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This is a newer version where each record is a unique combination of subjectID-predicate- objectID and contains a count of the unique pmids and predications supporting it.","termsOfService":"https://biothings.io/about","title":"BioThings SEMMEDDB API","version":"43_2024R","x-translator":{"biolink-version":"4.2.6","component":"KP","infores":"infores:biothings-semmeddb","team":["Service Provider"]}},"openapi":"3.0.3","paths":{"/association/{id}":{"get":{"description":"By default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. Multiple attributes should be separated by commas. If an attribute is not  available for a specific association, it will be ignored. 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If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. Multiple attributes should be separated by commas. If an attribute is not  available for a specific association, it will be ignored. Note that the attribute names are  case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"DB14539_C0151467","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["indication"]}},"/indication":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases,  there are some times you might find it easier to batch query (e.g., retrieving multiple associations).  Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple association ids separated by commas. Note that currently we only take ids up to  1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["DB14539_C0151467","DB14509_C0003873"]},"schema":{"properties":{"ids":{"description":"Accepts multiple association ids. 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In the output, \"total\" in the output gives the total number  of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained  [here for a core BioThings  API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"drug.drugbank:DB14006","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases,  there are times you might find it more efficient to make batch queries (e.g., retrieving data  for multiple inputs). 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A false discovery rate (FDR) threshold of <= 0.05 was applied to identify genes with a significant eQTL.","operationId":"egene","parameters":[{"description":"Page (slice) of entire results set to return. 0-based.","in":"query","name":"page","required":false,"schema":{"items":{"format":"int32","type":"integer"},"type":"array"}},{"description":"Number of records per page of results.  Max is 2000.","in":"query","name":"pageSize","required":false,"schema":{"default":250,"items":{"format":"int32","type":"integer"},"maximum":2000,"minimum":1,"type":"array"}},{"description":"Filter down results matching the specified term. 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Usually includes a data source and data release.","in":"query","name":"datasetId","required":true,"schema":{"default":"gtex_v7","items":{"type":"string"},"type":"array"}},{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Tissue ID of the tissue of interest.","in":"query","name":"tissueSiteDetailId","required":false,"schema":{"enum":["Adipose_Subcutaneous","Adipose_Visceral_Omentum","Adrenal_Gland","Artery_Aorta","Artery_Coronary","Artery_Tibial","Bladder","Brain_Amygdala","Brain_Anterior_cingulate_cortex_BA24","Brain_Caudate_basal_ganglia","Brain_Cerebellar_Hemisphere","Brain_Cerebellum","Brain_Cortex","Brain_Frontal_Cortex_BA9","Brain_Hippocampus","Brain_Hypothalamus","Brain_Nucleus_accumbens_basal_ganglia","Brain_Putamen_basal_ganglia","Brain_Spinal_cord_cervical_c-1","Brain_Substantia_nigra","Breast_Mammary_Tissue","Cells_EBV-transformed_lymphocytes","Cells_Transformed_fibroblasts","Cervix_Ectocervix","Cervix_Endocervix","Colon_Sigmoid","Colon_Transverse","Esophagus_Gastroesophageal_Junction","Esophagus_Mucosa","Esophagus_Muscularis","Fallopian_Tube","Heart_Atrial_Appendage","Heart_Left_Ventricle","Kidney_Cortex","Liver","Lung","Minor_Salivary_Gland","Muscle_Skeletal","Nerve_Tibial","Ovary","Pancreas","Pituitary","Prostate","Skin_Not_Sun_Exposed_Suprapubic","Skin_Sun_Exposed_Lower_leg","Small_Intestine_Terminal_Ileum","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina","Whole_Blood"],"items":{"type":"string"},"type":"array"}},{"description":"specifies whether or not to perform hierarchical clustering.","in":"query","name":"hcluster","required":false,"schema":{"type":"boolean"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find median gene expression data.","tags":["expression"]}},"/expression/medianJunctionExpression":{"get":{"description":"This service returns median junction read counts in tissues of a given gene from all known transcripts. Results may be filtered by dataset or tissue. When the optional parameter hcluster is set to true, the service will return the hierarchical clustering results of tissues, based on junction expression, in Newick format. The hierarchical clustering is performed by calculating Euclidean distances and using the average linkage method. By default, this service queries the latest GTEx release.","operationId":"medianJunctionExpression","parameters":[{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":true,"schema":{"default":"gtex_v7","items":{"type":"string"},"type":"array"}},{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"type":"string"}},{"description":"Tissue ID of the tissue of interest.","in":"query","name":"tissueSiteDetailId","required":false,"schema":{"enum":["Adipose_Subcutaneous","Adipose_Visceral_Omentum","Adrenal_Gland","Artery_Aorta","Artery_Coronary","Artery_Tibial","Bladder","Brain_Amygdala","Brain_Anterior_cingulate_cortex_BA24","Brain_Caudate_basal_ganglia","Brain_Cerebellar_Hemisphere","Brain_Cerebellum","Brain_Cortex","Brain_Frontal_Cortex_BA9","Brain_Hippocampus","Brain_Hypothalamus","Brain_Nucleus_accumbens_basal_ganglia","Brain_Putamen_basal_ganglia","Brain_Spinal_cord_cervical_c-1","Brain_Substantia_nigra","Breast_Mammary_Tissue","Cells_EBV-transformed_lymphocytes","Cells_Transformed_fibroblasts","Cervix_Ectocervix","Cervix_Endocervix","Colon_Sigmoid","Colon_Transverse","Esophagus_Gastroesophageal_Junction","Esophagus_Mucosa","Esophagus_Muscularis","Fallopian_Tube","Heart_Atrial_Appendage","Heart_Left_Ventricle","Kidney_Cortex","Liver","Lung","Minor_Salivary_Gland","Muscle_Skeletal","Nerve_Tibial","Ovary","Pancreas","Pituitary","Prostate","Skin_Not_Sun_Exposed_Suprapubic","Skin_Sun_Exposed_Lower_leg","Small_Intestine_Terminal_Ileum","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina","Whole_Blood"],"items":{"type":"string"},"type":"array"}},{"description":"specifies whether or not to perform hierarchical clustering.","in":"query","name":"hcluster","required":false,"schema":{"type":"boolean"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find median gene expression data.","tags":["expression"]}},"/expression/medianTranscriptExpression":{"get":{"description":"This service returns median normalized expression in tissues of all known transcripts of a given gene. Results may be filtered by dataset or tissue. When the optional parameter hcluster is set to true, the service will return the hierarchical