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This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"}},"type":"object"},"Dataset":{"properties":{"collections":{"description":"A list of collections that this dataset belongs to.","items":{"$ref":"#/components/schemas/Collection"},"readOnly":true,"type":"array"},"contacts":{"description":"A list of the people who are the main contacts to get information about the entity.","items":{"$ref":"#/components/schemas/Person"},"type":"array"},"contains_human_genetic_sequences":{"description":"True if the data contains any human genetic sequence information. Can only be set at CREATE/POST time","type":"boolean"},"contributors":{"description":"A list of people who contributed to the creation of this dataset. Returned as an array of contributor where the structure of a contributor is","items":{"$ref":"#/components/schemas/Person"},"readOnly":true,"type":"array"},"created_by_user_displayname":{"description":"The name of the person or process authenticated when creating the object","readOnly":true,"type":"string"},"created_by_user_email":{"description":"The email address of the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_by_user_sub":{"description":"The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_timestamp":{"description":"The timestamp of when the node was created.  The format is an integer representing milliseconds since midnight Jan 1, 1970","readOnly":true,"type":"integer"},"creation_action":{"description":"The associated action that represents the creation of that dataset","type":"string"},"creators":{"description":"A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication.","items":{"$ref":"#/components/schemas/Person"},"type":"array"},"data_access_level":{"description":"One of the values: public, consortium.","enum":["public","consortium"],"readOnly":true,"type":"string"},"dataset_type":{"description":"The data or assay type contained in this dataset.","enum":["Visium","seqFISH","RNAseq","ATACseq","10X Multiome","SNARE-seq2","CODEX","PhenoCycler","CyCIF","MERFISH","Cell Dive","Histology","MALDI","SIMS","DESI","MIBI","2D Imaging Mass Cytometry","LC-MS","nanoSPLITS","Auto-fluorescence","Light Sheet","Confocal","Thick section Multiphoton MxIF","Second Harmonic Generation (SHG)","Enhanced Stimulated Raman Spectroscopy (SRS)","Molecular Cartography","DARTfish","WGS","3D Imaging Mass Cytometry"],"type":"string"},"description":{"description":"Free text description of the dataset","type":"string"},"direct_ancestors":{"description":"A list of direct parent ancensters (one level above) that the Dataset was derived from.","items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"readOnly":true,"type":"array"},"doi_url":{"description":"The url from the doi registry for this entity. e.g. https://doi.org/10.35079/snt289.pcbm.487","readOnly":true,"type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group.  This property cannot be set via PUT (only on Create/POST).","type":"string"},"ingest_metadata":{"description":"The metadata returned from the ingest pipeline processing at data submission time. Provided as json.","type":"object"},"intended_dataset_type":{"description":"The dataset type of the intended datasets that will be uploaded as part of the Upload.","type":"string"},"intended_organ":{"description":"The organ code representing the organ type that the data contained in the upload will be registered/associated with.","type":"string"},"last_modified_timestamp":{"description":"The timestamp of when the object was last modified. 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If the direct ancestor is a Source, the sample must be of type organ.","type":"string","writeOnly":true},"doi_url":{"description":"The url from the doi registry for this entity. e.g. https://doi.org/10.35079/snt289.pcbm.487","readOnly":true,"type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).","type":"string"},"image_files":{"description":"List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array.","items":{"$ref":"#/components/schemas/File"},"readOnly":true,"type":"array"},"image_files_to_add":{"description":"List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {\"files\": [{\"temp_file_id\":\"dzevgd6xjs4d5grmcp4n\",\"description\":\"This is image file one\"},{\"temp_file_id\":\"yrahjadfhadf\",\"description\":\"This is image file two\"}]}","items":{"format":"temp_file_id","type":"string"},"type":"array","writeOnly":true},"image_files_to_remove":{"description":"List of image files previously uploaded to delete. 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Stored in db as a stringfied json array.","items":{"$ref":"#/components/schemas/File"},"readOnly":true,"type":"array"},"metadata_files_to_add":{"description":"List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {\"files\": [{\"temp_file_id\":\"dzevgd6xjs4d5grmcp4n\",\"description\":\"This is image file one\"},{\"temp_file_id\":\"yrahjadfhadf\",\"description\":\"This is image file two\"}]}","items":{"format":"temp_file_id","type":"string"},"type":"array"},"metadata_files_to_remove":{"description":"List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"format":"file_uuid","type":"string"},"type":"array"},"organ":{"description":"Organ code specifier, only set if sample_type == organ. Valid values found in: [organ types](https://ontology.api.hubmapconsortium.org/organs?application_context=sennet)","enum":["UBERON:0001013","UBERON:0000178","UBERON:0001474","UBERON:0002371","UBERON:0000955","UBERON:0000948","UBERON:0004538","UBERON:0004539","UBERON:0000059","UBERON:0002107","UBERON:0002168","UBERON:0002167","UBERON:0000029","UBERON:0001911","FMA:57991","FMA:57987","UBERON:0005090","UBERON:0010000","UBERON:0002119","UBERON:0002118","UBERON:0001264","UBERON:0001987","UBERON:0002097","UBERON:0002240","UBERON:0002106","UBERON:0002370","FMA:54974","FMA:54973","UBERON:0003126"],"type":"string"},"organ_other":{"description":"The organ type provided by the user if \"other\" organ type is selected","type":"string"},"registered_doi":{"description":"The doi of a the registered entity. e.g. 10.35079/snt289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets.","type":"string"},"rui_location":{"description":"The sample location and orientation in the ancestor organ as specified in the RUI tool. Returned as a json object.","type":"object"},"sample_category":{"description":"The category of the sample. Valid values found in: [sample categories](https://ontology.api.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C020076&child_sabs=SENNET)","enum":["Block","Organ","Section","Suspension"],"type":"string"},"sennet_id":{"description":"A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every entity.","readOnly":true,"type":"string"},"uuid":{"description":"The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"},"visit":{"description":"The visit id for the source/patient when the sample was obtained.","type":"string"}},"type":"object"},"Source":{"properties":{"contacts":{"description":"A list of the people who are the main contacts to get information about the entity.","items":{"$ref":"#/components/schemas/Person"},"type":"array"},"created_by_user_displayname":{"description":"The name of the person or process authenticated when creating the object","readOnly":true,"type":"string"},"created_by_user_email":{"description":"The email address of the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_by_user_sub":{"description":"The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_timestamp":{"description":"The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970","readOnly":true,"type":"integer"},"creators":{"description":"A list of the people who created the entity with full name, email, ORCID iD, institution, etc.. This is analogus to the author list on a publication.","items":{"$ref":"#/components/schemas/Person"},"type":"array"},"data_access_level":{"description":"One of the values: public, consortium","enum":["consortium","public"],"readOnly":true,"type":"string"},"description":{"description":"Free text description of the source","type":"string"},"doi_url":{"description":"The url from the doi registry for this entity. e.g. https://doi.org/10.35079/snt289.pcbm.487","readOnly":true,"type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source, Upload","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of.  This is required on Create/POST if the user creating the Source is a member of more than one write group.  