\nA response for a **Presentation** such as that for a <a href=\"#create\">**Create**</a>, <a href=\"#read\">**Read**</a> or <a href=\"#update\">**Update**</a> includes the additional information\n\n* ** An array of the versions of the Presentation**\n* ** A number indicating the latest version**\n* ** The time when the Presentation was created**\n* ** The last time the Presentation was updated**\n* A reference to the <a href=\"#people\">**Person**</a> who submitted the **Presentation**\n* References to the <a href=\"#investigations\">**Investigations**</a> associated with the **Presentation**\n* References to the <a href=\"#studies\">**Studies**</a> associated with the **Presentation**","name":"presentations"},{"description":"<a name=\"organisms\"></a>An **Organism** is a organism as identified by an entry in the [NCBI ontology](http://www.ncbi.nlm.nih.gov/taxonomy).\n\nThe response to a read of an **Organism** includes the following information:\n\n* **The title of the Organism**\n* **A URI referencing an ontology entry describing the Organism**\n* **The common abbreviation for the ontology**\n* **References to <a href=\"#projects\">Projects</a> that use the Organism**\n* **References to <a href=\"#assays\">Assays</a> that use the Organism**\n* **References to <a href=\"#models\">Models</a> that simulate the Organism**\n","name":"organisms"},{"description":"<a name=\"sampleTypes\"></a>A **SampleType** is a definition of the information that is held about a physical or virtual sample.\n\n**In the current release of the API it is only possible to list references to the SampleTypes. Additional functionality will be available in future versions.**\n","name":"sampleTypes"}],"x-tagGroups":[{"name":"operation types","tags":["list","create","read","update","delete","upload","download"]},{"name":"Search","tags":["search"]},{"name":"Yellow Pages","tags":["institutions","people","programmes","projects"]},{"name":"Experiments","tags":["investigations","studies","assays"]},{"name":"Assets","tags":["dataFiles","documents","models","publications","sops","contentBlobs"]},{"name":"Activities","tags":["events","presentations"]},{"name":"Samples","tags":["organisms","sampleTypes"]}],"x-types":{"CreateTypeT":{"400":{"description":"Bad request","schema":{"$ref":"#/definitions/bad_request"}},"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}},"DeleteTypeT":{"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"ListTypeT":{"501":{"description":"Not implemented"}},"ReadTypeT":{"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}}},"UpdateTypeT":{"403":{"description":"Forbidden","schema":{"$ref":"#/definitions/forbidden"}},"404":{"description":"Not found","schema":{"$ref":"#/definitions/not_found"}},"422":{"description":"Unprocessable entity","schema":{"$ref":"#/definitions/unprocessable_entity"}}}}},{"basePath":"/v2","definitions":{"ApiResponse":{"properties":{"code":{"format":"int32","type":"integer"},"message":{"type":"string"},"type":{"type":"string"}},"type":"object"},"Category":{"properties":{"id":{"format":"int64","type":"integer"},"name":{"type":"string"}},"type":"object","xml":{"name":"Category"}},"Order":{"properties":{"complete":{"default":false,"type":"boolean"},"id":{"format":"int64","type":"integer"},"petId":{"format":"int64","type":"integer"},"quantity":{"format":"int32","type":"integer"},"shipDate":{"format":"date-time","type":"string"},"status":{"description":"Order Status","enum":["placed","approved","delivered"],"type":"string"}},"type":"object","xml":{"name":"Order"}},"Pet":{"properties":{"category":{"$ref":"#/definitions/Category"},"id":{"format":"int64","type":"integer"},"name":{"example":"doggie","type":"string"},"photoUrls":{"items":{"type":"string"},"type":"array","xml":{"name":"photoUrl","wrapped":true}},"status":{"description":"pet status in the store","enum":["available","pending","sold"],"type":"string"},"tags":{"items":{"$ref":"#/definitions/Tag"},"type":"array","xml":{"name":"tag","wrapped":true}}},"required":["name","photoUrls"],"type":"object","xml":{"name":"Pet"}},"Tag":{"properties":{"id":{"format":"int64","type":"integer"},"name":{"type":"string"}},"type":"object","xml":{"name":"Tag"}},"User":{"properties":{"email":{"type":"string"},"firstName":{"type":"string"},"id":{"format":"int64","type":"integer"},"lastName":{"type":"string"},"password":{"type":"string"},"phone":{"type":"string"},"userStatus":{"description":"User Status","format":"int32","type":"integer"},"username":{"type":"string"}},"type":"object","xml":{"name":"User"}}},"externalDocs":{"description":"Find out more about Swagger","url":"http://swagger.io"},"host":"petstore.fancy.io","info":{"contact":{"email":"apiteam@fancy.io","x-chat":"https://de.wikipedia.org/wiki/Chat","x-issueTracker":"https://www.atlassian.com/de/software/jira"},"description":"This is a sample server Petstore server.","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"http://fancy.io/terms/","title":"Fancy Petstore","version":"1.0.0"},"paths":{"/pet":{"post":{"consumes":["application/json","application/xml"],"description":"","operationId":"addPet","parameters":[{"description":"Pet object that needs to be added to the store","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Pet"}}],"produces":["application/xml","application/json"],"responses":{"405":{"description":"Invalid input"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Add a new pet to the store","tags":["pet"]},"put":{"consumes":["application/json","application/xml"],"description":"","operationId":"updatePet","parameters":[{"description":"Pet object that needs to be added to the store","in":"body","name":"body","required":true,"schema":{"$ref":"#/definitions/Pet"}}],"produces":["application/xml","application/json"],"responses":{"400":{"description":"Invalid ID supplied"},"404":{"description":"Pet not found"},"405":{"description":"Validation exception"}},"security":[{"petstore_auth":["write:pets","read:pets"]}],"summary":"Update an existing pet","tags":["pet"]}},"/pet/findByStatus":{"get":{"description":"Multiple status values can be provided with comma separated strings","operationId":"findPetsByStatus","parameters":[{"collectionFormat":"multi","description":"Status values that need to be considered for 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The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.","properties":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/Edge"},"description":"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/Node"},"description":"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"}},"required":["edges","nodes"],"type":"object","x-nullable":true},"LogEntry":{"additionalProperties":true,"description":"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.","example":{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"},"properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":false,"type":"string"},"timestamp":{"description":"Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00).","example":"2020-09-03T18:13:49+00:00","format":"date-time","nullable":false,"type":"string"}},"required":["message","timestamp"],"title":"LogEntry","type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"example":"DEBUG","type":"string","x-nullable":true},"MeshNgdResponse":{"example":{"message":"Term 1 'malria' not found in MeSH","result_code":"TermNotFound","value":0.714},"properties":{"message":{"description":"Extended message denoting the success or mode of failure for request","example":"Term 1 'malria' not found in MeSH","title":"message","type":"string"},"result_code":{"description":"Set to OK for success, or some other short string to indicate and error (e.g., TermNotFound, etc.)","example":"TermNotFound","title":"result_code","type":"string"},"value":{"description":"Calculated Normalized Google Distance for the two supplied terms","example":0.714,"format":"float","title":"value","type":"number"}},"title":"MeshNgdResponse","type":"object"},"Message":{"additionalProperties":false,"description":"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.","example":{"query_graph":{"edges":{"e00":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"properties":{"auxiliary_graphs":{"additionalProperties":{"$ref":"#/components/schemas/AuxiliaryGraph"},"description":"Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key.","type":"object"},"knowledge_graph":{"description":"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message","nullable":true,"oneOf":[{"$ref":"#/components/schemas/KnowledgeGraph"}]},"query_graph":{"description":"QueryGraph object that contains a serialization of a query in the form of a graph","nullable":true,"oneOf":[{"$ref":"#/components/schemas/QueryGraph"}]},"results":{"description":"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property,\nif present, MAY be used to infer result rankings. If Results are\nnot expected (such as for a query Message), this property SHOULD\nbe null or absent. If Results are expected (such as for a response\nMessage) and no Results are available, this property SHOULD be an\narray with 0 Results in it.","items":{"$ref":"#/components/schemas/Result"},"nullable":true,"type":"array"}},"title":"Message","type":"object"},"MetaAttribute":{"example":{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"title":"attribute_source","type":"string"},"attribute_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"title":"constraint_name","type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","title":"constraint_use","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"title":"original_attribute_names","type":"array"}},"required":["attribute_type_id"],"title":"MetaAttribute","type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","example":{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","qualifiers":[{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"}],"subject":"biolink:PhenotypicFeature"},"properties":{"association":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"title":"attributes","type":"array"},"knowledge_types":{"description":"A list of knowledge_types that are supported by the service. If the knowledge_types is null, this means that only 'lookup' is supported. Currently allowed values are 'lookup' or 'inferred'.","items":{"type":"string"},"minItems":1,"nullable":true,"title":"knowledge_types","type":"array"},"object":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"},"predicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","title":"BiolinkPredicate","type":"string"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"title":"qualifiers","type":"array"},"subject":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"}},"required":["object","predicate","subject"],"title":"MetaEdge","type":"object"},"MetaKnowledgeGraph":{"description":"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.","example":{"edges":[{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","qualifiers":[{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"}],"subject":"biolink:PhenotypicFeature"},{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","qualifiers":[{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"}],"subject":"biolink:PhenotypicFeature"}],"nodes":{"key":{"attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"id_prefixes":["CHEMBL.COMPOUND","INCHIKEY"]}}},"properties":{"edges":{"description":"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.","items":{"$ref":"#/components/schemas/MetaEdge"},"title":"edges","type":"array"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/MetaNode"},"description":"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.","title":"nodes","type":"object"}},"required":["edges","nodes"],"title":"MetaKnowledgeGraph","type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","example":{"attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"id_prefixes":["CHEMBL.COMPOUND","INCHIKEY"]},"properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"title":"attributes","type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"title":"id_prefixes","type":"array"}},"required":["id_prefixes"],"title":"MetaNode","type":"object"},"MetaQualifier":{"example":{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":"[\"expression\",\"activity\",\"abundance\",\"degradation\"]","type":"string"},"title":"applicable_values","type":"array"},"qualifier_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"}},"required":["qualifier_type_id"],"title":"MetaQualifier","type":"object"},"Node":{"additionalProperties":false,"description":"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.","properties":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"title":"attributes","type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"nullable":true,"title":"categories","type":"array"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"title":"name","type":"string"}},"title":"Node","type":"object"},"NodeBinding":{"additionalProperties":true,"description":"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph.","properties":{"attributes":{"description":"A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"query_id":{"description":"An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided.","oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id"],"title":"NodeBinding","type":"object"},"OperationAnnotate":{"additionalProperties":false,"description":"This