clustering results of tissues and transcripts, based on expression, in Newick format. The hierarchical clustering is performed by calculating Euclidean distances and using the average linkage method. By default, this service queries the latest GTEx release.","operationId":"medianTranscriptExpression","parameters":[{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":true,"schema":{"default":"gtex_v7","items":{"type":"string"},"type":"array"}},{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"type":"string"}},{"description":"Tissue ID of the tissue of interest.","in":"query","name":"tissueSiteDetailId","required":false,"schema":{"enum":["Adipose_Subcutaneous","Adipose_Visceral_Omentum","Adrenal_Gland","Artery_Aorta","Artery_Coronary","Artery_Tibial","Bladder","Brain_Amygdala","Brain_Anterior_cingulate_cortex_BA24","Brain_Caudate_basal_ganglia","Brain_Cerebellar_Hemisphere","Brain_Cerebellum","Brain_Cortex","Brain_Frontal_Cortex_BA9","Brain_Hippocampus","Brain_Hypothalamus","Brain_Nucleus_accumbens_basal_ganglia","Brain_Putamen_basal_ganglia","Brain_Spinal_cord_cervical_c-1","Brain_Substantia_nigra","Breast_Mammary_Tissue","Cells_EBV-transformed_lymphocytes","Cells_Transformed_fibroblasts","Cervix_Ectocervix","Cervix_Endocervix","Colon_Sigmoid","Colon_Transverse","Esophagus_Gastroesophageal_Junction","Esophagus_Mucosa","Esophagus_Muscularis","Fallopian_Tube","Heart_Atrial_Appendage","Heart_Left_Ventricle","Kidney_Cortex","Liver","Lung","Minor_Salivary_Gland","Muscle_Skeletal","Nerve_Tibial","Ovary","Pancreas","Pituitary","Prostate","Skin_Not_Sun_Exposed_Suprapubic","Skin_Sun_Exposed_Lower_leg","Small_Intestine_Terminal_Ileum","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina","Whole_Blood"],"items":{"type":"string"},"type":"array"}},{"description":"specifies whether or not to perform hierarchical clustering.","in":"query","name":"hcluster","required":false,"schema":{"type":"boolean"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find median transcript expression data of all known transcripts of a gene.","tags":["expression"]}},"/expression/topExpressedGene":{"get":{"description":"This service returns top expressed genes for a specified tissue in a dataset. When the optional parameter filterMtGene is set to true, mitochondrial genes will be excluded from the results. By default, this service queries the latest GTEx release.","operationId":"topExpressedGene","parameters":[{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":true,"schema":{"default":"gtex_v7","type":"string"}},{"description":"Tissue ID of the tissue of interest.","in":"query","name":"tissueSiteDetailId","required":true,"schema":{"enum":["Adipose_Subcutaneous","Adipose_Visceral_Omentum","Adrenal_Gland","Artery_Aorta","Artery_Coronary","Artery_Tibial","Bladder","Brain_Amygdala","Brain_Anterior_cingulate_cortex_BA24","Brain_Caudate_basal_ganglia","Brain_Cerebellar_Hemisphere","Brain_Cerebellum","Brain_Cortex","Brain_Frontal_Cortex_BA9","Brain_Hippocampus","Brain_Hypothalamus","Brain_Nucleus_accumbens_basal_ganglia","Brain_Putamen_basal_ganglia","Brain_Spinal_cord_cervical_c-1","Brain_Substantia_nigra","Breast_Mammary_Tissue","Cells_EBV-transformed_lymphocytes","Cells_Transformed_fibroblasts","Cervix_Ectocervix","Cervix_Endocervix","Colon_Sigmoid","Colon_Transverse","Esophagus_Gastroesophageal_Junction","Esophagus_Mucosa","Esophagus_Muscularis","Fallopian_Tube","Heart_Atrial_Appendage","Heart_Left_Ventricle","Kidney_Cortex","Liver","Lung","Minor_Salivary_Gland","Muscle_Skeletal","Nerve_Tibial","Ovary","Pancreas","Pituitary","Prostate","Skin_Not_Sun_Exposed_Suprapubic","Skin_Sun_Exposed_Lower_leg","Small_Intestine_Terminal_Ileum","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina","Whole_Blood"],"type":"string"}},{"description":"Flag specifying whether or not to filter out mitochondrial genes","in":"query","name":"filterMtGene","required":false,"schema":{"type":"boolean"}},{"description":"Which column in the results should be used for sorting paginated results?","in":"query","name":"sortBy","required":false,"schema":{"default":"median","enum":["median"],"type":"string"}},{"description":"Sort direction for the returned data.","in":"query","name":"sortDirection","required":false,"schema":{"default":"desc","enum":["asc","desc"],"type":"string"}},{"description":"Page (slice) of entire results set to return. 0-based.","in":"query","name":"page","required":false,"schema":{"items":{"format":"int32","type":"integer"},"type":"array"}},{"description":"Number of records per page of results.  Max is 10000.","in":"query","name":"pageSize","required":false,"schema":{"default":100,"items":{"format":"int32","type":"integer"},"maximum":10000,"minimum":1,"type":"array"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find top expressed genes for a specified tissue.","tags":["expression"]}},"/expression/transcriptExpression":{"get":{"description":"This service returns normalized expression in tissues, at the individual sample level, of all known transcripts from one or more genes. Results may be filtered by dataset, gene, or tissue, but at least one gene must be provided. The optional boxplotDetail can be specified to report medians and quartiles. By default, this service queries the latest GTEx release.","operationId":"transcriptExpression","parameters":[{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":true,"schema":{"default":"gtex_v7","enum":["gtex_v7","gtex_v6p"],"items":{"type":"string"},"type":"array"}},{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Tissue ID of the tissue of interest.","in":"query","name":"tissueSiteDetailId","required":false,"schema":{"enum":["Adipose_Subcutaneous","Adipose_Visceral_Omentum","Adrenal_Gland","Artery_Aorta","Artery_Coronary","Artery_Tibial","Bladder","Brain_Amygdala","Brain_Anterior_cingulate_cortex_BA24","Brain_Caudate_basal_ganglia","Brain_Cerebellar_Hemisphere","Brain_Cerebellum","Brain_Cortex","Brain_Frontal_Cortex_BA9","Brain_Hippocampus","Brain_Hypothalamus","Brain_Nucleus_accumbens_basal_ganglia","Brain_Putamen_basal_ganglia","Brain_Spinal_cord_cervical_c-1","Brain_Substantia_nigra","Breast_Mammary_Tissue","Cells_EBV-transformed_lymphocytes","Cells_Transformed_fibroblasts","Cervix_Ectocervix","Cervix_Endocervix","Colon_Sigmoid","Colon_Transverse","Esophagus_Gastroesophageal_Junction","Esophagus_Mucosa","Esophagus_Muscularis","Fallopian_Tube","Heart_Atrial_Appendage","Heart_Left_Ventricle","Kidney_Cortex","Liver","Lung","Minor_Salivary_Gland","Muscle_Skeletal","Nerve_Tibial","Ovary","Pancreas","Pituitary","Prostate","Skin_Not_Sun_Exposed_Suprapubic","Skin_Sun_Exposed_Lower_leg","Small_Intestine_Terminal_Ileum","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina","Whole_Blood"],"items":{"type":"string"},"type":"array"}},{"description":"Subject attribute to subset data by.","in":"query","name":"attributeSubset","required":false,"schema":{"enum":["ageBracket","sex"],"type":"string"}},{"description":"Specifies amount of boxplot detail to return. Default empty string will simply return all expression values (no boxplot calculations performed).","in":"query","name":"boxplotDetail","required":false,"schema":{"enum":["full","median","quartiles"],"type":"string"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find