This property cannot be set via PUT (only on Create/POST).","type":"string"},"image_files":{"description":"List of uploaded image files and descriptions of the files. Stored in db as a stringfied json array.","items":{"$ref":"#/components/schemas/File"},"readOnly":true,"type":"array"},"image_files_to_add":{"description":"List of temporary file ids with an optional description. Provide as a json array with an temp_file_id and description attribute for each element like {\"files\": [{\"temp_file_id\":\"dzevgd6xjs4d5grmcp4n\",\"description\":\"This is image file one\"},{\"temp_file_id\":\"yrahjadfhadf\",\"description\":\"This is image file two\"}]}","items":{"format":"temp_file_id","type":"string"},"type":"array","writeOnly":true},"image_files_to_remove":{"description":"List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"format":"file_uuid","type":"string"},"type":"array","writeOnly":true},"lab_source_id":{"description":"A lab specific identifier for the source.","type":"string"},"label":{"description":"Lab provided, de-identified name for the source","type":"string"},"last_modified_timestamp":{"description":"The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970","readOnly":true,"type":"integer"},"last_modified_user_displayname":{"description":"The name of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_email":{"description":"The email address of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_sub":{"description":"The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.","readOnly":true,"type":"string"},"registered_doi":{"description":"The doi of a the registered entity. e.g. 10.35079/snt289.pcbm.487. This is set during the publication process and currently available for certain Collections and Datasets.","type":"string"},"sennet_id":{"description":"A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every entity.","readOnly":true,"type":"string"},"source_type":{"description":"A high level description of where this source originates from. Valid values found in: [source types](https://ontology.api.hubmapconsortium.org/valueset?parent_sab=SENNET&parent_code=C050020&child_sabs=SENNET)","enum":["Human","Human Organoid","Mouse","Mouse Organoid"],"type":"string"},"uuid":{"description":"The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal uuid e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"}},"type":"object"},"SourceMetadata":{"properties":{"code":{"description":"This is a Code from a source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS source vocabulary terms.","type":"string"},"concept_id":{"description":"This is the Concept ID from the SenNet Knowledge Graph.  Currently limited to UMLS concepts.","type":"string"},"data_type":{"description":"This is the data type of thw record. Numeric types will generally have non-null data_value. Nominal types will generally have null data_value.","enum":["Nominal","Numeric"],"type":"string"},"data_value":{"description":"The data value of the record.","type":"string"},"end_datetime":{"description":"This is the approximate time difference in seconds between the procurement and the end of this event (this is to construct time series records of clinical data for event-level data not source-level data). An empty of zero value designates missing data or that this field is not applicable for the concept","type":"integer"},"graph_version":{"description":"This is the version of the SenNet Knowledge Graph that the Concept appears in, currently the version of UMLS that is used.","type":"string"},"grouping_code":{"description":"This is a Code from a source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS vocabulary codes. This code corresponds to the grouping_concept.","type":"string"},"grouping_concept":{"description":"This is the Concept ID from the SenNet Knowledge Graph, currently limited to UMLS concetps, that is to be used for grouping the record.","type":"string"},"grouping_concept_preferred_term":{"description":"This is the preferred display term for the facet in which this record should be counted for faceted search in the portal. It may or may not correspond to a term in UMLS for the grouping concept.","type":"string"},"grouping_sab":{"description":"This is a grouping for the source vocabulary in the SenNet Knowledge Graph, currently limited to UMLS source vocabularies.. This sab corresponds to the grouping_code.","type":"string"},"numeric_operator":{"description":"This is the numeric operator for the data value .This enables inputing thresholds and ranges for data values by using greater than or less than.","enum":["EQ","GT","LT"],"type":"string"},"preferred_term":{"description":"This is the preferred display term for the item. It may or may not correspond to a term in UMLS for this concept.","type":"string"},"sab":{"description":"This is the source vocabulary in the SenNet Knowledge Graph.  Currently limited to UMLS source vocabularies.","type":"string"},"start_datetime":{"description":"This is the approximate time difference in seconds between the procurement and the start of this event (this is to construct time series records of clinical data for event-level data not source-level data). An empty or zero value designates missing data or that this field is not applicable for the concept.","type":"integer"},"units":{"description":"This are the units for the data value.","type":"string"}},"type":"object"},"Upload":{"properties":{"created_by_user_displayname":{"description":"The name of the person or process authenticated when creating the object","readOnly":true,"type":"string"},"created_by_user_email":{"description":"The email address of the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_by_user_sub":{"description":"The subject id as provided by the authorization mechanism for the person or process authenticated when creating the object.","readOnly":true,"type":"string"},"created_timestamp":{"description":"The timestamp of when the node was created. The format is an integer representing milliseconds since midnight Jan 1, 1970","readOnly":true,"type":"integer"},"dataset_uuids_to_link":{"description":"List of datasets to add to the Upload. Provide as a json array of the dataset UUIDs like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"type":"string"},"type":"array","writeOnly":true},"dataset_uuids_to_unlink":{"description":"List of datasets to remove from a Upload. Provide as a json array of the dataset UUIDs like: [\"232934234234234234234270c0ea6c51d604a850558ef2247d0b4\", \"230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa\"]","items":{"type":"string"},"type":"array","writeOnly":true},"datasets":{"description":"The datasets that are contained in this Upload.","items":{"$ref":"#/components/schemas/Dataset"},"readOnly":true,"type":"array"},"description":{"description":"Free text description of the data being submitted.","type":"string"},"entity_type":{"description":"One of the normalized entity types: Dataset, Collection, Sample, Source, Upload","readOnly":true,"type":"string"},"group_name":{"description":"The displayname of globus group which the user who created this entity is a member of","readOnly":true,"type":"string"},"group_uuid":{"description":"The UUID of globus group which the user who created this entity is a member of. This is required on Create/POST if the user creating the Source is a member of more than one write group. This property cannot be set via PUT (only on Create/POST).","type":"string"},"last_modified_timestamp":{"description":"The timestamp of when the object was last modified. The format is an integer representing milliseconds since midnight, Jan 1, 1970","readOnly":true,"type":"integer"},"last_modified_user_displayname":{"description":"The name of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_email":{"description":"The email address of the person or process which authenticated when the object was last modified.","readOnly":true,"type":"string"},"last_modified_user_sub":{"description":"The subject id of the user who last modified the entity as provided by the authorization mechanism for the person or process authenticated when the object was modified.","readOnly":true,"type":"string"},"sennet_id":{"description":"A SenNet Consortium wide unique identifier randomly generated in the format SNT###.ABCD.### for every entity.","readOnly":true,"type":"string"},"status":{"description":"One of: New|Valid|Invalid|Error|Submitted","type":"string"},"title":{"description":"Title of the datasets, a sentance or less","type":"string"},"uuid":{"description":"The SenNet unique identifier, intended for internal software use only. This is a 32 digit hexadecimal UUID e.g. 461bbfdc353a2673e381f632510b0f17","readOnly":true,"type":"string"},"validation_message":{"description":"A message from the validataion tools describing what is invalid with the upload.","type":"string"}},"type":"object"}},"securitySchemes":{"BearerAuth":{"description":"Globus Bearer token to authorize requests","scheme":"bearer","type":"http"}}},"info":{"contact":{"email":"help@sennetconsortium.org","name":"SenNet Help Desk"},"description":"The SenNet Entity API is a standard RESTful web service with create, update and read operations for the standard SenNet provenance graph entities.","license":{"name":"MIT License","url":"https://github.com/sennetconsortium/entity-api/blob/main/license.txt"},"title":"SenNet Entity API","version":"1.10.6"},"openapi":"3.0.0","paths":{"/entities/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID (32 digit hexadecimal number)","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"The properties to not be included in the JSON response of the entity.","in":"query","name":"exclude","required":false,"schema":{"type":"string"}},{"description":"Specifies a single property to be returned from the entity JSON.","in":"query","name":"property","required":false,"schema":{"enum":["data_access_level","status"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}},"description":"The json of the **[Source](http://somewhere.org)**, **[Sample](http://somewhere.org)**, **[Dataset](http://somewhere.org)**, or **[Upload](http://somewhere.org)**"},"400":{"description":"Invalid or misformatted entity identifier was provided."},"401":{"description":"The user's bearer token has expired or the user did not supply a valid token."},"403":{"description":"The user is not authorized to retrieve the referenced entity."},"404":{"description":"The target entity could not be found."},"500":{"description":"An unexpected error occurred."