operation adds attributes to knowledge graph elements.","properties":{"id":{"enum":["annotate"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationAnnotateEdges":{"additionalProperties":false,"description":"This operation adds attributes to knowledge graph edges.","properties":{"id":{"enum":["annotate_edges"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationAnnotateEdges_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationAnnotateEdges_parameters":{"properties":{"attributes":{"description":"A list of attributes to annotate the edges with. If not included then all available data will be annotated.","example":["pmids"],"items":{"type":"string"},"title":"attributes","type":"array"}},"title":"OperationAnnotateEdges_parameters","type":"object"},"OperationAnnotateNodes":{"additionalProperties":false,"description":"This operation adds attributes to knowledge graph nodes.","properties":{"id":{"enum":["annotate_nodes"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationAnnotateNodes_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationAnnotateNodes_parameters":{"properties":{"attributes":{"description":"A list of attributes to annotate the nodes with. If not included then all available data will be annotated.","example":["pmids"],"items":{"type":"string"},"title":"attributes","type":"array"}},"title":"OperationAnnotateNodes_parameters","type":"object"},"OperationBind":{"additionalProperties":false,"description":"This operation adds results binding kgraph elements to qgraph elements.","properties":{"id":{"enum":["bind"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationCompleteResults":{"additionalProperties":false,"description":"This operation combines partial results into complete results.","properties":{"id":{"enum":["complete_results"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationEnrichResults":{"additionalProperties":false,"description":"Create new results by applying enrichment analysis to existing results.  In particular, combines results by transforming a qnode into a set, formed of knodes that share a property or relation more often than expected by chance.","properties":{"id":{"enum":["enrich_results"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationEnrichResults_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationEnrichResults_parameters":{"properties":{"pvalue_threshold":{"default":1e-6,"description":"The cutoff p-value for enrichment.","example":1e-7,"maximum":1,"minimum":0,"title":"pvalue_threshold","type":"number"},"qnode_keys":{"description":"If specified, then only knodes bound to these qnodes will be examined for enrichment and combination.","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"}},"title":"OperationEnrichResults_parameters","type":"object"},"OperationFill":{"additionalProperties":false,"description":"This operation adds knodes and kedges. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected.","properties":{"id":{"enum":["fill"],"type":"string"},"parameters":{"oneOf":[{"additionalProperties":false,"properties":{"allowlist":{"description":"List of knowledge providers/sources that may be used to provide knowledge.","example":["icees"],"items":{"type":"string"},"minLength":1,"type":"array"},"qedge_keys":{"description":"A list of qedge keys. If included only edges corresponding to the given qedge keys, as well as their connected nodes, will be filled. If not included all edges will be filled.","example":["e00"],"items":{"type":"string"},"type":"array"}},"type":"object"},{"additionalProperties":false,"properties":{"denylist":{"description":"List of knowledge providers/sources that may NOT be used to provide knowledge.","example":["ctd"],"items":{"type":"string"},"minLength":1,"type":"array"},"qedge_keys":{"description":"A list of qedge keys. If included only edges corresponding to the given qedge keys, as well as their connected nodes, will be filled. If not included all edges will be filled.","example":["e00"],"items":{"type":"string"},"type":"array"}},"type":"object"}],"type":"object"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationFilterKgraph":{"additionalProperties":false,"description":"This operation removes kgraph elements (nodes and/or edges).","properties":{"id":{"enum":["filter_kgraph"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationFilterKgraphContinuousKedgeAttribute":{"additionalProperties":false,"description":"This operation removes kgraph edges based on the value of a continuous edge attribute. Edges without the given attribute are left alone.","properties":{"id":{"enum":["filter_kgraph_continuous_kedge_attribute"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterKgraphContinuousKedgeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterKgraphContinuousKedgeAttribute_parameters":{"properties":{"edge_attribute":{"description":"The name of the edge attribute to filter on.","example":"normalized_google_distance","title":"edge_attribute","type":"string"},"qedge_keys":{"description":"This indicates if you only want to remove edges with specific edge_keys. If not provided or empty, all edges will be filtered on.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"},"qnode_keys":{"default":[],"description":"This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed.","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"},"remove_above_or_below":{"description":"Indicates whether to remove above or below the given threshold.","enum":["above","below"],"title":"remove_above_or_below","type":"string"},"threshold":{"description":"The value to compare attribute values to.","example":1.2,"title":"threshold","type":"number"}},"required":["edge_attribute","remove_above_or_below","threshold"],"title":"OperationFilterKgraphContinuousKedgeAttribute_parameters","type":"object"},"OperationFilterKgraphDiscreteKedgeAttribute":{"additionalProperties":false,"description":"This operation removes kgraph edges which have a discrete attribute containing the specified value. Edges without the given attribute are left alone.","properties":{"id":{"enum":["filter_kgraph_discrete_kedge_attribute"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKedgeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterKgraphDiscreteKedgeAttribute_parameters":{"properties":{"edge_attribute":{"description":"The name of the edge attribute to filter on.","example":"provided_by","title":"edge_attribute","type":"string"},"qedge_keys":{"description":"This indicates if you only want to remove edges with specific edge_keys. If not provided or empty, all edges will be filtered on.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"},"qnode_keys":{"default":[],"description":"This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"},"remove_value":{"description":"The value for which all edges containing this value in the specified edge_attribute should be removed.","example":"infores:semmeddb","title":"remove_value"}},"required":["edge_attribute","remove_value"],"title":"OperationFilterKgraphDiscreteKedgeAttribute_parameters","type":"object"},"OperationFilterKgraphDiscreteKnodeAttribute":{"additionalProperties":false,"description":"This operation removes kgraph nodes which have a discrete attribute containing the specified value. In TRAPI 1.1+ this will look in the `attribute_type_id` and `original_attribute_name` attribute fields for the attribute name. Node without the given attribute are left alone. Edges connecting to the removed nodes will also be removed.","properties":{"id":{"enum":["filter_kgraph_discrete_knode_attribute"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKnodeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterKgraphDiscreteKnodeAttribute_parameters":{"properties":{"node_attribute":{"description":"The name of the node attribute to filter on.","example":"molecule_type","title":"node_attribute","type":"string"},"qnode_keys":{"description":"This indicates if you only want to remove nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, all nodes will be considered when filtering.","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"},"remove_value":{"description":"The value for which all edges containing this value in the specified edge_attribute should be removed.","example":"small_molecule","title":"remove_value"}},"required":["node_attribute","remove_value"],"title":"OperationFilterKgraphDiscreteKnodeAttribute_parameters","type":"object"},"OperationFilterKgraphOrphans":{"additionalProperties":false,"description":"This operation removes kgraph elements that are not referenced by any results.","properties":{"id":{"enum":["filter_kgraph_orphans"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationFilterKgraphPercentile":{"additionalProperties":false,"description":"This operation removes kgraph edges that have attribute values are below/above the given percentile.","properties":{"id":{"enum":["filter_kgraph_percentile"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterKgraphPercentile_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterKgraphPercentile_parameters":{"properties":{"edge_attribute":{"description":"The name of the edge attribute to filter on.","example":"normalized_google_distance","title":"edge_attribute","type":"string"},"qedge_keys":{"description":"This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"},"qnode_keys":{"default":[],"description":"This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed.","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"},"remove_above_or_below":{"default":"below","description":"Indicates whether to remove above or below the given threshold.","enum":["above","below"],"title":"remove_above_or_below","type":"string"},"threshold":{"default":95,"description":"The percentile to threshold on.","example":96.8,"maximum":100,"minimum":0,"title":"threshold","type":"number"}},"required":["edge_attribute"],"title":"OperationFilterKgraphPercentile_parameters","type":"object"},"OperationFilterKgraphStdDev":{"additionalProperties":false,"description":"This operation removes kgraph edges that have attribute values are below/above the mean +/- n standard deviations.","properties":{"id":{"enum":["filter_kgraph_std_dev"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterKgraphStdDev_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterKgraphStdDev_parameters":{"properties":{"edge_attribute":{"description":"The name of the edge attribute to filter on.","example":"normalized_google_distance","title":"edge_attribute","type":"string"},"num_sigma":{"default":1,"description":"The number of standard deviations to threshold on.","example":1.2,"minimum":0,"title":"num_sigma","type":"number"},"plus_or_minus_std_dev":{"default":"plus","description":"Indicate whether or not the threshold should be found using plus or minus the standard deviation. E.g. when plus_or_minus_std_dev is set to plus will set the cutoff for filtering as the mean + num_sigma * std_dev while setting plus_or_minus_std_dev to minus will set the cutoff as the mean - num_sigma * std_dev.","enum":["plus","minus"],"title":"plus_or_minus_std_dev","type":"string"},"qedge_keys":{"description":"This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"},"qnode_keys":{"default":[],"description":"This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering.","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"},"remove_above_or_below":{"default":"below","description":"Indictes whether to remove above or below the given threshold.","enum":["above","below"],"title":"remove_above_or_below","type":"string"}},"required":["edge_attribute"],"title":"OperationFilterKgraphStdDev_parameters","type":"object"},"OperationFilterKgraphTopN":{"additionalProperties":false,"description":"This operation removes kgraph edges that have attribute values are below/above the top/bottom n values.","properties":{"id":{"enum":["filter_kgraph_top_n"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterKgraphTopN_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterKgraphTopN_parameters":{"properties":{"edge_attribute":{"description":"The name of the edge attribute to filter on.","example":"normalized_google_distance","title":"edge_attribute","type":"string"},"keep_top_or_bottom":{"default":"top","description":"Indicate whether or not the the top or bottom n values should be kept.","enum":["top","bottom"],"title":"keep_top_or_bottom","type":"string"},"max_edges":{"default":50,"description":"The number of edges to keep.","example":10,"minimum":0,"title":"max_edges","type":"integer"},"qedge_keys":{"description":"This indicates if you only want to filter on specific edge_keys. If not provided or empty, all edges will be filtered on.