transcript expression data at the sample level.","tags":["expression"]}},"/metadata/dataset":{"get":{"description":"This service returns information and analysis summary of the datasets that GTEx web services provide. Results may be filtered by dataset ID or organization.","operationId":"dataset","parameters":[{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":false,"schema":{"type":"string"}},{"description":"Organization that owns datasets.","in":"query","name":"organizationName","required":false,"schema":{"type":"string"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}},{"description":"Which column in the results should be used for sorting paginated results?","in":"query","name":"sortBy","required":false,"schema":{"default":"datasetId","enum":["organizationName","dbgapId","datasetId"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find information about the datasets that GTEx web services provide.","tags":["metadata"]}},"/metadata/tissueSiteDetail":{"get":{"description":"This service returns information for each tissue subsite (tissueSiteDetail), including ID, name, and standard tissue colors published by the GTEx Consortium in both RGB and hexadecimal formats. TissueSiteDetails are grouped by tissue sites (tissueSite). Results may be filtered by tissue site (tissueSite), subsite name (tissueSiteDetail), subsite ID (tissueSiteId), or subsite abbreviation (tissueSiteDetailAbbr).","operationId":"tissueSiteDetail","parameters":[{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}},{"description":"Tissue Site is an anatomical grouping of Tissue Site Details.","in":"query","name":"tissueSite","required":false,"schema":{"enum":["Adipose Tissue","Adrenal Gland","Blood","Blood Vessel","Bladder","Brain","Breast","Cervix Uteri","Colon","Esophagus","Fallopian Tube","Heart","Kidney","Liver","Lung","Muscle","Nerve","Ovary","Pancreas","Pituitary","Prostate","Salivary Gland","Skin","Small Intestine","Spleen","Stomach","Testis","Thyroid","Uterus","Vagina"],"type":"string"}},{"description":"The formatted version of a tissueSiteDetail, e.g., Adipose - Subcutaneous","in":"query","name":"tissueSiteDetail","required":false,"schema":{"type":"string"}},{"description":"Standard abbreviation for the Tissue Site Detail, e.g., ADPSBQ.","in":"query","name":"tissueSiteDetailAbbr","required":false,"schema":{"type":"string"}},{"description":"The URL formatted version of a tissueSiteDetail, e.g., Adipose_Subcutaneous","in":"query","name":"tissueSiteDetailId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find metadata of each tissue site detail.","tags":["metadata"]}},"/reference/exon":{"get":{"deprecated":false,"description":"This service returns exons from all known transcripts of the given gene. A versioned GENCODE ID is required to ensure that all exons are from a single gene. A dataset ID or both GENCODE version and genome build must be provided. Although annotated exons are not dataset dependent, specifying a dataset here is equivalent to specifying the GENCODE version and genome build used by that dataset.","operationId":"exon","parameters":[{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"type":"string"}},{"description":"GENCODE annotation release.","in":"query","name":"gencodeVersion","required":false,"schema":{"enum":["v19"],"type":"string"}},{"description":"Reference genome assembly.","in":"query","name":"genomeBuild","required":false,"schema":{"enum":["GRCh37/hg19"],"type":"string"}},{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find exons from all known reference transcripts of the given gene.","tags":["reference"]}},"/reference/gene":{"get":{"description":"This service returns information about reference genes. A genome build and GENCODE version must be provided. Genes are searchable by gene symbol, GENCODE ID and versioned GENCODE ID. Versioned GENCODE ID is recommended to ensure unique ID matching. By default, this service queries the genome build and GENCODE version used by the latest GTEx release.","operationId":"gene","parameters":[{"description":"A gene symbol, versioned gencodeId, or unversioned gencodeId.","in":"query","name":"geneId","required":true,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"GENCODE annotation release.","in":"query","name":"gencodeVersion","required":false,"schema":{"default":"v19","enum":["v19"],"type":"string"}},{"description":"Reference genome assembly.","in":"query","name":"genomeBuild","required":false,"schema":{"default":"GRCh37/hg19","enum":["GRCh37/hg19"],"type":"string"}},{"description":"Page (slice) of entire results set to return. 0-based.","in":"query","name":"page","required":false,"schema":{"items":{"format":"int32","type":"integer"},"type":"array"}},{"description":"Number of records per page of results.  Max is 2000.","in":"query","name":"pageSize","required":false,"schema":{"default":250,"items":{"format":"int32","type":"integer"},"maximum":2000,"minimum":1,"type":"array"}},{"description":"Format of result.","in":"query","name":"format","required":false,"schema":{"default":"json","enum":["json","tsv","csv"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find reference genes.","tags":["reference"]}},"/reference/transcript":{"get":{"deprecated":false,"description":"This service returns information about transcripts of the given versioned GENCODE ID. A genome build and GENCODE version must be provided. By default, this service queries the genome build and GENCODE version used by the latest GTEx release.","operationId":"transcript","parameters":[{"description":"Versioned GENCODE ID of a gene, e.g. ENSG00000065613.9.","in":"query","name":"gencodeId","required":true,"schema":{"type":"string"}},{"description":"GENCODE annotation release.","in":"query","name":"gencodeVersion","required":false,"schema":{"enum":["v19"],"type":"string"}},{"description":"Reference genome assembly.","in":"query","name":"genomeBuild","required":false,"schema":{"enum":["GRCh37/hg19"],"type":"string"}},{"description":"Unique identifier of a dataset. Usually includes a data source and data release.","in":"query","name":"datasetId","required":false,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Success"},"default":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}},"text/plain":{"schema":{"items":{"type":"string"},"type":"array"}},"text/tab-separated-values":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"Unexpected error."}},"summary":"Find all transcripts of a reference gene.","tags":["reference"]}}},"servers":[{"url":"https://dev.gtexportal.org/rest/v1"}],"tags":[{"name":"NIHdatacommons"},{"name":"GTEx"}]},{"components":{"securitySchemes":{"tokenAuth":{"description":"FlyMine authentication token obtained from /user/token endpoint","in":"query","name":"token","type":"apiKey"}}},"info":{"contact":{"email":"support@flymine.org","name":"FlyMine Support","url":"https://www.flymine.org/"},"description":"FlyMine is an integrated database for Drosophila genomics providing powerful search and\ndata warehousing capabilities for accessing integrated genomic, proteomic, and genetic data\nfor Drosophila and related organisms. This API provides RESTful web services powered by\nInterMine, an open-source biological data warehouse system.