}},"summary":"Retrieve a provenance entity by id. Entity types of Source, Sample, Dataset, and Upload.","tags":["entities"]},"put":{"parameters":[{"description":"The SenNet ID (e.g. SNT123.ABCD.456) or UUID of target entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}},"description":"The entity was successfully updated and is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Update the properties of a given Source, Sample, Dataset or Upload","tags":["entities"]}},"/entity-types":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"An array of entity types is returned"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to use this method"},"500":{"description":"Internal error"}},"summary":"Get a list of all the available entity types defined in the schema yaml","tags":["entities types"]}},"/ancestors/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the ancestor list for an Entity. The ancestors are the nodes connected \"upstream\" from the current node. This list traverses all the levels in the graph.","tags":["ancestors"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the ancestor list for an Entity. The ancestors are the nodes connected \"upstream\" from the current node. This list traverses all the levels in the graph.","tags":["ancestors"]}},"/descendants/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of descendants is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the descendant list for an Entity. The descendants are the nodes \"downstream\" from the current node.  This list traverses all the levels in the graph. Returns all descendants as an array of Entities.","tags":["descendants"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the descendant list for an Entity. The descendants are the nodes \"downstream\" from the current node.  This list traverses all the levels in the graph. Returns all descendants as an array of Entities.","tags":["descendants"]}},"/parents/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of parent entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the immediate parent list for an Entity. The parents are the nodes connected one level \"upstream\" from the current node.  This list only goes to the next higher level in the graph.","tags":["parents"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the immediate parent list for an Entity. The parents are the nodes connected one level \"upstream\" from the current node.  This list only goes to the next higher level in the graph.","tags":["parents"]}},"/children/{id}":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of children entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the list of children directly connected to an Entity. The children are the nodes one level below the current node. This list only returns the items one level below in the graph.","tags":["children"]},"post":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"filter_properties":{"description":"A list of properties to include or exclude","items":{"type":"string"},"type":"array"},"is_include":{"description":"Used to determine if the list provided is inclusion or exclusion","type":"boolean"}},"type":"object"}}},"description":"A json body with \"filter_properties\" (a list of properties to include or exclude) and \"is_include\" (a boolean value for if the list provided is inclusion or exclusion)."},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of ancestors is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the list of children directly connected to an Entity. The children are the nodes one level below the current node. This list only returns the items one level below in the graph.","tags":["children"]}},"/entities/{id}/siblings":{"get":{"parameters":[{"description":"The unique identifier of entity.  This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides true will have no effect. If the string is 'true', datasets that are have newer revisions will be included, otherwise by default they are not included.","in":"query","name":"include-old-revisions","required":false,"schema":{"enum":["true","false"],"type":"string"}},{"description":"A case insensitive string. Any value besides 'new', 'qa', and 'published' will raise an error. If a valid status is provided, only results matching that status (if they are datasets) will be returned","in":"query","name":"status","required":false,"schema":{"enum":["new","qa","published"],"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. If property_key=uuid is provided, rather than entire dictionary representations of each node, only the list of matching uuid's will be returned","in":"query","name":"property_key","required":false,"schema":{"enum":["uuid"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of sibling entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the siblings list for an Entity.  The siblings have the same direct ancestor.  This list does not include all nodes whom have common ancestors, only the direct ancestor.","tags":["entities"]}},"/entities/{id}/tuplets":{"get":{"parameters":[{"description":"The unique identifier of entity.  This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'new', 'qa', and 'published' will raise an error. If a valid status is provided, only results matching that status (if they are datasets) will be returned","in":"query","name":"status","required":false,"schema":{"enum":["new","qa","published"],"type":"string"}},{"description":"A case insensitive string. Any value besides 'uuid' will raise an error. If property_key=uuid is provided, rather than entire dictionary representations of each node, only the list of matching uuid's will be returned","in":"query","name":"property_key","required":false,"schema":{"enum":["uuid"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"}]},"type":"array"}}},"description":"An array of tuplet entities is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the tuplets list for an Entity.  The tuplets have the same parent activity node.","tags":["entities"]}},"/entities/{id}/provenance":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"Determines which node labels are allowed or not allowed to be returned in the provenance result. Formatting of filter follows the syntax of 'labelFilter' config param of the neo4j subgraph method. (e.g. -Publication|-Collection)","in":"query","name":"filter","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{}},"description":"Successful operation"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the provenance of the given entity."},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get Provenance Data for Entity. This returns a PROV JSON compliant representation of the entity's provenance. Refer to this document for more information regarding [PROV JSON format](https://www.w3.org/Submission/2013/SUBM-prov-json-20130424/)","tags":["entities"]}},"/entities/type/{type_a}/instanceof/{type_b}":{"get":{"parameters":[{"description":"The unique identifier of entity (e.g. Published)","in":"path","name":"type_a","required":true,"schema":{"type":"string"}},{"description":"The Entity Type Class as defined in entity-api-spec.yaml (e.g. Dataset)","in":"path","name":"type_b","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Instanceof"}}},"description":"An object with the attribute 'instanceof' that has a value of either 'true' of 'false'"},"400":{"description":"Invalid or misformatted entity identifie"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to retrieve the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Determines if the Entity type type_a is an instance of type_b","tags":["entities"]}},"/entities/{id}/ancestor-organs":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"$ref":"#/components/schemas/Sample"},"type":"array"}}},"description":"An array of Samples (sub-type organ) are returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to retrieve the entity"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve a list of ancestor organ(s) of a given UUID","tags":["entities"]}},"/entities/{entity_type}":{"post":{"parameters":[{"description":"One of the target entity types (case-insensitive since will be normalized): Source, Sample, Dataset, Upload","in":"path","name":"entity_type","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"oneOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]}}}},"responses":{"200":{"content":{"application/json":{"schema":{"items":{"anyOf":[{"$ref":"#/components/schemas/Source"},{"$ref":"#/components/schemas/Sample"},{"$ref":"#/components/schemas/Dataset"},{"$ref":"#/components/schemas/Upload"}]},"type":"array"}}},"description":"The entity was successfully created and is returned"},"400":{"description":"Invalid entity type provided"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to create the entity"},"500":{"description":"Internal error"}},"summary":"Create a new entity of the target type","tags":["entities"]}},"/entities/multiple-samples/{count}":{"post":{"parameters":[{"description":"The number of samples to be created","in":"path","name":"count","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"properties":{"sennet_id":{"type":"string"},"uuid":{"type":"string"}},"type":"object"},"type":"array"}}},"description":"The samples were successfully created. An array of objects each containing a UUID and SenNet ID associated with each newly created sample."},"400":{"description":"Invalid json input"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"500":{"description":"Internal error"}},"summary":"Create multiple samples from the same source entity. 