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"},"qnode_keys":{"default":[],"description":"This indicates if you only want nodes corresponding to a specific list of qnode_keys to be removed. If not provided or empty, no nodes will be removed when filtering. Allows us to know what to do with the nodes connected to edges that are removed.","example":["n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"}},"required":["edge_attribute"],"title":"OperationFilterKgraphTopN_parameters","type":"object"},"OperationFilterResults":{"additionalProperties":false,"description":"This operation allows the TRAPI server to remove elements from the list of results.","properties":{"id":{"enum":["filter_results"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationFilterResultsTopN":{"additionalProperties":false,"description":"This operation truncates the results to at most `max_results` that appear in the TRAPI JSON message.","properties":{"id":{"enum":["filter_results_top_n"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationFilterResultsTopN_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationFilterResultsTopN_parameters":{"properties":{"max_results":{"description":"The maximum number of results to return.","example":50,"minimum":0,"title":"max_results","type":"integer"}},"required":["max_results"],"title":"OperationFilterResultsTopN_parameters","type":"object"},"OperationLookup":{"additionalProperties":false,"description":"This operation adds knodes/kedges and (complete) results. It is equivalent to the workflow fill + bind + complete_results. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected.","properties":{"id":{"enum":["lookup"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationLookupAndScore":{"additionalProperties":false,"description":"This operation adds knodes/kedges, (complete) results, and scores (to the results). It is equivalent to the workflow fill + bind + complete_results + score. Any constraints attached to QNodes and QEdges specified in the TRAPI must be respected.","properties":{"id":{"enum":["lookup_and_score"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationOverlay":{"additionalProperties":false,"description":"This operation adds additional qedges and/or kedges and/or result edge bindings.","properties":{"id":{"enum":["overlay"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationOverlayComputeJaccard":{"additionalProperties":false,"description":"This operation computes the Jaccard Similarity which measures how many intermediate_node_key nodes are directly connected to both the end_node_keys nodes for all pairs of nodes with corresponding keys. It will then add edges to the knowledge graph along with edge attributes (with the property name jaccard_index) between each start_node_key and object_node_key. A query graph edge will also be added using the key specified by virtual_relation_label. This is used for purposes such as \"find me all drugs (start_node_key) that have many proteins (intermediate_node_key) in common with this disease (end_node_key).\" This can be used for downstream filtering to concentrate on relevant bioentities.","properties":{"id":{"enum":["overlay_compute_jaccard"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationOverlayComputeJaccard_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationOverlayComputeJaccard_parameters":{"properties":{"end_node_keys":{"description":"A list of qnode keys specifying the ending nodes.","example":["n0","n2"],"items":{"type":"string"},"title":"end_node_keys","type":"array"},"intermediate_node_key":{"description":"A qnode key specifying the intermediate node.","example":"n1","title":"intermediate_node_key","type":"string"},"virtual_relation_label":{"description":"The key of the query graph edge that corresponds to the knowledge graph edges that were added by this operation.","example":"J1","title":"virtual_relation_label","type":"string"}},"required":["end_node_keys","intermediate_node_key","virtual_relation_label"],"title":"OperationOverlayComputeJaccard_parameters","type":"object"},"OperationOverlayComputeNgd":{"additionalProperties":false,"description":"This operation computes the normalized Google distance (co-occurrence frequency) in PubMed abstracts and adds virual edges between qnodes AND/OR knodes AND/OR results edge bindings. If no publications are found infinity is returned.","properties":{"id":{"enum":["overlay_compute_ngd"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationOverlayComputeNgd_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationOverlayComputeNgd_parameters":{"properties":{"qnode_keys":{"description":"A list of qnode keys to overlay pairwise edges onto. Must be be a list of at least 2 valid qnodes.","example":["n00","n01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"},"virtual_relation_label":{"description":"An label to help identify the virtual edge in the relation field","example":"NGD1","title":"virtual_relation_label","type":"string"}},"required":["qnode_keys","virtual_relation_label"],"title":"OperationOverlayComputeNgd_parameters","type":"object"},"OperationOverlayConnectKnodes":{"additionalProperties":false,"description":"Given a TRAPI message, create new kedges between existing knodes.  These may be created using arbitrary methods or data sources, though provenance should be attached to the new kedges.   Each new kedge is also added to all results containing node bindings to both the subject and object knodes.  This may be independent of any qedge connections, i.e. kedges can be created between any nodes in the kgraph.","properties":{"id":{"enum":["overlay_connect_knodes"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationOverlayFisherExactTest":{"additionalProperties":false,"description":"Fisher exact test computes the Fisher's Exact Test p-values of the connection between a list of given nodes with specified query id (subject_qnode_key e.g. n01) to their adjacent nodes with specified query id (object_qnode_key e.g. n02) in the message knowledge graph. This information is then added as an edge attribute to a virtual edge which is then added to the query graph and knowledge graph. It can also allow you to filter out the user-defined insignificance of connections based on a specified p-value cutoff or return the top n smallest p-value of connections and only add their corresponding virtual edges to the knowledge graph.","properties":{"id":{"enum":["overlay_fisher_exact_test"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationOverlayFisherExactTest_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationOverlayFisherExactTest_parameters":{"properties":{"object_qnode_key":{"description":"A specific object query node id.","example":"n2","title":"object_qnode_key","type":"string"},"rel_edge_key":{"description":"A specific Qedge id connected to both subject nodes and object nodes in message KG (optional, otherwise all edges connected to both subject nodes and object nodes in message KG are considered).","example":"e01","title":"rel_edge_key","type":"string"},"subject_qnode_key":{"description":"A specific subject query node id.","example":"n1","title":"subject_qnode_key","type":"string"},"virtual_relation_label":{"description":"An label to help identify the virtual edge.","example":"f1","title":"virtual_relation_label","type":"string"}},"required":["object_qnode_key","subject_qnode_key","virtual_relation_label"],"title":"OperationOverlayFisherExactTest_parameters","type":"object"},"OperationRestate":{"additionalProperties":false,"description":"This operation modifies the query graph.","properties":{"id":{"enum":["restate"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationScore":{"additionalProperties":false,"description":"This operation adds scores to results.","properties":{"id":{"enum":["score"],"type":"string"},"parameters":{},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. 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A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id"],"type":"object"},"OperationSortResultsEdgeAttribute":{"additionalProperties":false,"description":"This operation sorts the results by the given edge attribute. If in ascending order, the minimum value of the results edges with the given attribute will be taken while the maximum will be taken for descending order. If a result has no edges with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value.","properties":{"id":{"enum":["sort_results_edge_attribute"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationSortResultsEdgeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationSortResultsEdgeAttribute_parameters":{"properties":{"ascending_or_descending":{"description":"Indicates whether results should be sorted in ascending or descending order.","enum":["ascending","descending"],"title":"ascending_or_descending","type":"string"},"edge_attribute":{"description":"The name of the edge attribute to order by.","example":"normalized_google_distance","title":"edge_attribute","type":"string"},"qedge_keys":{"description":"This indicates if you only want to consider edges with specific edge_keys. If not provided or empty, all edges will be looked at.","example":["e01"],"items":{"type":"string"},"title":"qedge_keys","type":"array"}},"required":["ascending_or_descending","edge_attribute"],"title":"OperationSortResultsEdgeAttribute_parameters","type":"object"},"OperationSortResultsNodeAttribute":{"additionalProperties":false,"description":"This operation sorts the results by the given node attribute. If in ascending order, the minimum value of the results nodes with the given attribute will be taken while the maximum will be taken for descending order. If a result has no nodes with the given attribute, it will be listed last. If `max_results` is given, it truncates the results to at most the given value.","properties":{"id":{"enum":["sort_results_node_attribute"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationSortResultsNodeAttribute_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationSortResultsNodeAttribute_parameters":{"properties":{"ascending_or_descending":{"description":"Indicates whether results should be sorted in ascending or descending order.","enum":["ascending","descending"],"title":"ascending_or_descending","type":"string"},"node_attribute":{"description":"The name of the node attribute to order by.","example":"normalized_google_distance","title":"node_attribute","type":"string"},"qnode_keys":{"description":"This indicates if you only want to consider nodes with specific node_keys. If not provided or empty, all nodes will be looked at.","example":["e01"],"items":{"type":"string"},"title":"qnode_keys","type":"array"}},"required":["ascending_or_descending","node_attribute"],"title":"OperationSortResultsNodeAttribute_parameters","type":"object"},"OperationSortResultsScore":{"additionalProperties":false,"description":"This operation sorts the results by the result score. If `max_results` is given, it truncates the results to at most the given