\n\n## Authentication\nSome endpoints require authentication via API token. Obtain a token using the /user/token endpoint\nwith username and password, then include it as a query parameter in subsequent requests.\n\n## Formats\nMost endpoints support multiple output formats including JSON, XML, TSV, and CSV.\n","license":{"name":"LGPL-2.1","url":"https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html"},"title":"FlyMine Web Services API","version":"31.0.0"},"openapi":"3.0.3","paths":{"/query/results":{"get":{"description":"Execute a PathQuery to retrieve data from FlyMine. Queries can be submitted\nin XML or JSON format and results can be returned in various formats.\n","operationId":"queryResultsGet","parameters":[{"description":"A definition of the query to execute in Path-Query XML or JSON format","examples":{"eveGeneQuery":{"summary":"Query for even-skipped gene","value":"<query name=\"eve gene query\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.name Gene.length Gene.chromosome.primaryIdentifier Gene.chromosomeLocation.start Gene.chromosomeLocation.end\">\n  <constraint path=\"Gene.symbol\" op=\"=\" value=\"eve\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"},"notchPathwayGenes":{"summary":"Genes in Notch signaling pathway","value":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\", \"symbol\", \"name\", \"pathways.name\"],\n  \"where\": [\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"},\n    {\"path\": \"pathways.name\", \"op\": \"CONTAINS\", \"value\": \"Notch\"}\n  ]\n}\n"},"shortGenesXChromosome":{"summary":"Short genes on X chromosome (from original service.json)","value":"<query model=\"genomic\" view=\"Gene.name Gene.symbol Gene.id Gene.length Gene.chromosome.primaryIdentifier\" constraintLogic=\"(nil and B)\" sortOrder=\"\">\n <constraint path=\"Gene.chromosome.primaryIdentifier\" value=\"X\" op=\"=\" code=\"A\"/>\n <constraint path=\"Gene.length\" value=\"100\" op=\"&lt;=\" code=\"B\"/>\n </query>\n"},"transcriptionFactorGenes":{"summary":"Genes with transcription factor activity","value":"<query name=\"transcription factor genes\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.name Gene.goAnnotation.ontologyTerm.name\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription factor\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"},"winglessProteinDomains":{"summary":"Protein domains of wingless gene","value":"<query name=\"wingless protein domains\" model=\"genomic\" view=\"Gene.symbol Gene.proteins.primaryIdentifier Gene.proteins.proteinDomains.name Gene.proteins.proteinDomains.description\">\n  <constraint path=\"Gene.symbol\" op=\"=\" value=\"wingless\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"}},"in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Output format","in":"query","name":"format","schema":{"default":"tab","enum":["tab","csv","count","json","jsonobjects","jsoncount","xml","html","rdf+xml"],"type":"string"}},{"description":"The index of the first result to return","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"The maximum size of the result 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query","value":{"executionTime":234,"results":[["FBgn0000008","a","893","X"],["FBgn0000606","eve","7784","2R"],["FBgn0001077","ftz","1062","3R"],["FBgn0004053","zen","583","3R"],["FBgn0001180","hb","746","3R"]],"statusCode":200,"wasSuccessful":true}},"transcriptionFactorResponse":{"summary":"Response for transcription factor genes","value":{"executionTime":567,"results":[["FBgn0000606","eve","even-skipped","DNA-binding transcription factor activity"],["FBgn0001077","ftz","fushi tarazu","DNA-binding transcription factor activity"],["FBgn0004053","zen","zerknüllt","DNA-binding transcription factor activity"],["FBgn0001180","hb","hunchback","DNA-binding transcription factor 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value=\"14615455\"/>\n  <constraint path=\"Gene.chromosomeLocation.end\" op=\"<\" value=\"14619002\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","size":50}},"eveGenePost":{"summary":"POST query for eve gene with JSON format","value":{"format":"jsonobjects","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\", \"symbol\", \"name\", \"proteins.primaryIdentifier\", \"proteins.proteinDomains.name\"],\n  \"where\": [\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"},\n    {\"path\": \"symbol\", \"op\": \"=\", \"value\": \"eve\"}\n  ]\n}\n","size":10}},"transcriptionFactors":{"summary":"Query for transcription factors","value":{"format":"json","query":"<query model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.goAnnotation.ontologyTerm.name\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription factor\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","size":20}}},"schema":{"properties":{"columnheaders":{"default":"none","enum":["none","path","friendly"],"type":"string"},"format":{"default":"tab","enum":["tab","csv","count","json","jsonobjects","jsoncount","xml","html","rdf+xml"],"type":"string"},"query":{"type":"string"},"size":{"default":10,"type":"integer"},"start":{"default":0,"type":"integer"},"token":{"type":"string"}},"required":["query"],"type":"object"}}}},"responses":{"200":{"description":"Query results"}},"summary":"Execute a query","tags":["query"]}},"/query/results/gff3":{"get":{"description":"Export sequence features from a query in GFF3 format. Suitable for queries\nreturning SequenceFeature objects.\n","operationId":"queryGFF3Get","parameters":[{"description":"PathQuery in XML or JSON format selecting sequence features","example":"<query model=\"genomic\" view=\"Gene.id Gene.exons.id\">\n  <constraint path=\"Gene.chromosome.primaryIdentifier\" op=\"=\" value=\"2L\"/>\n  <constraint path=\"Gene.chromosomeLocation.start\" op=\">\" value=\"10000000\"/>\n  <constraint path=\"Gene.chromosomeLocation.end\" op=\"<\" value=\"11000000\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Extra columns to include in the ninth column","example":["Gene.symbol","Gene.length"],"in":"query","name":"view","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"content":{"text/plain":{"example":"##gff-version 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]\n}\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"example":["Gene.length","Gene.chromosome.primaryIdentifier"],"in":"query","name":"view","schema":{"items":{"type":"string"},"type":"array"}}],"responses":{"200":{"content":{"text/plain":{"example":">FBgn0000606 type=gene; loc=2R:9979319..9984780; name=eve; length=5462;\nATGGAGATCAAACAAGCGAAGAGTGGAGAGAAGTGGAGAAGCAGCCAAGCAAG\nCAACAGCACAAGGGCTCGTCGAGCAAGTCCAGCGAGGAGGATCTGCTGAGCGG\n>FBgn0001077 type=gene; loc=3R:2648685..2653456; name=ftz; length=4772;\nATGGCAATGGAAGTGTCCAGCAGTCCCGTGATGGTTCATCACGTCGGTCGCTC\n","schema":{"type":"string"}}},"description":"FASTA formatted sequences"}},"summary":"Export sequences as FASTA","tags":["query","export"]}},"/query/results/bed":{"get":{"description":"Export genomic locations from a query in UCSC BED format.