'count' samples will be generated each with individual UUIDs and SenNet IDs.","tags":["entities"]}},"/doi/redirect/{id}":{"get":{"parameters":[{"description":"The SenNet ID (e.g. SNT123.ABCD.456) or UUID of the target collection","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"307":{"description":"Redirect to the entities landing page"},"400":{"description":"Invalid or misformatted collection identifier"},"500":{"description":"Internal error"}},"summary":"Redirect a request from a doi service","tags":["doi"]}},"/entities/{id}/globus-url":{"get":{"parameters":[{"description":"The ID (e.g. SNT123.ABCD.456) or UUID of the given entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"schema":{"format":"url","type":"string"}}},"description":"Returns the Globus service URL pointing to the Dataset or Upload data is returned"},"400":{"description":"Invalid or misformatted entity identifier"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the data"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the Globus URL to the given Dataset or Upload entity","tags":["entities"]}},"/entities/{id}/pipeline-message":{"get":{"parameters":[{"description":"The ID (e.g. SNT123.ABCD.456) or UUID of the given entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"schema":{"format":"text","type":"string"}}},"description":"Returns the pipeline message for the given Dataset"},"400":{"description":"Invalid or misformatted entity identifier or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the data"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the pipeline message for the given Dataset","tags":["entities"]}},"/entities/{id}/validation-message":{"get":{"parameters":[{"description":"The ID (e.g. SNT123.ABCD.456) or UUID of the given entity","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"schema":{"format":"text","type":"string"}}},"description":"Returns the validation message for the given Upload"},"400":{"description":"Invalid or misformatted entity identifier or the given entity is not an Upload"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to access the data"},"404":{"description":"The target entity could not be found"},"500":{"description":"Internal error"}},"summary":"Get the validation message for the given Upload","tags":["entities"]}},"/datasets/{id}/latest-revision":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Dataset"}}},"description":"Successful operation"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the latest revision of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve the latest (newest) revision of a given Dataset. Public/Consortium access rules apply - if no token/consortium access then must be for a public dataset and the returned Dataset must be the latest public version. If the given dataset itself is the latest revision, meaning it has no next revisions, this dataset gets returned.","tags":["datasets"]}},"/datasets/{id}/revision":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"The revision number (integer) on successful operation"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retrieve the calculated revision number of a Dataset. The calculated revision is number is based on the [:REVISION_OF] relationships to the oldest dataset in a revision chain. Where the oldest dataset = 1 and each newer version is incremented by one (1, 2, 3 ...). Public/Consortium access rules apply, if is for a non-public dataset and no token or a token without membership in SenNet-Read group is sent with the request then a 403 response should be returned.","tags":["datasets"]}},"/datasets/{id}/revisions":{"get":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides true will have no effect. If the string is 'true', the full dataset for each revision will be included in the response","in":"query","name":"include_dataset","required":false,"schema":{"enum":["true","false"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"dataset":{"$ref":"#/components/schemas/Dataset"},"revision_number":{"description":"The number in the revision chain of this dataset where 1 is the oldest revision","type":"integer"},"uuid":{"description":"The uuid of a dataset","type":"string"}},"type":"object"}}},"description":"The list of revised datasets that the referenced dataset is a member of including the index number of the revision, where 1 is the oldest version of any revision chain"},"400":{"description":"Invalid or misformatted entity identifier, or the given entity is not a Dataset"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the revision number of the given dataset."},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"From a given ID of a versioned dataset, retrieve a list of every dataset in the chain ordered from most recent to oldest. The revision number, as well as the dataset UUID will be included. An optional parameter ?include_dataset=true will include the full dataset for each revision as well. Public/Consortium access rules apply, if is for a non-public dataset and no token or a token without membership in SenNet-Read group is sent with the request then a 403 response should be returned. If the given id is published, but later revisions are not and the user is not in SenNet-Read group, only published revisions will be returned. The field next_revision_uuid will not be returned if the next revision is unpublished","tags":["datasets"]}},"/datasets/{id}/retract":{"put":{"parameters":[{"description":"The unique identifier of entity. This identifier can be either a SenNet ID (e.g. SNT123.ABCD.456) or UUID","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"retraction_reason":{"description":"Free text describing why the dataset was retracted","type":"string"}},"type":"object"}}},"description":"A json body with a single, required retraction_reason parameter contianing the reason why the dataset is being retracted."},"responses":{"200":{"description":"The complete dataset with modified sub_status and retraction_reason"},"400":{"description":"Invalid or misformatted entity identifier, the given entity is not a Dataset, is not published or the required retraction_reason was not included in a json body"},"401":{"description":"The user's token has expired or the user did not supply a valid token"},"403":{"description":"The user is not authorized to query the retract the given dataset. The user must be a member of the SenNet-Data-Admin group"},"404":{"description":"The target dataset could not be found"},"500":{"description":"Internal error"}},"summary":"Retracts a dataset after it has been published. Requires a json body with a single field {retraction_reason: string}. The dataset for the given id is modified to include this new retraction_reason field and sets the dataset property sub_status to Retracted. The complete modified dataset is returned. Requires that the dataset being retracted has already been published (dataset.status == Published. Requires a user token with membership in the SenNet-Data-Admin group otherwise then a 403 will be returned.","tags":["datasets"]}},"/datasets/prov-info":{"get":{"parameters":[{"description":"A case insensitive string. Any value besides 'json' will have no effect. If the string is 'json', provenance info will be returned as a json. Otherwise, it will be returned as a tsv file","in":"query","name":"format","required":false,"schema":{"enum":["json","tsv"],"type":"string"}},{"description":"The UUID of the group","in":"query","name":"group_uuid","required":false,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides true or false will cause a 400 exception.","in":"query","name":"has_rui_info","required":false,"schema":{"enum":["true","false"],"type":"string"}},{"description":"Case insensitive string for 2 character organ code. Values must be present on organ yaml or a 400 exception is raised","in":"query","name":"organ","required":false,"schema":{"type":"string"}},{"description":"Case insensitive string indicating the current status of a dataset","in":"query","name":"dataset_status","required":false,"schema":{"enum":["qa","new","published"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"dataset_created_by_email":{"description":"The email address of the person who created the dataset","type":"string"},"dataset_data_types":{"description":"The data/assay types (can be multiple types for pipeline derived data, so a comma separated list for tsv output or a json array for json output)","type":"string"},"dataset_date_time_created":{"description":"The date/time that the dataset was created","type":"string"},"dataset_date_time_modified":{"description":"The date/time that the dataset was last modified","type":"string"},"dataset_group_name":{"description":"The name of the 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This identifier can be either an SenNet ID (e.g. SNT123.ABCD.456) or UUID (32 digit hexadecimal number)","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A case insensitive string. Any value besides 'json' will have no effect. If the string is 'json', provenance info will be returned as a json. 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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.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["callback","message"],"type":"object","x-body-name":"request_body"},"AsyncQueryResponse":{"additionalProperties":true,"description":"The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the result of the async_query submission.","example":"Async_query has been queued","nullable":true,"type":"string"},"job_id":{"description":"An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job.","nullable":false,"type":"string"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"type":"object"},"AsyncQueryStatusResponse":{"additionalProperties":true,"description":"The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the current state or summary of the problem if the status is Failed.","example":"Callback URL returned 500","nullable":false,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. The most recent entry should be last. Its timestamp will be compared against the current time to see if there is still activity.