value.","properties":{"id":{"enum":["sort_results_score"],"type":"string"},"parameters":{"$ref":"#/components/schemas/OperationSortResultsScore_parameters"},"runner_parameters":{"oneOf":[{"properties":{"allowlist":{"description":"List of operation providers (by infores ID) that may be used to complete operation. No others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the workflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}},{"properties":{"denylist":{"description":"List of operation providers (by infores ID) that may not be used to complete operation. All others will be used. A full list of operation providers for each operation with infores ID's is available through the '/services' endpoint of the worflow runner.","example":["infores:aragorn"],"items":{"type":"string"},"minLength":1,"type":"array"}}}],"type":"object"},"unique":{"default":true,"type":"boolean"}},"required":["id","parameters"],"type":"object"},"OperationSortResultsScore_parameters":{"properties":{"ascending_or_descending":{"description":"Indicates whether results should be sorted in ascending or descending order.","enum":["ascending","descending"],"title":"ascending_or_descending","type":"string"}},"required":["ascending_or_descending"],"title":"OperationSortResultsScore_parameters","type":"object"},"Operations":{"additionalProperties":true,"description":"Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned","nullable":true,"properties":{"actions":{"description":"List of order-dependent operations to execute","example":["add_qnode(name=acetaminophen, key=n00)","add_qnode(category=biolink:Protein, key=n01)","add_qedge(subject=n01, object=n00, key=e00)","expand(edge_key=e00)","resultify()","filter_results(action=limit_number_of_results, max_results=10)"],"items":{"type":"string"},"type":"array"},"message_uris":{"description":"List of URIs for Message or Response objects to fetch and process","example":["https://arax.ncats.io/api/arax/v1.3/response/38"],"items":{"type":"string"},"type":"array"},"messages":{"description":"List of Message objects to process","items":{"$ref":"#/components/schemas/Message"},"type":"array"},"options":{"additionalProperties":true,"description":"Map of order independent options that apply during processing","example":{"halt_on_warning":false},"type":"object"}},"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute contraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"exclude":{"description":"If set to true, then all subgraphs containing this edge are excluded from the final results. (optional)","type":"boolean"},"knowledge_type":{"description":"Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future.","example":"lookup","nullable":true,"type":"string"},"object":{"description":"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.","example":"https://www.uniprot.org/uniprot/P00738","type":"string"},"option_group_id":{"description":"Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ","nullable":true,"type":"string"},"predicates":{"description":"These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided.","items":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"qualifier_constraints":{"default":[],"description":"A list of QualifierConstraints that provide nuance to the QEdge. If multiple QualifierConstraints are provided, there is an OR relationship between them. If the QEdge has multiple predicates or if the QNodes that correspond to the subject or object of this QEdge have multiple categories or multiple curies, then qualifier_constraints MUST NOT be specified because these complex use cases are not supported at this time.","items":{"$ref":"#/components/schemas/QualifierConstraint"},"type":"array"},"subject":{"description":"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.","example":"https://omim.org/entry/603903","type":"string"}},"required":["object","subject"],"title":"QEdge","type":"object"},"QNode":{"additionalProperties":true,"description":"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.","properties":{"categories":{"description":"These should be Biolink Model categories and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' categories should be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"CURIE identifier for this node","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"is_set":{"default":false,"description":"Set to true if this QNode is a set (deprecated)","type":"boolean"},"option_group_id":{"description":"Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ","nullable":true,"type":"string"},"set_id":{"description":"A client-provided identifier for the set described in this QNode","nullable":true,"type":"string"},"set_interpretation":{"description":"Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH.","enum":["BATCH","ALL","MANY"],"nullable":true,"type":"string"}},"title":"QNode","type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"qualifier_value":{"description":"The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge.","example":"expression","nullable":false,"title":"qualifier_value","type":"string"}},"required":["qualifier_type_id","qualifier_value"],"title":"Qualifier","type":"object"},"QualifierConstraint":{"additionalProperties":false,"description":"Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. For example, it can constrain a \"ChemicalX - affects - ?Gene\" query to return only edges where ChemicalX specifically affects the 'expression' of the Gene, by constraining on the qualifier_type \"biolink:object_aspect_qualifier\" with a qualifier_value of \"expression\".","properties":{"qualifier_set":{"description":"A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"title":"qualifier_set","type":"array"}},"required":["qualifier_set"],"title":"QualifierConstraint","type":"object"},"Query":{"additionalProperties":true,"description":"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.","example":{"bypass_cache":false,"enforce_edge_directionality":false,"log_level":"","max_results":100,"message":{"query_graph":{"edges":{"e00":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"operations":"","page_number":1,"page_size":100,"return_minimal_metadata":false,"stream_progress":false,"submitter":"submitter","workflow":["",""]},"properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"enforce_edge_directionality":{"default":false,"description":"Set to true in order to enforce edge directionality during queries. By default, edge directionality can be reversed without penalty.","type":"boolean"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"max_results":{"default":100,"description":"Maximum number of individual results to return","example":100,"type":"integer"},"message":{"nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"operations":{"description":"Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned","nullable":true,"oneOf":[{"$ref":"#/components/schemas/Operations"}]},"page_number":{"default":1,"description":"Page number of results when the number of results exceeds the page_size, with page 1 as the first page","example":1,"type":"integer"},"page_size":{"default":100,"description":"Split the results into pages with this number of results each","example":100,"type":"integer"},"return_minimal_metadata":{"default":false,"description":"Set to true in order to return only the most minimal metadata. By default, rich metadata for nodes and edges are supplied, which may cause a very large and slower Response.","type":"boolean"},"stream_progress":{"default":false,"description":"Set to true in order to receive a stream of LogEntry objects as the query is progressing","type":"boolean"},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","items":{"oneOf":[{"$ref":"#/components/schemas/OperationAnnotate"},{"$ref":"#/components/schemas/OperationAnnotateEdges"},{"$ref":"#/components/schemas/OperationAnnotateNodes"},{"$ref":"#/components/schemas/OperationBind"},{"$ref":"#/components/schemas/OperationCompleteResults"},{"$ref":"#/components/schemas/OperationEnrichResults"},{"$ref":"#/components/schemas/OperationFill"},{"$ref":"#/components/schemas/OperationFilterKgraph"},{"$ref":"#/components/schemas/OperationFilterKgraphContinuousKedgeAttribute"},{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKedgeAttribute"},{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKnodeAttribute"},{"$ref":"#/components/schemas/OperationFilterKgraphOrphans"},{"$ref":"#/components/schemas/OperationFilterKgraphPercentile"},{"$ref":"#/components/schemas/OperationFilterKgraphStdDev"},{"$ref":"#/components/schemas/OperationFilterKgraphTopN"},{"$ref":"#/components/schemas/OperationFilterResults"},{"$ref":"#/components/schemas/OperationFilterResultsTopN"},{"$ref":"#/components/schemas/OperationLookup"},{"$ref":"#/components/schemas/OperationOverlay"},{"$ref":"#/components/schemas/OperationOverlayComputeJaccard"},{"$ref":"#/components/schemas/OperationOverlayComputeNgd"},{"$ref":"#/components/schemas/OperationOverlayConnectKnodes"},{"$ref":"#/components/schemas/OperationOverlayFisherExactTest"},{"$ref":"#/components/schemas/OperationRestate"},{"$ref":"#/components/schemas/OperationScore"},{"$ref":"#/components/schemas/OperationSortResults"},{"$ref":"#/components/schemas/OperationSortResultsEdgeAttribute"},{"$ref":"#/components/schemas/OperationSortResultsNodeAttribute"},{"$ref":"#/components/schemas/OperationSortResultsScore"}]},"nullable":true,"type":"array"}},"required":["message"],"title":"Query","type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/QEdge"},"description":"The edge specifications. The keys of this map are unique edge identifiers and the corresponding values include the constraints on bound edges, in addition to specifying the subject and object QNodes.","type":"object"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/QNode"},"description":"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.","type":"object"}},"required":["edges","nodes"],"type":"object"},"Question":{"additionalProperties":true,"properties":{"language":{"description":"Human language in which the question is posed","enum":["English"],"example":"English","type":"string"},"text":{"description":"Free text question","example":"what genetic conditions offer protection against malaria","type":"string"}},"type":"object"},"ResourceRoleEnum":{"description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.  This enumeration is found in Biolink Model, but is repeated here for convenience.","enum":["primary_knowledge_source","aggregator_knowledge_source","supporting_data_source"],"title":"ResourceRoleEnum","type":"string"},"Response":{"additionalProperties":true,"description":"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.","example":{"biolink_version":"3.1.2","context":"https://rtx.ncats.io/ns/translator.jsonld","datetime":"2021-01-09T12:34:45","description":"Success. 42 results found.","id":"https://arax.ncats.io/api/rtx/v1.3/response/123","info":"info","job_id":"rXEOAosN3L","logs":[{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"},{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"}],"message":{"query_graph":{"edges":{"e00":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"operations":"","original_question":"what proteins are affected by sickle cell anemia","query_options":{"coalesce":true,"threshold":0.9},"resource_id":"ARAX","restated_question":"Which proteins are affected by sickle cell anemia?","schema_version":"1.4.0","status":"Success","submitter":"submitter","table_column_names":["chemical_substance.name","chemical_substance.id"],"tool_version":"ARAX 0.8.0","total_results_count":0,"type":"TranslatorAPIResponse","validation_result":"{}","workflow":["",""]},"properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","type":"string"},"context":{"description":"JSON-LD context URI","example":"https://rtx.ncats.io/ns/translator.jsonld","type":"string"},"datetime":{"description":"Datetime string for the time that this response was generated","example":"2021-01-09T12:34:45","type":"string"},"description":{"description":"A brief human-readable description of the outcome","example":"Success. 