\n","operationId":"queryBEDGet","parameters":[{"description":"PathQuery selecting sequence features","example":"<query model=\"genomic\" view=\"Gene.id\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"=\" value=\"wing disc development\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"example":"# UCSC BED format\n# Source: FlyMine\ntrack name=FlyMine_Wing_Development description=\"Wing Development Genes\"\nchr2L\t7529\t9484\tCG11023\t1000\t+\nchr2R\t9979319\t9984780\teve\t1000\t-\nchrX\t2648220\t2653456\trunt\t1000\t+\n","schema":{"type":"string"}}},"description":"BED formatted results"}},"summary":"Export genomic locations as BED","tags":["query","export"]}},"/template/results":{"get":{"description":"Execute a pre-configured template query with parameters.\n","operationId":"templateResults","parameters":[{"description":"The name of the template to run","examples":{"flyAtlas":{"summary":"Template for FlyAtlas expression","value":"Gene_AdultFlyAtlas"},"genePathways":{"summary":"Template for gene pathways","value":"Gene_Pathways"},"proteinDomains":{"summary":"Template for gene protein domains","value":"Gene_Protein"}},"in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Constraint path for parameter 1","examples":{"geneConstraint":{"summary":"Gene constraint","value":"Gene"},"geneSymbol":{"summary":"Gene symbol constraint","value":"Gene.symbol"}},"in":"query","name":"constraint1","schema":{"type":"string"}},{"description":"Constraint operator for parameter 1","examples":{"equals":{"summary":"Equals operator","value":"="},"lookup":{"summary":"Lookup operator","value":"LOOKUP"}},"in":"query","name":"op1","schema":{"type":"string"}},{"description":"Constraint value for parameter 1","examples":{"eveGene":{"summary":"even-skipped gene","value":"eve"},"ftzGene":{"summary":"fushi tarazu gene","value":"ftz"},"hbGene":{"summary":"hunchback 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transcription factors","value":"transcription factor"},"winglessPathway":{"summary":"Search for wingless/Wnt pathway","value":"wingless wnt"}},"in":"query","name":"q","schema":{"type":"string"}},{"description":"Maximum number of results","example":20,"in":"query","name":"size","schema":{"default":10,"type":"integer"}},{"description":"Index of first result","in":"query","name":"start","schema":{"default":0,"type":"integer"}},{"description":"Filter by category facet","example":"Gene","in":"query","name":"facet_Category","schema":{"type":"string"}},{"description":"Search within a specific list","example":"PL_FlyBase_IDs","in":"query","name":"list","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"examples":{"developmentalGenesSearch":{"summary":"Search results for developmental genes","value":{"facets":{"Category":{"GOTerm":45,"Gene":5,"Publication":1234},"organism":{"D. 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3\n2R\tFlyMine\tgene\t5865334\t5873117\t.\t+\t.\tID=FBgn0000606;Name=eve;symbol=eve;biotype=protein_coding\n2R\tFlyMine\tmRNA\t5865334\t5873117\t.\t+\t.\tID=FBtr0070607;Parent=FBgn0000606;Name=eve-RA\n2R\tFlyMine\texon\t5865334\t5865475\t.\t+\t.\tID=FBgn0000606:1;Parent=FBtr0070607\n2R\tFlyMine\texon\t5866646\t5868384\t.\t+\t.\tID=FBgn0000606:2;Parent=FBtr0070607\n2R\tFlyMine\texon\t5872855\t5873117\t.\t+\t.\tID=FBgn0000606:3;Parent=FBtr0070607\n"},"originalRegionsGFF3":{"summary":"GFF3 output for original genomic regions","value":"##gff-version 3\n2L\tFlyMine\tgene\t14615552\t14618902\t.\t+\t.\tID=FBgn0000055;Name=Adh;symbol=Adh;biotype=protein_coding\n2L\tFlyMine\tmRNA\t14615552\t14618902\t.\t+\t.\tID=FBtr0070000;Parent=FBgn0000055;Name=Adh-RA\n2L\tFlyMine\texon\t14615552\t14615700\t.\t+\t.\tID=FBgn0000055:1;Parent=FBtr0070000\n2L\tFlyMine\texon\t14616300\t14618902\t.\t+\t.\tID=FBgn0000055:2;Parent=FBtr0070000\n"}}}},"description":"GFF3 formatted features"}},"summary":"Get features overlapping genomic regions as GFF3","tags":["genomic-regions","export"]}},"/regions/sequence":{"post":{"operationId":"regionsFASTAPost","requestBody":{"content":{"application/json":{"examples":{"eveGeneSequence":{"summary":"Sequences from eve gene region","value":{"featureTypes":["Gene","Exon","CDS"],"organism":"D. melanogaster","regions":["2R:5865334..5873117"]}},"multipleChromosomeSequences":{"summary":"Sequences from multiple chromosomes","value":{"featureTypes":["Gene"],"organism":"D. melanogaster","regions":["2L:14615455..14619002","3R:2578486..2580016","X:1000000..1002000"]}},"xChromosomeSequences":{"summary":"Sequences from X chromosome regions","value":{"featureTypes":["Gene","CDS"],"organism":"D. 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X:15001000-15003500 symbol=Notch length=2501\nATGCCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGA\nTCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCGATCG\n"}}}},"description":"FASTA formatted sequences"}},"summary":"Get sequences from genomic regions as FASTA","tags":["genomic-regions","export"]}},"/regions/bed":{"post":{"operationId":"regionsBEDPost","requestBody":{"content":{"application/json":{"example":{"featureTypes":["Gene","TransposableElement"],"organism":"D. melanogaster","regions":["2L:10000000..11000000","2R:5000000..6000000"]},"schema":{"properties":{"featureTypes":{"items":{"type":"string"},"type":"array"},"organism":{"type":"string"},"regions":{"items":{"type":"string"},"type":"array"}},"required":["regions","featureTypes","organism"],"type":"object"}}},"required":true},"responses":{"200":{"content":{"text/plain":{"example":"track name=FlyMine_Regions description=\"Selected genomic regions\"\nchr2L\t10234567\t10245678\tCG11023\t1000\t+\nchr2L\t10456789\t10467890\tCG2187\t1000\t-\nchr2R\t5234567\t5245678\t1360{}1224\t500\t+\n"}},"description":"BED formatted features"}},"summary":"Get features overlapping genomic regions as BED","tags":["genomic-regions","export"]}},"/model":{"get":{"description":"Retrieve the FlyMine data model\n","operationId":"getModel","parameters":[{"description":"Output 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The query must return\nobjects of a single type that can be stored in a list.\n","operationId":"queryToListGet","parameters":[{"description":"PathQuery in XML or JSON format","example":"<query model=\"genomic\" view=\"Gene.primaryIdentifier\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"transcription\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Name for the new list (must be unique)","example":"Transcription_Factors_Query","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Description for the new list","example":"Genes involved in transcription regulation","in":"query","name":"description","schema":{"type":"string"}},{"description":"Tags to categorize the list","example":["gene-function","transcription"],"in":"query","name":"tags","schema":{"items":{"type":"string"},"type":"array"}},{"description":"Whether to replace existing list with same name","in":"query","name":"replaceExisting","schema":{"default":false,"type":"boolean"}},{"description":"Authentication token","in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"executionTime":876,"listName":"Transcription_Factors_Query","size":234,"type":"Gene","wasSuccessful":true},"schema":{"properties":{"executionTime":{"type":"integer"},"listName":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"List created from query results"}},"summary":"Save query results as a list","tags":["query","list"]},"post":{"description":"Execute a query and save the results as a new list using POST method.