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":1,"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":["status","description","logs"],"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,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.","example":"biolink:synonym"},"attributes":{"description":"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"description":{"description":"Human-readable description for the attribute and its value.","example":"Assertion Authored By Dr. Trans L. Ator","nullable":true,"type":"string"},"original_attribute_name":{"description":"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. 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,"type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153},"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. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_1187","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"value_url":{"description":"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).","example":"https://pubmed.ncbi.nlm.nih.gov/32529952","nullable":true,"type":"string"}},"required":["attribute_type_id","value"],"type":"object"},"AttributeConstraint":{"additionalProperties":false,"description":"Generic query constraint for a query node or query edge","properties":{"id":{"description":"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_0844","oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"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","type":"string"},"not":{"default":false,"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","==="],"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},"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},"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}},"required":["name","id","operator","value"],"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":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"edges":{"description":"List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge","items":{"type":"string"},"minItems":1,"nullable":false,"type":"array"}},"required":["edges","attributes"],"type":"object"},"BiolinkEntity":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","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_]*$","type":"string"},"CURIE":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"type":"string"},"Edge":{"additionalProperties":false,"description":"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \"thought\" graph resulting from a query upon the underlying knowledge source.","properties":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"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":[{"$ref":"#/components/schemas/CURIE"}]},"predicate":{"description":"The type of relationship between the subject and object for the statement expressed in an Edge. These should be Biolink Model predicate terms and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' predicate terms should also be avoided.","example":"biolink:gene_associated_with_condition","nullable":false,"oneOf":[{"$ref":"#/components/schemas/BiolinkPredicate"}]},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":true,"type":"array"},"sources":{"description":"A list of RetrievalSource objects that provide information about how a particular Information Resource served as a source from which the knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","items":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"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":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["object","predicate","subject","sources"],"type":"object"},"EdgeBinding":{"additionalProperties":true,"description":"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized). Edge bindings are captured within a specific reasoner's Analysis object because the Edges in the Knowledge Graph that get bound to the input Query Graph may differ between reasoners.","properties":{"attributes":{"description":"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","nullable":false,"type":"string"}},"required":["id","attributes"],"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":["nodes","edges"],"type":"object"},"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.","properties":{"code":{"description":"One of a standardized set of short codes e.g. QueryNotTraversable, KPNotAvailable, KPResponseMalformed","nullable":true,"type":"string"},"level":{"nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"A human-readable log message","nullable":false,"type":"string"},"timestamp":{"description":"Timestamp in ISO 8601 format, providing the LogEntry time either in univeral coordinated time (UTC) using the 'Z' tag (e.g 2020-09-03T18:13:49Z), or, if local time is provided, the timezone offset must be provided (e.g. 2020-09-03T18:13:49-04:00).","example":"2020-09-03T18:13:49+00:00","format":"date-time","nullable":false,"type":"string"}},"required":["timestamp","message"],"type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"},"Message":{"additionalProperties":false,"description":"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.","properties":{"auxiliary_graphs":{"additionalProperties":{"$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.","nullable":true,"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, if present, MAY be used to infer result rankings. If Results are not expected (such as for a query Message), this property SHOULD be null or absent. If Results are expected (such as for a response Message) and no Results are available, this property SHOULD be an array with 0 Results in it.","items":{"$ref":"#/components/schemas/Result"},"minItems":0,"nullable":true,"type":"array"}},"type":"object"},"MetaAttribute":{"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)","example":"biolink:p_value"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"}},"required":["attribute_type_id"],"type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","properties":{"association":{"$ref":"#/components/schemas/BiolinkEntity","description":"The Biolink association type (entity) that this edge represents. Associations are classes in Biolink that represent a relationship between two entities. For example, the association 'gene interacts with gene' is represented by the Biolink class, 'biolink:GeneToGeneAssociation'.  If association is filled out, then the testing harness can help validate that the qualifiers are being used correctly.","example":"biolink:ChemicalToGeneAssociation"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"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,"type":"array"},"object":{"$ref":"#/components/schemas/BiolinkEntity","description":"Object node category of this relationship edge.","example":"biolink:Protein"},"predicate":{"$ref":"#/components/schemas/BiolinkPredicate","description":"Biolink relationship between the subject and object categories.","example":"biolink:affects"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"type":"array"},"subject":{"$ref":"#/components/schemas/BiolinkEntity","description":"Subject node category of this relationship edge.","example":"biolink:ChemicalEntity"}},"required":["subject","predicate","object"],"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.","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":{"$ref":"#/components/schemas/MetaEdge"},"type":"array"},"nodes":{"additionalProperties":{"$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.","type":"object"}},"required":["nodes","edges"],"type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"type":"array"}},"required":["id_prefixes"],"type":"object"},"MetaQualifier":{"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":["expression","activity","abundance","degradation"],"type":"string"},"type":"array"},"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE of the qualifier type.","example":"biolink:subject_aspect_qualifier","nullable":false}},"required":["qualifier_type_id"],"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":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":false,"type":"array"},"is_set":{"description":"Indicates that the node represents a set of entities. If this property is missing or null, it is assumed to be false.","nullable":true,"type":"boolean"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"type":"string"}},"required":["categories","attributes"],"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":{"$ref":"#/components/schemas/Attribute"},"minItems":0,"nullable":false,"type":"array"},"id":{"description":"The CURIE of a Node within the Knowledge Graph.","nullable":false,"oneOf":[{"$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.","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id","attributes"],"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute constraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"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"},"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":["subject","object"],"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":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"A CURIE identifier (or list of identifiers) for this node.  