42 results found.","nullable":true,"type":"string"},"id":{"description":"URI for this response","example":"https://arax.ncats.io/api/rtx/v1.3/response/123","type":"string"},"info":{"description":"A placholder for including some additional information","nullable":true,"type":"string"},"job_id":{"description":"An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job.","example":"rXEOAosN3L","nullable":true,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first.","items":{"$ref":"#/components/schemas/LogEntry"},"nullable":true,"type":"array"},"message":{"nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"operations":{"description":"Container for one or more Message objects or identifiers for one or more Messages along with the processing plan and options for how those messages were processed and returned","oneOf":[{"$ref":"#/components/schemas/Operations"}]},"original_question":{"description":"The original question text typed in by the user","example":"what proteins are affected by sickle cell anemia","type":"string"},"query_options":{"description":"Dict of options that can be sent with the query. Options are tool specific and not stipulated here","example":{"coalesce":true,"threshold":0.9},"type":"object"},"resource_id":{"description":"Identifier string of the resource that provided this response (one of ARAX, Aragorn, etc.)","example":"ARAX","nullable":true,"type":"string"},"restated_question":{"description":"A precise restatement of the question, as understood by the Translator, for which the answer applies. The user should verify that the restated question matches the intent of their original question (it might not).","example":"Which proteins are affected by sickle cell anemia?","type":"string"},"schema_version":{"description":"Version label of this TRAPI schema","example":"1.4.0","type":"string"},"status":{"description":"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable","example":"Success","nullable":true,"type":"string"},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"table_column_names":{"description":"List of column names that corresponds to the row_data for each result","example":["chemical_substance.name","chemical_substance.id"],"items":{"type":"string"},"type":"array"},"tool_version":{"description":"Version label of the tool that generated this response","example":"ARAX 0.8.0","type":"string"},"total_results_count":{"description":"The total number of results that were generated prior to any filtering.","nullable":true,"type":"integer"},"type":{"description":"Entity type of this response","example":"TranslatorAPIResponse","type":"string"},"validation_result":{"description":"Validation results and other summary stats computed for this Response.","type":"object"},"workflow":{"description":"A list of operations that were executed.","items":{"oneOf":[{"$ref":"#/components/schemas/OperationAnnotate"},{"$ref":"#/components/schemas/OperationAnnotateEdges"},{"$ref":"#/components/schemas/OperationAnnotateNodes"},{"$ref":"#/components/schemas/OperationBind"},{"$ref":"#/components/schemas/OperationCompleteResults"},{"$ref":"#/components/schemas/OperationEnrichResults"},{"$ref":"#/components/schemas/OperationFill"},{"$ref":"#/components/schemas/OperationFilterKgraph"},{"$ref":"#/components/schemas/OperationFilterKgraphContinuousKedgeAttribute"},{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKedgeAttribute"},{"$ref":"#/components/schemas/OperationFilterKgraphDiscreteKnodeAttribute"},{"$ref":"#/components/schemas/OperationFilterKgraphOrphans"},{"$ref":"#/components/schemas/OperationFilterKgraphPercentile"},{"$ref":"#/components/schemas/OperationFilterKgraphStdDev"},{"$ref":"#/components/schemas/OperationFilterKgraphTopN"},{"$ref":"#/components/schemas/OperationFilterResults"},{"$ref":"#/components/schemas/OperationFilterResultsTopN"},{"$ref":"#/components/schemas/OperationLookup"},{"$ref":"#/components/schemas/OperationLookupAndScore"},{"$ref":"#/components/schemas/OperationOverlay"},{"$ref":"#/components/schemas/OperationOverlayComputeJaccard"},{"$ref":"#/components/schemas/OperationOverlayComputeNgd"},{"$ref":"#/components/schemas/OperationOverlayConnectKnodes"},{"$ref":"#/components/schemas/OperationOverlayFisherExactTest"},{"$ref":"#/components/schemas/OperationRestate"},{"$ref":"#/components/schemas/OperationScore"},{"$ref":"#/components/schemas/OperationSortResults"},{"$ref":"#/components/schemas/OperationSortResultsEdgeAttribute"},{"$ref":"#/components/schemas/OperationSortResultsNodeAttribute"},{"$ref":"#/components/schemas/OperationSortResultsScore"}]},"type":"array"}},"required":["message"],"title":"Response","type":"object"},"Result":{"additionalProperties":true,"description":"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings).","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"type":"array"},"confidence":{"description":"Confidence metric for this result, a value between (inclusive)\n 0.0 (no confidence) and 1.0 (highest confidence)","example":0.9234,"format":"float","nullable":true,"type":"number"},"description":{"description":"A free text description of this result answer from the reasoner","example":"The genetic condition sickle cell anemia may provide protection from cerebral malaria via genetic alterations of proteins HBB (P68871) and HMOX1 (P09601).","nullable":true,"type":"string"},"essence":{"description":"A single string that is the terse essence of the result (useful for simple answers)","example":"ibuprofen","nullable":true,"type":"string"},"essence_category":{"description":"A Translator BioLink bioentity category of the essence","example":"biolink:ChemicalEntity","nullable":true,"type":"string"},"id":{"description":"URI for this result","example":"result:234","nullable":true,"type":"string"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"type":"array"},"description":"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.","type":"object"},"resource_id":{"description":"Identifier string of the resource that provided this result (one of ARAX, Aragorn, etc.)","example":"ARAX","nullable":true,"type":"string"},"result_group":{"description":"An integer group number for results for use in cases where several results should be grouped together. Also useful to control sorting ascending.","example":1,"nullable":true,"type":"integer"},"result_group_similarity_score":{"description":"A score that denotes the similarity of this result to other members of the result_group","example":0.95,"format":"float","nullable":true,"type":"number"},"row_data":{"description":"An arbitrary list of values that captures the essence of the result that can be turned into a tabular result across all answers (each result is a row) for a user that wants simplified tabular output","example":["ibuprofen","CHEMBL:CHEMBL521"],"items":{"oneOf":[{"type":"string"},{"type":"number"}]},"nullable":true,"type":"array"},"score":{"description":"A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. Higher MUST be better.","example":163.233,"format":"float","nullable":true,"type":"number"},"score_direction":{"description":"Sorting indicator for the score: one of higher_is_better or lower_is_better","example":"lower_is_better","nullable":true,"type":"string"},"score_name":{"description":"Name for the score","example":"Jaccard distance","nullable":true,"type":"string"}},"required":["analyses","node_bindings"],"title":"Result","type":"object"},"RetrievalSource":{"additionalProperties":true,"description":"Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","properties":{"resource_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"resource_role":{"$ref":"#/components/schemas/ResourceRoleEnum"},"source_record_urls":{"description":"A URL linking to a specific web page or document provided by the  source, that contains a record of the knowledge expressed in the  Edge. If the knowledge is contained in more than one web page on  an Information Resource's site, urls MAY be provided for each.  For example, Therapeutic Targets Database (TTD) has separate web  pages for 'Imatinib' and its protein target KIT, both of which hold  the claim that 'the KIT protein is a therapeutic target for Imatinib'.         ","example":"[https://db.idrblab.net/ttd/data/drug/details/d0az3c,  https://db.idrblab.net/ttd/data/target/details/t57700]","items":{"type":"string"},"type":"array"},"upstream_resource_ids":{"description":"An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.","example":["infores:automat-mychem-info","infores:molepro"],"items":{"$ref":"#/components/schemas/CURIE"},"type":"array"}},"required":["resource_id","resource_role"],"title":"RetrievalSource","type":"object"}}},"externalDocs":{"description":"Documentation for the NCATS Biomedical Translator Reasoners web services","url":"https://github.com/NCATSTranslator/ReasonerAPI"},"info":{"contact":{"email":"edeutsch@systemsbiology.org"},"description":"TRAPI 1.6 endpoint for the NCATS Biomedical Translator Reasoner called ARAX","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://github.com/RTXteam/RTX/blob/master/LICENSE","title":"ARAX Translator Reasoner - TRAPI 1.6.0","version":"1.6.2","x-translator":{"biolink-version":"4.2.5","component":"ARA","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/production/x-translator/"},"infores":"infores:arax","team":["Expander Agent"]},"x-trapi":{"asyncquery":true,"externalDocs":{"description":"The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/production/x-trapi/"},"multicuriequery":false,"operations":["lookup","lookup_and_score","overlay_compute_ngd","overlay_compute_jaccard","overlay_fisher_exact_test","overlay_connect_knodes","filter_results_top_n","bind","fill","filter_kgraph_orphans","filter_kgraph_top_n","filter_kgraph_std_dev","filter_kgraph_percentile","filter_kgraph_discrete_kedge_attribute","filter_kgraph_continuous_kedge_attribute","sort_results_score","sort_results_edge_attribute","sort_results_node_attribute","annotate_nodes","score","complete_results"],"pathfinderquery":true,"version":"1.6.0"}},"openapi":"3.0.1","paths":{"/PubmedMeshNgd/{term1}/{term2}":{"get":{"operationId":"pubmed_mesh_ngd","parameters":[{"description":"First of two terms. Order not important.","example":"PTGS2","explode":false,"in":"path","name":"term1","required":true,"schema":{"type":"string"},"style":"simple"},{"description":"Second of two terms. Order not important.","example":"acetaminophen","explode":false,"in":"path","name":"term2","required":true,"schema":{"type":"string"},"style":"simple"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MeshNgdResponse"}}},"description":"successful operation"},"400":{"description":"Invalid terms"}},"summary":"Query to get the Normalized Google Distance between two MeSH terms based on co-occurrence in all PubMed article annotations","tags":["PubmedMeshNgd"],"x-openapi-router-controller":"openapi_server.controllers.pubmed_mesh_ngd_controller"}},"/asyncquery":{"post":{"operationId":"asyncquery","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing and the Response will be sent to the callback url when complete."