\n","operationId":"queryToListPost","requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Genes in hedgehog signaling pathway","name":"Hedgehog_Pathway_Genes","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"primaryIdentifier\"],\n  \"where\": [\n    {\"path\": \"pathways.name\", \"op\": \"CONTAINS\", \"value\": \"hedgehog\"},\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"}\n  ]\n}\n","tags":["pathway","signaling"]},"schema":{"properties":{"description":{"description":"Description for the new list","type":"string"},"name":{"description":"Name for the new list","type":"string"},"query":{"description":"PathQuery in XML or JSON format","type":"string"},"replaceExisting":{"default":false,"description":"Whether to replace existing list","type":"boolean"},"tags":{"description":"Tags to categorize the list","items":{"type":"string"},"type":"array"},"token":{"description":"Authentication token","type":"string"}},"required":["query","name"],"type":"object"}}}},"responses":{"200":{"description":"List created from query results"}},"summary":"Save query results as a list","tags":["query","list"]}},"/lists/append":{"post":{"description":"Add items to an existing list by providing identifiers. 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data","tags":["export"]}},"/summaryfields":{"get":{"description":"Get the fields used to summarize each class in the data model.\nSummary fields are the key attributes displayed in search results and object summaries.\n","operationId":"getSummaryFields","parameters":[{"description":"Whether to exclude reference fields from summary","in":"query","name":"norefs","schema":{"default":false,"type":"boolean"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"classes":{"Gene":["primaryIdentifier","symbol","name","organism.name"],"Protein":["primaryIdentifier","name","organism.name"],"Publication":["firstAuthor","title","year","journal"]}},"schema":{"properties":{"classes":{"additionalProperties":{"items":{"type":"string"},"type":"array"},"type":"object"}},"type":"object"}}},"description":"Summary fields for all classes"}},"summary":"Get summary fields for classes","tags":["model"]}},"/path/values":{"get":{"description":"Get possible values for a given path in the data model. Useful for auto-complete\nand discovering valid constraint values for queries.\n","operationId":"getPathValues","parameters":[{"description":"Path in the data model (e.g., Gene.symbol, Organism.name)","example":"Gene.organism.name","in":"query","name":"path","required":true,"schema":{"type":"string"}},{"description":"JSON object with type constraints","example":"{\"Gene\": \"SequenceFeature\"}","in":"query","name":"typeConstraints","schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"results":[{"count":35807,"value":"Drosophila melanogaster"},{"count":15420,"value":"Drosophila simulans"},{"count":14520,"value":"Drosophila pseudoobscura"}]},"schema":{"properties":{"results":{"items":{"properties":{"count":{"type":"integer"},"value":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"List of possible values"}},"summary":"Get possible values for a path","tags":["model"]}},"/classkeys":{"get":{"description":"Get the keys used to uniquely identify objects of each class in the data model.\nThese keys are used for object lookups and deduplication.\n","operationId":"getClassKeys","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"classes":{"Gene":[["primaryIdentifier"],["symbol","organism.name"],["name","organism.name"]],"Protein":[["primaryIdentifier"],["primaryAccession"],["name","organism.name"]],"Publication":[["pubMedId"],["doi"]]}},"schema":{"properties":{"classes":{"additionalProperties":{"items":{"items":{"type":"string"},"type":"array"},"type":"array"},"type":"object"}},"type":"object"}}},"description":"Class keys for all classes"}},"summary":"Get class keys","tags":["model"]}},"/web-properties":{"get":{"description":"Get configuration properties for the web application interface, including\nsettings for display, behavior, and available features.\n","operationId":"getWebProperties","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"properties":{"externallink.flybase.url":"http://flybase.org/reports/<<attributeValue>>.html","externallink.uniprot.url":"https://www.uniprot.org/uniprot/<<attributeValue>>","project.contact":"support@flymine.org","project.releaseVersion":"52.0","project.subTitle":"An integrated database for Drosophila and Anopheles genomics","project.title":"FlyMine","webapp.listchooser.size":"10","webapp.max.bag.size":"100000"}},"schema":{"properties":{"properties":{"additionalProperties":{"type":"string"},"type":"object"}},"type":"object"}}},"description":"Web application properties"}},"summary":"Get web application properties","tags":["model"]}},"/query/append/tolist":{"post":{"description":"Execute a query and append the results to an existing list. The query must return\nobjects of the same type as the target list.\n","operationId":"queryAppendToList","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"listName":"Signaling_Genes","query":"<query model=\"genomic\" view=\"Gene.primaryIdentifier\">\n  <constraint path=\"Gene.pathways.name\" op=\"CONTAINS\" value=\"insulin\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n</query>\n"},"schema":{"properties":{"listName":{"description":"Name of the existing list to append to","type":"string"},"query":{"description":"PathQuery in XML or JSON format","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["query","listName"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"added":23,"duplicates":5,"listName":"Signaling_Genes","newSize":467,"wasSuccessful":true},"schema":{"properties":{"added":{"type":"integer"},"duplicates":{"type":"integer"},"listName":{"type":"string"},"newSize":{"type":"integer"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Query results appended to list"}},"summary":"Append query results to existing list","tags":["query","list"]}},"/list/tags":{"delete":{"description":"Remove one or more tags from an existing list.\n","operationId":"removeListTags","parameters":[{"description":"Name of the list","example":"Gap_Genes","in":"query","name":"name","required":true,"schema":{"type":"string"}},{"description":"Semicolon-separated list of tags to remove","example":"old;deprecated","in":"query","name":"tags","required":true,"schema":{"type":"string"}},{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"Tags removed successfully"}},"summary":"Remove tags from a list","tags":["list"]},"get":{"description":"Get all tags used across lists in the system. Tags help organize and categorize lists.\n","operationId":"getListTags","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml","text"],"type":"string"}},{"description":"Authentication token for private tags","in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"tags":[{"count":142,"tagName":"im:public"},{"count":67,"tagName":"im:aspect:Genes"},{"count":23,"tagName":"development"},{"count":18,"tagName":"signaling"},{"count":12,"tagName":"transcription"}]},"schema":{"properties":{"tags":{"items":{"properties":{"count":{"type":"integer"},"tagName":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"Available list tags"}},"summary":"Get available list tags","tags":["list"]},"post":{"description":"Add one or more tags to an existing list to help with organization and discovery.