The 'ids' field will hold a list of CURIEs only in the case of a BATCH set_interpretation, where each CURIE is queried  separately. If a list of queried CURIEs is to be considered as a   set (as under a MANY or ALL set_interpretation), the 'ids' field  will hold a single id representing this set, and the individual members  of this set will be captured in a separate 'member_ids' field.  Note that the set id MUST be created as a UUID by the system that  defines the queried set, using a centralized nodenorm service.  Note also that downstream systems MUST re-use the original set UUID  in the messages they create/send, which will facilitate merging or  caching operations.","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"member_ids":{"description":"A list of CURIE identifiers for members of a queried set. This  field MUST be populated under a set_interpretation of MANY or ALL, when the 'ids' field holds a UUID representing the set  itself. This field MUST NOT be used under a set_interpretation  of BATCH.","items":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"},"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"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"CURIE for a Biolink 'qualifier' association slot, generally taken from Biolink association slots designated for this purpose (that is, association slots with names ending in 'qualifier') e.g. biolink:subject_aspect_qualifier,  biolink:subject_direction_qualifier, biolink:object_aspect_qualifier, etc. Such qualifiers are used to elaborate a second layer of meaning of a knowledge graph edge. Available qualifiers are edge properties in the Biolink Model (see https://biolink.github.io/biolink-model/docs/edge_properties.html) which have slot names with the suffix string 'qualifier'.","example":"biolink:subject_aspect_qualifier","nullable":false,"pattern":"^biolink:[a-z][a-z_]*$"},"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,"type":"string"}},"required":["qualifier_type_id","qualifier_value"],"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":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"type":"array"}},"required":["qualifier_set"],"type":"object"},"Query":{"additionalProperties":true,"description":"The Query class is used to package a user request for information. A Query object consists of a required Message object with optional additional properties. Additional properties are intended to convey implementation-specific or query-independent parameters. For example, an additional property specifying a log level could allow a user to override the default log level in order to receive more fine-grained log information when debugging an issue.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. 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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":{"$ref":"#/definitions/unprocessable_entity"}}}}},{"components":{"schemas":{"Analysis":{"additionalProperties":true,"description":"An analysis is a dictionary that contains information about the result tied to a particular service. Each Analysis is generated by a single reasoning service, and describes the outputs of analyses performed by the reasoner on a particular Result (e.g. a result score), along with provenance information supporting the analysis (e.g. method or data that supported generation of the score).","properties":{"attributes":{"description":"The attributes of this particular Analysis.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edge_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/EdgeBinding"},"type":"array"},"description":"The dictionary of input Query Graph to Knowledge Graph edge bindings where the dictionary keys are the key identifiers of the Query Graph edges and the associated values of those keys are instances of EdgeBinding schema type (see below). This value is an array of EdgeBindings since a given query edge may resolve to multiple Knowledge Graph Edges.","type":"object"},"resource_id":{"$ref":"#/components/schemas/CURIE","description":"The id of the resource generating this Analysis"},"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"},"scoring_method":{"description":"An identifier and link to an explanation for the method used to generate the score","nullable":true,"type":"string"},"support_graphs":{"description":"This is a list of references to Auxiliary Graph instances that supported the analysis of a Result as performed by the reasoning service. Each item in the list is the key of a single Auxiliary Graph.","items":{"type":"string"},"nullable":true,"type":"array"}},"required":["resource_id","edge_bindings"],"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,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"The 'key' of the attribute object, holding a CURIE of an ontology property defining the attribute (preferably the CURIE of a Biolink association slot). This property captures the relationship asserted to hold between the value of the attribute, and the node or edge from  which it hangs. For example, that a value of '0.000153' represents a p-value supporting an edge, or that a value of 'ChEMBL' represents the original source of the knowledge expressed in the edge.","example":"biolink:synonym"},"attributes":{"description":"A list of attributes providing further information about the parent attribute (for example to provide provenance information about the parent attribute).","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"description":{"description":"Human-readable description for the attribute and its value.","example":"Assertion Authored By Dr. Trans L. Ator","nullable":true,"type":"string"},"original_attribute_name":{"description":"The term used by the original source of an attribute to describe the meaning or significance of the value it captures. 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,"type":"string"},"value":{"description":"Value of the attribute. May be any data type, including a list.","example":0.000153},"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. If a suitable CURIE/identifier does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_1187","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"value_url":{"description":"Human-consumable URL linking to a web document that provides additional information about an  attribute's value (not the node or the edge fom which it hangs).","example":"https://pubmed.ncbi.nlm.nih.gov/32529952","nullable":true,"type":"string"}},"required":["attribute_type_id","value"],"type":"object"},"AttributeConstraint":{"additionalProperties":false,"description":"Generic query constraint for a query node or query edge","properties":{"id":{"description":"CURIE of the concept being constrained. For properties defined by the Biolink model this SHOULD be a biolink CURIE. otherwise, if possible, from the EDAM ontology. If a suitable CURIE does not exist, enter a descriptive phrase here and submit the new type for consideration by the appropriate authority.","example":"EDAM:data_0844","oneOf":[{"$ref":"#/components/schemas/CURIE"}]},"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","type":"string"},"not":{"default":false,"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","==="],"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},"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},"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}},"required":["name","id","operator","value"],"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":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"edges":{"description":"List of edges that form the Auxiliary Graph. Each item is a reference to a single Knowledge Graph edge","items":{"type":"string"},"minItems":1,"nullable":false,"type":"array"}},"required":["edges"],"type":"object"},"BiolinkEntity":{"description":"Compact URI (CURIE) for a Biolink class, biolink:NamedThing or a child thereof. The CURIE must use the prefix 'biolink:' followed by the PascalCase class name.","example":"biolink:PhenotypicFeature","externalDocs":{"description":"Biolink model entities","url":"https://biolink.github.io/biolink-model/docs/NamedThing.html"},"pattern":"^biolink:[A-Z][a-zA-Z]*$","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_]*$","type":"string"},"CURIE":{"description":"A Compact URI, consisting of a prefix and a reference separated by a colon, such as UniProtKB:P00738. Via an external context definition, the CURIE prefix and colon may be replaced by a URI prefix, such as http://identifiers.org/uniprot/, to form a full URI.","externalDocs":{"url":"https://www.w3.org/TR/2010/NOTE-curie-20101216/"},"type":"string"},"Edge":{"additionalProperties":false,"description":"A specification of the semantic relationship linking two concepts that are expressed as nodes in the knowledge \"thought\" graph resulting from a query upon the underlying knowledge source.","properties":{"attributes":{"description":"A list of additional attributes for this edge","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"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":[{"$ref":"#/components/schemas/CURIE"}]},"predicate":{"description":"The type of relationship between the subject and object for the statement expressed in an Edge. These should be Biolink Model predicate terms and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' predicate terms should also be avoided.","example":"biolink:gene_associated_with_condition","nullable":false,"oneOf":[{"$ref":"#/components/schemas/BiolinkPredicate"}]},"qualifiers":{"description":"A set of Qualifiers that act together to add nuance or detail to the statement expressed in an Edge.