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"],"x-openapi-router-controller":"openapi_server.controllers.asyncquery_controller"}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","example":800000,"explode":false,"in":"path","name":"job_id","required":true,"schema":{"type":"string"},"style":"simple"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"],"x-openapi-router-controller":"openapi_server.controllers.asyncquery_status_controller"}},"/entity":{"get":{"operationId":"get_entity","parameters":[{"description":"A string to search by (name, abbreviation, CURIE, etc.). The parameter may be repeated for multiple search strings.","explode":true,"in":"query","name":"q","required":true,"schema":{"example":["MESH:D014867","NCIT:C34373"],"items":{"type":"string"},"type":"array"},"style":"form"}],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"successful operation"},"404":{"description":"Entity not found"}},"summary":"Obtain CURIE and synonym information about a search term","tags":["entity"],"x-openapi-router-controller":"openapi_server.controllers.entity_controller"},"post":{"operationId":"post_entity","requestBody":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"List of terms to get information about","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/EntityQuery"}}},"description":"successful operation"},"404":{"description":"Entity not found"}},"summary":"Obtain CURIE and synonym information about search terms","tags":["entity"],"x-openapi-router-controller":"openapi_server.controllers.entity_controller"}},"/exampleQuestions":{"get":{"operationId":"example_questions","responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"object"},"type":"array"}}},"description":"successful operation"}},"summary":"Request a list of example questions that ARAX can answer","tags":["exampleQuestions"],"x-openapi-router-controller":"openapi_server.controllers.example_questions_controller"}},"/meta_knowledge_graph":{"get":{"operationId":"meta_knowledge_graph","parameters":[{"description":"Provide meta_knowledge_graph information in a format other than the default. Default value is 'full'. Also permitted is 'simple'","explode":true,"in":"query","name":"format","required":false,"schema":{"type":"string"},"style":"form"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"],"x-openapi-router-controller":"openapi_server.controllers.meta_knowledge_graph_controller"}},"/query":{"post":{"operationId":"query","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"],"x-openapi-router-controller":"openapi_server.controllers.query_controller"}},"/response":{"post":{"operationId":"post_response","requestBody":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"Object that provides annotation information","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"successful operation"},"400":{"description":"Invalid request"}},"summary":"Annotate a response","tags":["response"],"x-openapi-router-controller":"openapi_server.controllers.response_controller"}},"/response/{response_id}":{"get":{"operationId":"get_response","parameters":[{"description":"Identifier of the response to return","example":41651,"explode":false,"in":"path","name":"response_id","required":true,"schema":{"type":"string"},"style":"simple"}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"successful operation"},"404":{"description":"response_id not found"}},"summary":"Request a previously stored response from the server","tags":["response"],"x-openapi-router-controller":"openapi_server.controllers.response_controller"}},"/status":{"get":{"operationId":"get_status","parameters":[{"description":"Limit results to the past N hours","explode":true,"in":"query","name":"last_n_hours","required":false,"schema":{"example":6,"type":"integer"},"style":"form"},{"description":"Identifier of the log entry","explode":true,"in":"query","name":"id","required":false,"schema":{"example":10,"type":"integer"},"style":"form"},{"description":"PID of an ongoing query to terminate","explode":true,"in":"query","name":"terminate_pid","required":false,"schema":{"type":"integer"},"style":"form"},{"description":"Authorization string required for certain calls to status","explode":true,"in":"query","name":"authorization","required":false,"schema":{"type":"string"},"style":"form"},{"description":"Switch to control the type of returned status information Possible values are: activity: Show query activity on server [default] smartapi: Summarize Translator endpoints at SmartAPI","explode":true,"in":"query","name":"mode","required":false,"schema":{"type":"string"},"style":"form"}],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"successful operation"},"404":{"description":"Entity not found"}},"summary":"Obtain status information about the endpoint","tags":["status"],"x-openapi-router-controller":"openapi_server.controllers.status_controller"}},"/status/logs":{"get":{"operationId":"get_logs","parameters":[{"description":"Specify the log sending mode","explode":true,"in":"query","name":"mode","required":false,"schema":{"example":"tail","type":"string"},"style":"form"}],"responses":{"200":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":"successful operation"},"404":{"description":"Logs not found"}},"summary":"Get log information from the server","tags":["status"],"x-openapi-router-controller":"openapi_server.controllers.status_controller"}},"/translate":{"post":{"operationId":"translate","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Question"}}},"description":"Question information to be translated","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Query"},"type":"array"}}},"description":"successful operation"},"400":{"description":"Invalid status value"}},"summary":"Translate natural language question into a standardized query","tags":["translate"],"x-openapi-router-controller":"openapi_server.controllers.translate_controller"}}},"servers":[{"description":"ARAX TRAPI 1.6 endpoint - 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ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","externalDocs":{"description":"Documentation for the reasoner predicates function","url":"https://arax.ncats.io/overview.html#predicates"},"name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","externalDocs":{"description":"Documentation for the reasoner query function","url":"https://arax.ncats.io/overview.html#query"},"name":"query"},{"description":"Initiate a query with a callback to receive the response","externalDocs":{"description":"Documentation for the reasoner asynchquery function","url":"https://arax.ncats.io/overview.html#asyncquery"},"name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"},{"description":"Request a previously stored response from the server","externalDocs":{"description":"Documentation for the reasoner response function","url":"https://arax.ncats.io/overview.html#response"},"name":"response"},{"description":"Translate natural language question into a standardized query","externalDocs":{"description":"Documentation for the reasoner translate function","url":"https://arax.ncats.io/overview.html#translate"},"name":"translate"},{"description":"Return identifier and type of some entity in the knowledge graph","externalDocs":{"description":"Documentation for the reasoner entity function","url":"https://arax.ncats.io/overview.html#entity"},"name":"entity"},{"description":"Return a list of example questions that the reasoner can answer","externalDocs":{"description":"Documentation for the reasoner exampleQuestions function","url":"https://arax.ncats.io/overview.html#exampleQuestions"},"name":"exampleQuestions"},{"description":"Query to get the Normalized Google Distance between two MeSH terms based on co-occurance in all PubMed article annotations","externalDocs":{"description":"Documentation for the reasoner PubmedMeshNgd function","url":"https://arax.ncats.io/overview.html#PubmedMeshNgd"},"name":"PubmedMeshNgd"},{"description":"Return status information about the endpoint","name":"status"}]},{"components":{"schemas":{"Analysis":{"additionalProperties":true,"description":"An analysis is a dictionary that contains information about the result tied to a particular service. Each Analysis is generated by a single reasoning service, and describes the outputs of analyses performed by the reasoner on a particular Result (e.g. a result score), along with provenance information supporting the analysis (e.g. method or data that supported generation of the score).","properties":{"attributes":{"description":"The attributes of this particular Analysis.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edge_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/EdgeBinding"},"type":"array"},"description":"The dictionary of input Query Graph to Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple Knowledge Graph Edges.","type":"object"},"resource_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"score":{"description":"A numerical score associated with this result indicating the relevance or confidence of this result relative to others in the returned set. 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Each item in the list is the key of a single Auxiliary Graph.","items":{"type":"string"},"nullable":true,"type":"array"}},"required":["edge_bindings","resource_id"],"title":"Analysis","type":"object"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"callback":{"description":"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.","format":"uri","pattern":"^https?://","type":"string"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","items":{"oneOf":[{"$ref":"#/components/schemas/OperationLookup"}]},"type":"array"}},"required":["callback","message"],"type":"object","x-body-name":"request_body"},"AsyncQueryResponse":{"additionalProperties":true,"description":"The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query.","example":{"description":"Async_query has been queued","job_id":"rXEOAosN3L","status":"Accepted"},"properties":{"description":{"description":"A brief human-readable description of the result of the async_query submission.","example":"Async_query has been queued","nullable":true,"type":"string"},"job_id":{"description":"An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job.","example":"rXEOAosN3L","nullable":false,"type":"string"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"title":"AsyncQueryResponse","type":"object"},"AsyncQueryStatusResponse":{"additionalProperties":true,"description":"The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query.","example":{"description":"Callback URL returned 500","logs":[{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"},{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"}],"response_url":"https://arax.ncats.io/api/arax/v1.3/response/116481","status":"Running"},"properties":{"description":{"description":"A brief human-readable description of the current state or summary of the problem if the status is Failed.","example":"Callback URL returned 500","nullable":false,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. The most recent entry should be last. Its timestamp will be compared against the current time to see if there is still activity.","items":{"$ref":"#/components/schemas/LogEntry"},"nullable":false,"type":"array"},"response_url":{"description":"Optional URL that can be queried to restrieve the full TRAPI Response.","example":"https://arax.ncats.io/api/arax/v1.3/response/116481","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes: Queued, Running, Completed, Failed","example":"Running","nullable":false,"type":"string"}},"required":["description","logs","status"],"title":"AsyncQueryStatusResponse","type":"object"},"Attribute":{"additionalProperties":false,"description":"Generic attribute for a node or an edge that expands the key-value pair concept by including fields for additional metadata. These fields can be used to describe the source of the statement made in a key-value pair of the attribute object, or describe the attribute's value itself including its semantic type, or a url providing additional information about it. An attribute may be further qualified with sub-attributes (for example to provide confidence intervals on a value).","properties":{"attribute_source":{"description":"The source of the core assertion made by the key-value pair of an attribute object. Use a CURIE or namespace designator for this resource where possible.","example":"UniProtKB","nullable":true,"title":"attribute_source","type":"string"},"attribute_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. 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This may be a column name in a source tsv file, or a key in a source json document for the field in the data that held the attribute's value. Capturing this information  where possible lets us preserve what the original source said. Note that the data type is string' but the contents of the field could also be a CURIE of a third party ontology term.","example":"p-value","nullable":true,"title":"original_attribute_name","type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153,"title":"value"},"value_type_id":{"description":"CURIE describing the semantic type of an  attribute's value. Use a Biolink class if possible, otherwise a term from an external ontology. 