\n","operationId":"addListTags","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"name":"Gap_Genes","tags":"development;segmentation;maternal"},"schema":{"properties":{"name":{"description":"Name of the list to tag","type":"string"},"tags":{"description":"Semicolon-separated list of tags to add","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["name","tags"],"type":"object"}}}},"responses":{"200":{"description":"Tags added successfully"}},"summary":"Add tags to a list","tags":["list"]}},"/lists/rename":{"post":{"description":"Rename an existing list. The list must belong to the authenticated user.\n","operationId":"renameList","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"newname":"Validated_Gap_Genes","oldname":"My_Test_Genes"},"schema":{"properties":{"newname":{"description":"New name for the list (must be unique)","type":"string"},"oldname":{"description":"Current name of the list","type":"string"},"token":{"description":"Authentication token","type":"string"}},"required":["oldname","newname"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"newname":"Validated_Gap_Genes","oldname":"My_Test_Genes","wasSuccessful":true},"schema":{"properties":{"newname":{"type":"string"},"oldname":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"List renamed successfully"},"400":{"description":"List not found or name already exists"}},"summary":"Rename a list","tags":["list"]}},"/user/preferences":{"get":{"description":"Retrieve user preferences and settings.\n","operationId":"getUserPreferences","parameters":[{"description":"Authentication token","in":"query","name":"token","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"preferences":{"default-query-format":"json","do_not_spam":"true","email-notifications":"false","galaxy-url":"https://usegalaxy.org/"}},"schema":{"properties":{"preferences":{"additionalProperties":{"type":"string"},"type":"object"}},"type":"object"}}},"description":"User preferences"},"401":{"description":"Authentication required"}},"security":[{"tokenAuth":[]}],"summary":"Get user preferences","tags":["user"]},"post":{"description":"Update user preferences and settings.\n","operationId":"setUserPreferences","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"key":"do_not_spam","value":"false"},"schema":{"properties":{"key":{"description":"Preference key to update","type":"string"},"value":{"description":"New preference value","type":"string"}},"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"message":"Preference updated successfully","wasSuccessful":true},"schema":{"properties":{"message":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Preference updated successfully"}},"security":[{"tokenAuth":[]}],"summary":"Update user preferences","tags":["user"]}},"/facets":{"get":{"description":"Get available facets for search results. Facets provide categorized counts\nof search results for filtering and navigation.\n","operationId":"getFacets","parameters":[{"description":"Search query string","example":"transcription factor","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"facets":{"Category":{"Gene":234,"Protein":89,"Publication":567},"Organism":{"D. melanogaster":456,"D. simulans":123}}},"schema":{"properties":{"facets":{"additionalProperties":{"type":"object"},"type":"object"}},"type":"object"}}},"description":"Available facets"}},"summary":"Get search facets","tags":["search"]}},"/list/chart":{"get":{"description":"Generate chart data for visualization widgets based on list contents.\nDifferent widget types provide different chart visualizations.\n","operationId":"listChart","parameters":[{"description":"Name of the list to analyze","example":"PL FlyTF_site_specific_TFs","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"description":"Name of the chart widget","example":"flyatlas_for_gene","in":"query","name":"widget","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"results":{"chartData":{"datasets":[{"data":[45.2,67.8,23.1,34.5],"label":"Expression Level"}],"labels":["Brain","Eye","Wing","Leg"]},"chartType":"BarChart"}},"schema":{"properties":{"results":{"type":"object"}},"type":"object"}}},"description":"Chart data"}},"summary":"Get chart widget data for a list","tags":["widget","list"]}},"/list/table":{"get":{"description":"Generate tabular data for table widgets based on list contents.\nProvides structured data for display in table format.\n","operationId":"listTable","parameters":[{"description":"Name of the list","example":"Gap_Genes","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"description":"Name of the table widget","example":"interactions_for_gene","in":"query","name":"widget","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml","tsv","csv"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"results":[{"confidence":"high","gene1":"eve","gene2":"ftz","type":"genetic"},{"confidence":"medium","gene1":"eve","gene2":"hb","type":"physical"}]},"schema":{"properties":{"results":{"items":{"type":"object"},"type":"array"}},"type":"object"}}},"description":"Table data"}},"summary":"Get table widget data for a list","tags":["widget","list"]}},"/query/upload":{"post":{"description":"Upload a saved query in XML or JSON format and execute it.\nUseful for running complex saved queries.\n","operationId":"queryUpload","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml","tsv","csv"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"example":{"from":"Gene","select":["primaryIdentifier","symbol","length"],"where":[{"op":"CONTAINS","path":"goAnnotation.ontologyTerm.name","value":"DNA binding"},{"op":"=","path":"organism.name","value":"Drosophila melanogaster"}]},"schema":{"type":"object"}},"application/xml":{"example":"<query name=\"Complex Gene Query\" model=\"genomic\" view=\"Gene.primaryIdentifier Gene.symbol Gene.length\">\n  <constraint path=\"Gene.goAnnotation.ontologyTerm.name\" op=\"CONTAINS\" value=\"DNA binding\"/>\n  <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n  <constraint path=\"Gene.length\" op=\">\" value=\"1000\"/>\n  <constraint path=\"Gene.length\" op=\"<\" value=\"10000\"/>\n</query>\n","schema":{"format":"xml","type":"string"}}},"required":true},"responses":{"200":{"description":"Query results"}},"summary":"Upload and execute a saved query","tags":["query"]}},"/template/tags":{"get":{"description":"Get all tags used for categorizing and organizing templates.\n","operationId":"getTemplateTags","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"tags":["im:aspect:Genomics","im:aspect:Proteins","im:aspect:Function","im:aspect:Homology","im:aspect:Publications","im:frontpage","im:converter"]},"schema":{"properties":{"tags":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Template tags"}},"summary":"Get template tags","tags":["template"]}},"/template/tolist":{"post":{"description":"Execute a template query and save the results as a new list.