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":true,"type":"array"},"sources":{"description":"A list of RetrievalSource objects that provide information about how a particular Information Resource served as a source from which the knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","items":{"$ref":"#/components/schemas/RetrievalSource"},"minItems":1,"nullable":false,"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":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["object","predicate","subject","sources"],"type":"object"},"EdgeBinding":{"additionalProperties":true,"description":"A instance of EdgeBinding is a single KnowledgeGraph Edge mapping, identified by the corresponding 'id' object key identifier of the Edge within the Knowledge Graph. Instances of EdgeBinding may include extra annotation (such annotation is not yet fully standardized). Edge bindings are captured within a specific reasoner's Analysis object because the Edges in the Knowledge Graph that get bound to the input Query Graph may differ between reasoners.","properties":{"attributes":{"description":"A list of attributes providing further information about the edge binding. This is not intended for capturing edge attributes and should only be used for properties that vary from result to result.","items":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"description":"The key identifier of a specific KnowledgeGraph Edge.","type":"string"}},"required":["id"],"type":"object"},"HTTPValidationError":{"properties":{"detail":{"items":{"$ref":"#/components/schemas/ValidationError"},"title":"Detail","type":"array"}},"title":"HTTPValidationError","type":"object"},"KnowledgeGraph":{"additionalProperties":true,"description":"The knowledge graph associated with a set of results. The instances of Node and Edge defining this graph represent instances of biolink:NamedThing (concept nodes) and biolink:Association (relationship edges) representing (Attribute) annotated knowledge returned from the knowledge sources and inference agents wrapped by the given TRAPI implementation.","properties":{"edges":{"additionalProperties":{"$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":{"$ref":"#/components/schemas/Node"},"description":"Dictionary of Node instances used in the KnowledgeGraph, referenced elsewhere in the TRAPI output by the dictionary key.","type":"object"}},"required":["nodes","edges"],"type":"object"},"LogLevel":{"description":"Logging level","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"},"Message":{"additionalProperties":false,"description":"The message object holds the main content of a Query or a Response in three properties: query_graph, results, and knowledge_graph. The query_graph property contains the query configuration, the results property contains any answers that are returned by the service, and knowledge_graph property contains lists of edges and nodes in the thought graph corresponding to this message. The content of these properties is context-dependent to the encompassing object and the TRAPI operation requested.","properties":{"auxiliary_graphs":{"additionalProperties":{"$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,\n if present, MAY be used to infer result rankings.","items":{"$ref":"#/components/schemas/Result"},"nullable":true,"type":"array"}},"type":"object"},"MetaAttribute":{"properties":{"attribute_source":{"description":"Source of an attribute provided by this TRAPI web service.","example":"infores:chembl","nullable":true,"type":"string"},"attribute_type_id":{"$ref":"#/components/schemas/CURIE","description":"Type of an attribute provided by this TRAPI web service (preferably the CURIE of a Biolink association slot)","example":"biolink:p_value"},"constraint_name":{"description":"Human-readable name or label for the constraint concept. Required whenever constraint_use is true.","example":"p-value","nullable":true,"type":"string"},"constraint_use":{"default":false,"description":"Indicates whether this attribute can be used as a query constraint.","type":"boolean"},"original_attribute_names":{"description":"Names of an the attribute as provided by the source.","items":{"type":"string"},"minItems":1,"nullable":true,"type":"array"}},"required":["attribute_type_id"],"type":"object"},"MetaEdge":{"additionalProperties":false,"description":"Edge in a meta knowledge map describing relationship between a subject Biolink class and an object Biolink class.","properties":{"association":{"$ref":"#/components/schemas/BiolinkEntity","description":"The Biolink association type (entity) that this edge represents. Associations are classes in Biolink that represent a relationship between two entities. For example, the association 'gene interacts with gene' is represented by the Biolink class, 'biolink:GeneToGeneAssociation'.  If association is filled out, then the testing harness can help validate that the qualifiers are being used correctly.","example":"biolink:ChemicalToGeneAssociation","type":"object"},"attributes":{"description":"Edge attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"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,"type":"array"},"object":{"$ref":"#/components/schemas/BiolinkEntity","description":"Object node category of this relationship edge.","example":"biolink:Protein"},"predicate":{"$ref":"#/components/schemas/BiolinkPredicate","description":"Biolink relationship between the subject and object categories.","example":"biolink:affects"},"qualifiers":{"description":"Qualifiers that are possible to be found on this edge type.","items":{"$ref":"#/components/schemas/MetaQualifier"},"nullable":true,"type":"array"},"subject":{"$ref":"#/components/schemas/BiolinkEntity","description":"Subject node category of this relationship edge.","example":"biolink:ChemicalEntity"}},"required":["subject","predicate","object"],"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.","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":{"$ref":"#/components/schemas/MetaEdge"},"type":"array"},"nodes":{"additionalProperties":{"$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.","type":"object"}},"required":["nodes","edges"],"type":"object"},"MetaNode":{"additionalProperties":false,"description":"Description of a node category provided by this TRAPI web service.","properties":{"attributes":{"description":"Node attributes provided by this TRAPI web service.","items":{"$ref":"#/components/schemas/MetaAttribute"},"nullable":true,"type":"array"},"id_prefixes":{"description":"List of CURIE prefixes for the node category that this TRAPI web service understands and accepts on the input.","example":["CHEMBL.COMPOUND","INCHIKEY"],"items":{"type":"string"},"minItems":1,"type":"array"}},"required":["id_prefixes"],"type":"object"},"MetaQualifier":{"properties":{"applicable_values":{"description":"The list of values that are possible for this qualifier.","items":{"example":["expression","activity","abundance","degradation"],"type":"string"},"type":"array"},"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE of the qualifier type.","example":"biolink:subject_aspect_qualifier","nullable":false}},"required":["qualifier_type_id"],"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":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"categories":{"description":"These should be Biolink Model categories and are NOT allowed to be of type 'abstract' or 'mixin'. Returning 'deprecated' categories should also be avoided.","items":{"$ref":"#/components/schemas/BiolinkEntity"},"nullable":true,"type":"array"},"name":{"description":"Formal name of the entity","example":"Haptoglobin","nullable":true,"type":"string"}},"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":{"$ref":"#/components/schemas/Attribute"},"nullable":true,"type":"array"},"id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE of a Node within the Knowledge Graph."},"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.","nullable":true,"oneOf":[{"$ref":"#/components/schemas/CURIE"}]}},"required":["id"],"type":"object"},"QEdge":{"additionalProperties":true,"description":"An edge in the QueryGraph used as a filter pattern specification in a query. If the optional predicate property is not specified, it is assumed to be a wildcard match to the target knowledge space. If specified, the ontological inheritance hierarchy associated with the term provided is assumed, such that edge bindings returned may be an exact match to the given QEdge predicate term, or to a term that is a descendant of the QEdge predicate term.","properties":{"attribute_constraints":{"default":[],"description":"A list of attribute constraints applied to a query edge. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"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"},"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":["subject","object"],"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":{"$ref":"#/components/schemas/BiolinkEntity"},"minItems":1,"nullable":true,"type":"array"},"constraints":{"default":[],"description":"A list of constraints applied to a query node. If there are multiple items, they must all be true (equivalent to AND)","items":{"$ref":"#/components/schemas/AttributeConstraint"},"type":"array"},"ids":{"description":"CURIE identifier for this node","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"is_set":{"default":false,"description":"Boolean that if set to true, indicates that this QNode MAY have multiple KnowledgeGraph Nodes bound to it within each Result. The nodes in a set should be considered as a set of independent nodes, rather than a set of dependent nodes, i.e., the answer would still be valid if the nodes in the set were instead returned individually. Multiple QNodes may have is_set=True. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=False, each n1 must be connected to n2. If a QNode (n1) with is_set=True is connected to a QNode (n2) with is_set=True, each n1 must be connected to at least one n2.","type":"boolean"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$ref":"#/components/schemas/CURIE","description":"CURIE for a Biolink 'qualifier' association slot, generally taken from Biolink association slots designated for this purpose (that is, association slots with names ending in 'qualifier') e.g. biolink:subject_aspect_qualifier,  biolink:subject_direction_qualifier, biolink:object_aspect_qualifier, etc. Such qualifiers are used to elaborate a second layer of meaning of a knowledge graph edge. Available qualifiers are edge properties in the Biolink Model (see https://biolink.github.io/biolink-model/docs/edge_properties.html) which have slot names with the suffix string 'qualifier'.","example":"biolink:subject_aspect_qualifier","nullable":false,"pattern":"^biolink:[a-z][a-z_]*$"},"qualifier_value":{"description":"The value associated with the type of the qualifier, drawn from a set of controlled values by the type as specified in the Biolink model (e.g. 'expression' or 'abundance' for the qualifier type 'biolink:subject_aspect_qualifier', etc). The enumeration of qualifier values for a given qualifier type is generally going to be constrained by the category of edge (i.e. biolink:Association subtype) of the (Q)Edge.","example":"expression","nullable":false,"type":"string"}},"required":["qualifier_type_id","qualifier_value"],"type":"object"},"QualifierConstraint":{"additionalProperties":false,"description":"Defines a query constraint based on the qualifier_types and qualifier_values of a set of Qualifiers attached to an edge. For example, it can constrain a \"ChemicalX - affects - ?Gene\" query to return only edges where ChemicalX specifically affects the 'expression' of the Gene, by constraining on the qualifier_type \"biolink:object_aspect_qualifier\" with a qualifier_value of \"expression\".","properties":{"qualifier_set":{"description":"A set of Qualifiers that serves to add nuance to a query, by constraining allowed values held by Qualifiers on queried Edges.","items":{"$ref":"#/components/schemas/Qualifier"},"nullable":false,"type":"array"}},"required":["qualifier_set"],"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.","properties":{"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"$ref":"#/components/schemas/Message","description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields."},"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.","nullable":true,"oneOf":[{"$ref":"http://standards.ncats.io/workflow/1.3.2/schema"}]}},"required":["message"],"type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$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":{"$ref":"#/components/schemas/QNode"},"description":"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.","type":"object"}},"required":["nodes","edges"],"type":"object"},"ResourceRoleEnum":{"description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.  This enumeration is found in Biolink Model, but is repeated here for convenience.","enum":["primary_knowledge_source","aggregator_knowledge_source","supporting_data_source"],"type":"string"},"Result":{"additionalProperties":true,"description":"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and an EdgeBindings object (list of query graph edge to knowledge graph edge mappings).","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"type":"array"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"type":"array"},"description":"The dictionary of Input Query Graph to Result Knowledge Graph node bindings where the dictionary keys are the key identifiers of the Query Graph nodes and the associated values of those keys are instances of NodeBinding schema type (see below). This value is an array of NodeBindings since a given query node may have multiple knowledge graph Node bindings in the result.","type":"object"}},"required":["node_bindings","analyses"],"type":"object"},"RetrievalSource":{"additionalProperties":true,"description":"Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved.","properties":{"resource_id":{"$ref":"#/components/schemas/CURIE","description":"The CURIE for an Information Resource that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge.","example":"infores:drugbank","nullable":false},"resource_role":{"$ref":"#/components/schemas/ResourceRoleEnum","description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources."},"source_record_urls":{"description":"A URL linking to a specific web page or document provided by the  source, that contains a record of the knowledge expressed in the  Edge. If the knowledge is contained in more than one web page on  an Information Resource's site, urls MAY be provided for each.  For example, Therapeutic Targets Database (TTD) has separate web  pages for 'Imatinib' and its protein target KIT, both of which hold  the claim that 'the KIT protein is a therapeutic target for Imatinib'.","example":"[https://db.idrblab.net/ttd/data/drug/details/d0az3c,  https://db.idrblab.net/ttd/data/target/details/t57700]","items":{"type":"string"},"type":"array"},"upstream_resource_ids":{"description":"An upstream InformationResource from which the resource being described directly retrieved a record of the knowledge expressed in the Edge, or data used to generate this knowledge. This is an array because there are cases where a merged Edge holds knowledge that was retrieved from multiple sources. e.g. an Edge provided by the ARAGORN ARA can expressing knowledge it retrieved from both the automat-mychem-info and molepro KPs, which both provided it with records of this single fact.","example":["infores:automat-mychem-info","infores:molepro"],"items":{"$ref":"#/components/schemas/CURIE"},"type":"array"}},"required":["resource_id","resource_role"],"type":"object"},"ValidationError":{"properties":{"loc":{"items":{"type":"string"},"title":"Location","type":"array"},"msg":{"title":"Message","type":"string"},"type":{"title":"Error Type","type":"string"}},"required":["loc","msg","type"],"title":"ValidationError","type":"object"}}},"info":{"contact":{"email":"edgar.gatica@cuanschutz.edu","name":"Edgar Gatica","x-id":"https://github.com/edgargaticaCU","x-role":"responsible developer"},"description":"A KG linking concepts that cooccur in scientific text, scored  at different levels, e.g. title, sentence, document, using  a suite of cooccurrence metrics.","license":{"name":"MIT License","url":"https://github.com/UCDenver-ccp/Translator-TM-Provider-Cooccurrence/blob/main/LICENSE"},"title":"Text Mined Cooccurrence API","version":"1.0.0","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:text-mining-provider-cooccurrence","team":["Text Mining Provider"]},"x-trapi":{"asyncquery":false,"operations":["lookup","overlay"],"test_data_location":{"development":{"url":"https://raw.githubusercontent.com/UCDenver-ccp/Translator-TM-Provider-Cooccurrence/main/src/test/data/test_triples.json"}},"version":"1.4.0"}},"openapi":"3.0.2","paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/overlay":{"post":{"description":"Given a ReasonerAPI graph, add support edges for any nodes.","requestBody":{"content":{"application/json":{"schema":{"allOf":[{"$ref":"#/components/schemas/Query"}],"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"ms\": {\n          \"id\": \"MONDO:0005301\"\n        },\n        \"ce\": {\n          \"category\": \"biolink:ChemicalEntity\"\n        }\n      },\n      \"edges\": {\n        \"treats\": {\n          \"subject\": \"ce\",\n          \"predicate\": \"biolink:treats\",\n          \"object\": \"ms\"\n        }\n      }\n    },\n    \"knowledge_graph\": {\n      \"nodes\": {\n        \"MONDO:0005301\": {\n          \"name\": \"multiple sclerosis\",\n          \"categories\": [\n            \"biolink:Disease\",\n            \"biolink:DiseaseOrPhenotypicFeature\",\n            \"biolink:ThingWithTaxon\",\n            \"biolink:BiologicalEntity\",\n            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\"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n            \"biolink:NamedThing\",\n            \"biolink:Entity\",\n            \"biolink:PhysicalEssenceOrOccurrent\"\n          ]\n        },\n        \"DRUGBANK:DB11811\": {\n          \"name\": \"Arhalofenate\",\n          \"categories\": [\n            \"biolink:SmallMolecule\",\n            \"biolink:MolecularEntity\",\n            \"biolink:ChemicalEntity\",\n            \"biolink:PhysicalEssence\",\n            \"biolink:ChemicalOrDrugOrTreatment\",\n            \"biolink:ChemicalEntityOrGeneOrGeneProduct\",\n            \"biolink:ChemicalEntityOrProteinOrPolypeptide\",\n            \"biolink:NamedThing\",\n            \"biolink:Entity\",\n            \"biolink:PhysicalEssenceOrOccurrent\"\n          ]\n        }\n      },\n      \"edges\": {\n        \"2fa653819ad7c4d42e49aced752e4b466e5cd7951b2ed30975f9ab13acc4d862-treats\": {\n          \"subject\": \"DRUGBANK:DB05266\",\n          \"object\": \"MONDO:0005301\",\n          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