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If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_0844","oneOf":[{"$ref":"#/components/schemas/CURIE"}],"title":"id"},"name":{"description":"Human-readable name or label for the constraint concept. If appropriate, it SHOULD be the term name of the CURIE used as the 'id'. This is redundant but required for human readability.","example":"molecular mass","title":"name","type":"string"},"not":{"default":false,"title":"not","type":"boolean"},"operator":{"description":"Relationship between the database value and the constraint value for the specified id. The operators ==, >, and < mean is equal to, is greater than, and is less than, respectively. The 'matches' operator indicates that the value is a regular expression to be evaluated. If value is a list type, then at least one evaluation must be true (equivalent to OR). This means that the == operator with a list acts like a SQL 'IN' clause. If the value of the compared attribute is a list, then comparisons are performed between each of the constraint values and each of the attribute values, and any one true evaluation counts as an overall true (e.g., [1,2,3] == [6,7,2] is true). The == operator is therefore a broad interpretation of inclusion. The '===' operator requires that the constraint value and the attribute value be the same data type, length, content, and order (e.g. only [1,2,3] === [1,2,3]). The 'not' property negates the operator such that not and == means 'not equal to' (or 'not in' for a list), and not > means <=, and not < means >=, not matches means does not match, and not === means the match between the constraint and attribute values are not exact. The '==' operator SHOULD NOT be used in a manner that describes an \"is a\" subclass relationship for the parent QNode.","enum":["==",">","<","matches","==="],"title":"operator","type":"string"},"unit_id":{"description":"CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) should be used if possible. The unit_id MUST be provided for (lists of) numerical values that correspond to a quantity that has units.","example":"UO:0000222","nullable":true,"title":"unit_id"},"unit_name":{"description":"Term name that is associated with the CURIE of the units of the value or list of values in the 'value' property. The Units of Measurement Ontology (UO) SHOULD be used if possible. This property SHOULD be provided if a unit_id is provided. This is redundant but recommended for human readability.","example":"kilodalton","nullable":true,"title":"unit_name"},"value":{"description":"Value of the attribute. May be any data type, including a list. If the value is a list and there are multiple items, at least one comparison must be true (equivalent to OR) unless the '===' operator is used. If 'value' is of data type 'object', the keys of the object MAY be treated as a list. A 'list' data type paired with the '>' or '<' operators will encode extraneous comparisons, but this is permitted as it is in SQL and other languages.","example":57.0,"title":"value"}},"required":["id","name","operator","value"],"title":"AttributeConstraint","type":"object"},"AuxiliaryGraph":{"additionalProperties":true,"description":"A single AuxiliaryGraph instance that is used by Knowledge Graph Edges and Result Analyses. Edges comprising an Auxiliary Graph are a subset of the Knowledge Graph in the message. Data creators can create an AuxiliaryGraph to assemble a specific collections of edges from the Knowledge Graph into a named graph that can be referenced from an Edge as evidence/explanation supporting that Edge, or from a Result Analysis as information used to generate a score.","properties":{"attributes":{"description":"Attributes of the Auxiliary Graph","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edges":{"description":"List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge","items":{"type":"string"},"minItems":1,"nullable":false,"type":"array"}},"required":["edges"],"type":"object"},"BiolinkEntity":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"},"BiolinkPredicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","title":"BiolinkPredicate","type":"string"},"CURIE":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"Edge":{"additionalProperties":false,"description":"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \"thought\" graph resulting from a query upon the underlying knowledge source.","properties":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"title":"attributes","type":"array"},"object":{"description":"Corresponds to the map key CURIE of the object concept node of this relationship edge.","example":"UniProtKB:P00738","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}],"title":"object"},"predicate":{"description":"The type of relationship between the subject and object for the statement expressed in an Edge. These should be Biolink Model predicate terms and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' predicate terms should also be avoided.","example":"biolink:gene_associated_with_condition","nullable":false,"oneOf":[{"$ref":"#/components/schemas/BiolinkPredicate"}],"title":"predicate"},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":true,"title":"qualifiers","type":"array"},"sources":{"description":"A list of RetrievalSource objects that provide information about how a particular Information Resource served as a source from which the knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","items":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"title":"sources","type":"array"},"subject":{"description":"Corresponds to the map key CURIE of the subject concept node of this relationship edge.","example":"MONDO:0011382","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}],"title":"subject"}},"required":["object","predicate","sources","subject"],"title":"Edge","type":"object"},"EdgeBinding":{"additionalProperties":true,"description":"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized). Edge bindings are captured within a specific reasoner's Analysis object because the Edges in the Knowledge Graph that get bound to the input Query Graph may differ between reasoners.","properties":{"attributes":{"description":"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","type":"string"}},"required":["id"],"title":"EdgeBinding","type":"object"},"EntityQuery":{"example":{"format":"format","terms":["terms","terms"]},"properties":{"format":{"description":"Format of the response (full or compact)","title":"format","type":"string"},"terms":{"description":"List of term strings to search for","items":{"type":"string"},"title":"terms","type":"array"}},"title":"EntityQuery","type":"object"},"KnowledgeGraph":{"additionalProperties":true,"description":"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.","properties":{"edges":{"additionalProperties":{"$ref":"#/components/schemas/Edge"},"description":"Dictionary of Edge instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/Node"},"description":"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"}},"required":["edges","nodes"],"type":"object","x-nullable":true},"LogEntry":{"additionalProperties":true,"description":"The LogEntry object contains information useful for tracing and debugging across Translator components.  Although an individual component (for example, an ARA or KP) may have its own logging and debugging infrastructure, this internal information is not, in general, available to other components. In addition to a timestamp and logging level, LogEntry includes a string intended to be read by a human, along with one of a standardized set of codes describing the condition of the component sending the message.","example":{"code":"code","level":"","message":"message","timestamp":"2020-09-03T18:13:49+00:00"},"properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":false,"type":"string"},"timestamp":{"description":"Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00).","example":"2020-09-03T18:13:49+00:00","format":"date-time","nullable":false,"type":"string"}},"required":["message","timestamp"],"title":"LogEntry","type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"example":"DEBUG","type":"string","x-nullable":true},"Message":{"additionalProperties":false,"description":"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.","example":{"query_graph":{"edges":{"e00":{"object":"n01","predicates":["biolink:physically_interacts_with"],"subject":"n00"}},"nodes":{"n00":{"ids":["CHEMBL.COMPOUND:CHEMBL112"]},"n01":{"categories":["biolink:Protein"]}}}},"properties":{"auxiliary_graphs":{"additionalProperties":{"$ref":"#/components/schemas/AuxiliaryGraph"},"description":"Dictionary of AuxiliaryGraph instances that are used by Knowledge Graph Edges and Result Analyses. These are referenced elsewhere by the dictionary key.","type":"object"},"knowledge_graph":{"description":"KnowledgeGraph object that contains lists of nodes and edges in the thought graph corresponding to the message","nullable":true,"oneOf":[{"$ref":"#/components/schemas/KnowledgeGraph"}]},"query_graph":{"description":"QueryGraph object that contains a serialization of a query in the form of a graph","nullable":true,"oneOf":[{"$ref":"#/components/schemas/QueryGraph"}]},"results":{"description":"List of all returned Result objects for the query posed. The list SHOULD NOT be assumed to be ordered. The 'score' property,\nif present, MAY be used to infer result rankings. If Results are\nnot expected (such as for a query Message), this property SHOULD\nbe null or absent. If Results are expected (such as for a response\nMessage) and no Results are available, this property SHOULD be an\narray with 0 Results in it.","items":{"$ref":"#/components/schemas/Result"},"nullable":true,"type":"array"}},"title":"Message","type":"object"},"MetaAttribute":{"example":{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"title":"attribute_source","type":"string"},"attribute_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"title":"constraint_name","type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","title":"constraint_use","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"title":"original_attribute_names","type":"array"}},"required":["attribute_type_id"],"title":"MetaAttribute","type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","example":{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","qualifiers":[{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"}],"subject":"biolink:PhenotypicFeature"},"properties":{"association":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"title":"attributes","type":"array"},"knowledge_types":{"description":"A list of knowledge_types that are supported by the service. If the knowledge_types is null, this means that only 'lookup' is supported. Currently allowed values are 'lookup' or 'inferred'.","items":{"type":"string"},"minItems":1,"nullable":true,"title":"knowledge_types","type":"array"},"object":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"},"predicate":{"description":"CURIE for a Biolink 'predicate' slot, taken from the Biolink slot ('is_a') hierarchy rooted in biolink:related_to (snake_case). This predicate defines the Biolink relationship between the subject and object nodes of a biolink:Association defining a knowledge graph edge.","example":"biolink:interacts_with","externalDocs":{"description":"Biolink model predicates","url":"https://biolink.github.io/biolink-model/docs/related_to.html"},"pattern":"^biolink:[a-z][a-z_]*$","title":"BiolinkPredicate","type":"string"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"title":"qualifiers","type":"array"},"subject":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","title":"BiolinkEntity","type":"string"}},"required":["object","predicate","subject"],"title":"MetaEdge","type":"object"},"MetaKnowledgeGraph":{"description":"Knowledge-map representation of this TRAPI web service. The meta knowledge graph is composed of the union of most specific categories and predicates for each node and edge.","example":{"edges":[{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","qualifiers":[{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"}],"subject":"biolink:PhenotypicFeature"},{"association":"biolink:PhenotypicFeature","attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"knowledge_types":["knowledge_types","knowledge_types"],"object":"biolink:PhenotypicFeature","predicate":"biolink:interacts_with","qualifiers":[{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"}],"subject":"biolink:PhenotypicFeature"}],"nodes":{"key":{"attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"id_prefixes":["CHEMBL.COMPOUND","INCHIKEY"]}}},"properties":{"edges":{"description":"List of the most specific edges/predicates provided by this TRAPI web service. A predicate is only exposed here if there is an edge for which the predicate is the most specific available.","items":{"$ref":"#/components/schemas/MetaEdge"},"title":"edges","type":"array"},"nodes":{"additionalProperties":{"$ref":"#/components/schemas/MetaNode"},"description":"Collection of the most specific node categories provided by this TRAPI web service, indexed by Biolink class CURIEs. A node category is only exposed here if there is node for which that is the most specific category available.","title":"nodes","type":"object"}},"required":["edges","nodes"],"title":"MetaKnowledgeGraph","type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","example":{"attributes":[{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]},{"attribute_source":"infores:chembl","attribute_type_id":"attribute_type_id","constraint_name":"p-value","constraint_use":false,"original_attribute_names":["original_attribute_names","original_attribute_names"]}],"id_prefixes":["CHEMBL.COMPOUND","INCHIKEY"]},"properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"title":"attributes","type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"title":"id_prefixes","type":"array"}},"required":["id_prefixes"],"title":"MetaNode","type":"object"},"MetaQualifier":{"example":{"applicable_values":["[\"expression\",\"activity\",\"abundance\",\"degradation\"]","[\"expression\",\"activity\",\"abundance\",\"degradation\"]"],"qualifier_type_id":"qualifier_type_id"},"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":"[\"expression\",\"activity\",\"abundance\",\"degradation\"]","type":"string"},"title":"applicable_values","type":"array"},"qualifier_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"}},"required":["qualifier_type_id"],"title":"MetaQualifier","type":"object"},"Node":{"additionalProperties":false,"description":"A node in the KnowledgeGraph which represents some biomedical concept. Nodes are identified by the keys in the KnowledgeGraph Node mapping.","properties":{"attributes":{"description":"A list of attributes describing the node","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"title":"attributes","type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"nullable":true,"title":"categories","type":"array"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"title":"name","type":"string"}},"title":"Node","type":"object"},"NodeBinding":{"additionalProperties":true,"description":"An instance of NodeBinding is a single KnowledgeGraph Node mapping, identified by the corresponding 'id' object key identifier of the Node within the Knowledge Graph. Instances of NodeBinding may include extra annotation in the form of additional properties. (such annotation is not yet fully standardized). Each Node Binding must bind directly to node in the original Query Graph.","properties":{"attributes":{"description":"A list of attributes providing further information about the node binding. This is not intended for capturing node attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"query_id":{"description":"An optional property to provide the CURIE in the QueryGraph to which this binding applies. If the bound QNode does not have an an 'id' property or if it is empty, then this query_id MUST be null or absent. If the bound QNode has one or more CURIEs as an 'id' and this NodeBinding's 'id' refers to a QNode 'id' in a manner where the CURIEs are different (typically due to the NodeBinding.id being a descendant of a QNode.id), then this query_id MUST be provided. In other cases, there is no ambiguity, and this query_id SHOULD NOT be provided.","oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id"],"title":"NodeBinding","type":"object"},"OperationLookup":{"additionalProperties":false,"properties":{"id":{"enum":["lookup"],"type":"string"},"parameters":{}},"required":["id"],"type":"object"},"Operations":{"additionalProperties":true,"description":"Container for one or more Message objects or identifiers for one or more Messages along with a processing plan and options for how those messages should be processed and returned","nullable":true,"properties":{"actions":{"description":"List of order-dependent operations to execute","example":["add_qnode(name=acetaminophen, key=n00)","add_qnode(category=biolink:Protein, key=n01)","add_qedge(subject=n01, object=n00, key=e00)","expand(edge_key=e00)","resultify()","filter_results(action=limit_number_of_results, max_results=10)"],"items":{"type":"string"},"type":"array"},"message_uris":{"description":"List of URIs for Message or Response objects to fetch and process","example":["https://arax.ncats.io/api/arax/v1.3/response/38"],"items":{"type":"string"},"type":"array"},"messages":{"description":"List of Message objects to process","items":{"$ref":"#/components/schemas/Message"},"type":"array"},"options":{"additionalProperties":true,"description":"Map of order independent options that apply during processing","example":{"halt_on_warning":false},"type":"object"}},"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute contraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"exclude":{"description":"If set to true, then all subgraphs containing this edge are excluded from the final results. (optional)","type":"boolean"},"knowledge_type":{"description":"Indicates the type of knowledge that the client wants from the server between the subject and object. If the value is 'lookup', then the client wants direct lookup information from knowledge sources. If the value is 'inferred', then the client wants the server to get creative and connect the subject and object in more speculative and non-direct-lookup ways. If this property is absent or null, it MUST be assumed to mean 'lookup'. This feature is currently experimental and may be further extended in the future.","example":"lookup","nullable":true,"type":"string"},"object":{"description":"Corresponds to the map key identifier of the object concept node anchoring the query filter pattern for the query relationship edge.","example":"https://www.uniprot.org/uniprot/P00738","type":"string"},"option_group_id":{"description":"Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ","nullable":true,"type":"string"},"predicates":{"description":"These should be Biolink Model predicates and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' predicates should be avoided.","items":{"$ref":"#/components/schemas/BiolinkPredicate"},"minItems":1,"nullable":true,"type":"array"},"qualifier_constraints":{"default":[],"description":"A list of QualifierConstraints that provide nuance to the QEdge. If multiple QualifierConstraints are provided, there is an OR relationship between them. If the QEdge has multiple predicates or if the QNodes that correspond to the subject or object of this QEdge have multiple categories or multiple curies, then qualifier_constraints MUST NOT be specified because these complex use cases are not supported at this time.","items":{"$ref":"#/components/schemas/QualifierConstraint"},"type":"array"},"subject":{"description":"Corresponds to the map key identifier of the subject concept node anchoring the query filter pattern for the query relationship edge.","example":"https://omim.org/entry/603903","type":"string"}},"required":["object","subject"],"title":"QEdge","type":"object"},"QNode":{"additionalProperties":true,"description":"A node in the QueryGraph used to represent an entity in a query. If a CURIE is not specified, any nodes matching the category of the QNode will be returned in the Results.","properties":{"categories":{"description":"These should be Biolink Model categories and are allowed to be of type 'abstract' or 'mixin' (only in QGraphs!). Use of 'deprecated' categories should be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of contraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"CURIE identifier for this node","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"is_set":{"default":false,"description":"Boolean that if set to true, indicates that this QNode MAY have multiple KnowledgeGraph Nodes bound to it within each Result. The nodes in a set should be considered as a set of independent nodes, rather than a set of dependent nodes, i.e., the answer would still be valid if the nodes in the set were instead returned individually. Multiple QNodes may have is_set=True. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=False, each n1 must be connected to n2. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True, each n1 must be connected to at least one n2.","type":"boolean"},"option_group_id":{"description":"Optional string acting as a label on a set of nodes and/or edges indicating that they belong to a group that are to be evaluated as a group. ","nullable":true,"type":"string"},"set_id":{"description":"A client-provided identifier for the set described in this QNode","nullable":true,"type":"string"},"set_interpretation":{"description":"Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH.","enum":["BATCH","ALL","MANY"],"nullable":true,"type":"string"}},"title":"QNode","type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"qualifier_value":{"description":"The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge.","example":"expression","nullable":false,"title":"qualifier_value","type":"string"}},"required":["qualifier_type_id","qualifier_value"],"title":"Qualifier","type":"object"},"QualifierConstraint":{"additionalProperties":false,"description":"Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. 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Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"title":"CURIE","type":"string"},"resource_role":{"$ref":"#/components/schemas/ResourceRoleEnum"},"source_record_urls":{"description":"A URL linking to a specific web page or document provided by the  source, that contains a record of the knowledge expressed in the  Edge. If the knowledge is contained in more than one web page on  an Information Resource's site, urls MAY be provided for each.  For example, Therapeutic Targets Database (TTD) has separate web  pages for 'Imatinib' and its protein target KIT, both of which hold  the claim that 'the KIT protein is a therapeutic target for Imatinib'.         ","example":"[https://db.idrblab.net/ttd/data/drug/details/d0az3c,  https://db.idrblab.net/ttd/data/target/details/t57700]","items":{"type":"string"},"type":"array"},"upstream_resource_ids":{"description":"An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. 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The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. 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Metadata: Metadata on the OARD database, including dataset descriptions, number of concepts, etc. \n\n\n2. Vocabulary: Access to the OMOP (pseudo), HPO, MONDO vocabulary for concept name concept identifier, and concept code (e.g. HP:xxxx) mapping\n\n\n3. Clinical Frequencies: Access to the counts, frequencies, and co-occurrences of phenotypes and disease. Frequency was determined as the number of patients with the code(s) / total number of patients. \n\n\n4. Concept Associations: Inferred associations between concepts using chi-square analysis, ratio between observed to expected frequency, and relative frequency. If multiple concepts supplied. A weighted statistics will be generated based on the statistics selected.\n\n\nA [Python notebook](https://github.com/WengLab-InformaticsResearch/XXX) demonstrates simple examples of how to use the COHD API.\n\n\nOARD was developed based upon [COHD](https://cohd.smart-api.info/ui/70117385218edc9bc01633829011dfcf) at the [Columbia University Department of Biomedical Informatics](https://www.dbmi.columbia.edu/) as a collaboration between the [Weng Lab](http://people.dbmi.columbia.edu/~chw7007/), [Tatonetti Lab](http://tatonettilab.org/), and the [NCATS Biomedical Data Translator](https://ncats.nih.gov/translator) program (Red Team). This work was supported in part by grants: NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM10714, and NLM/NHGRI R01XXXXX.\n","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"title":"Open Real-world-based Annotation for Rare Disease (OARD)","version":"1.0.0"},"openapi":"3.0.1","paths":{"/metadata/datasets":{"get":{"description":"Returns a list of datasets, including dataset ID, clinical_site, name, and description, etc.","operationId":"datasets","responses":{"default":{"description":"An array of dataset descriptions."}},"summary":"Enumerates the datasets available in OARD","tags":["Metadata"]}},"/metadata/domainCounts":{"get":{"description":"Returns a list of domains and the number of concepts in each domain.","operationId":"domainCounts","parameters":[{"description":"The dataset_id of the dataset to query. 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