\n","operationId":"templateToList","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"constraint1":"Gene.pathways.name","description":"Genes in hedgehog signaling pathway","extra1":"D. melanogaster","listName":"Hedgehog_Pathway_Genes_List","name":"Gene_Pathways","op1":"CONTAINS","value1":"hedgehog"},"schema":{"properties":{"constraint1":{"type":"string"},"description":{"type":"string"},"extra1":{"type":"string"},"listName":{"description":"Name for the new list","type":"string"},"name":{"description":"Name of the template to execute","type":"string"},"op1":{"type":"string"},"tags":{"items":{"type":"string"},"type":"array"},"token":{"type":"string"},"value1":{"type":"string"}},"required":["name","listName"],"type":"object"}}}},"responses":{"200":{"content":{"application/json":{"example":{"listName":"Hedgehog_Pathway_Genes_List","size":42,"type":"Gene"},"schema":{"properties":{"listName":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"}},"type":"object"}}},"description":"List created from template results"}},"summary":"Save template results as list","tags":["template","list"]}},"/query/code":{"get":{"description":"Generate client code in various programming languages for executing a query.\nUseful for integrating FlyMine queries into custom applications.\n","operationId":"queryCode","parameters":[{"description":"PathQuery in XML or JSON format","example":"<query model=\"genomic\" view=\"Gene.symbol Gene.primaryIdentifier\">\n  <constraint path=\"Gene.symbol\" op=\"=\" value=\"eve\"/>\n</query>\n","in":"query","name":"query","required":true,"schema":{"type":"string"}},{"description":"Target programming language","example":"python","in":"query","name":"lang","required":true,"schema":{"enum":["python","perl","java","ruby","javascript","curl"],"type":"string"}}],"responses":{"200":{"content":{"text/plain":{"example":"#!/usr/bin/env python\n\nfrom intermine.webservice import Service\n\nservice = Service(\"https://www.flymine.org/flymine/service\")\nquery = service.new_query(\"Gene\")\nquery.add_view(\"symbol\", \"primaryIdentifier\")\nquery.add_constraint(\"symbol\", \"=\", \"eve\")\n\nfor row in query:\n    print(row[\"symbol\"], row[\"primaryIdentifier\"])\n","schema":{"type":"string"}}},"description":"Generated code"}},"summary":"Generate code for a query","tags":["query"]}},"/facet-list":{"get":{"description":"Get faceted search results for items in a specific list.\n","operationId":"getFacetList","parameters":[{"description":"Name of the list","example":"PL FlyBase_Annotation_IDs","in":"query","name":"list","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"description":"Faceted list data"}},"summary":"Get facets for a list","tags":["search"]}},"/user/queries":{"get":{"description":"Get all saved queries for the authenticated user.\n","operationId":"getUserQueries","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"queries":[{"created":"2023-10-15T14:30:00Z","description":"Transcription factors with DNA binding","name":"My_TF_Search"},{"created":"2023-10-20T09:15:00Z","description":"Genes involved in wing morphogenesis","name":"Wing_Development_Genes"}]},"schema":{"properties":{"queries":{"items":{"properties":{"created":{"format":"date-time","type":"string"},"description":{"type":"string"},"name":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"User's saved queries"}},"security":[{"tokenAuth":[]}],"summary":"Get saved queries","tags":["user","query"]},"post":{"description":"Save a query for later use by the authenticated user.\n","operationId":"saveUserQuery","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/x-www-form-urlencoded":{"example":{"description":"Genes involved in neural development","name":"Neural_Genes","query":"{\n  \"from\": \"Gene\",\n  \"select\": [\"symbol\", \"primaryIdentifier\"],\n  \"where\": [\n    {\"path\": \"goAnnotation.ontologyTerm.name\", \"op\": \"CONTAINS\", \"value\": \"neural\"},\n    {\"path\": \"organism.name\", \"op\": \"=\", \"value\": \"Drosophila melanogaster\"}\n  ]\n}\n"},"schema":{"properties":{"description":{"type":"string"},"name":{"description":"Name for the saved query","type":"string"},"query":{"description":"Query in XML or JSON format","type":"string"},"token":{"type":"string"}},"required":["name","query"],"type":"object"}}}},"responses":{"200":{"description":"Query saved successfully"}},"security":[{"tokenAuth":[]}],"summary":"Save a query","tags":["user","query"]}},"/branding":{"get":{"description":"Get branding and customization information for the FlyMine instance,\nincluding colors, logos, and project information.\n","operationId":"getBranding","responses":{"200":{"content":{"application/json":{"example":{"properties":{"logos":{"favicon":"/images/favicon.ico","header":"/images/logo.png"},"project":{"description":"An integrated database for Drosophila and Anopheles genomics","name":"FlyMine","version":"52.0"},"theme":{"primaryColor":"#00539F","secondaryColor":"#FF6600"}}},"schema":{"properties":{"properties":{"type":"object"}},"type":"object"}}},"description":"Branding information"}},"summary":"Get branding information","tags":["model"]}},"/bluegenes-properties":{"get":{"description":"Get configuration properties for the BlueGenes user interface.\nBlueGenes is the modern web interface for InterMine databases.\n","operationId":"getBlueGenesProperties","responses":{"200":{"content":{"application/json":{"example":{"properties":{"listWidgets":["go_enrichment","pathway_enrichment"],"mineName":"FlyMine","reportWidgets":["ProteinAtlasExpression","FlyAtlas","Publications"],"toolsPath":"/tools"}},"schema":{"properties":{"properties":{"type":"object"}},"type":"object"}}},"description":"BlueGenes configuration"}},"summary":"Get BlueGenes properties","tags":["model"]}},"/lists/jaccard-index":{"get":{"description":"Calculate the Jaccard similarity coefficient between two lists.\nThe Jaccard index measures similarity as the size of the intersection\ndivided by the size of the union of the lists.\n","operationId":"listsJaccardIndex","parameters":[{"description":"Semicolon-separated list names to compare","example":"Gap_Genes;Hox_Genes","in":"query","name":"lists","required":true,"schema":{"type":"string"}},{"in":"query","name":"token","schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"intersection":2,"jaccardIndex":0.125,"list1Size":9,"list2Size":9,"union":16},"schema":{"properties":{"intersection":{"type":"integer"},"jaccardIndex":{"maximum":1,"minimum":0,"type":"number"},"list1Size":{"type":"integer"},"list2Size":{"type":"integer"},"union":{"type":"integer"}},"type":"object"}}},"description":"Jaccard similarity coefficient"}},"summary":"Calculate Jaccard index between lists","tags":["list"]}},"/listswithobject":{"get":{"description":"Find all lists that contain a specific object identified by its database ID.\nUseful for discovering which lists include a particular gene or other entity.\n","operationId":"listsWithObject","parameters":[{"description":"Database ID of the object","example":1007656,"in":"query","name":"id","required":true,"schema":{"type":"integer"}},{"in":"query","name":"token","schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"lists":[{"description":"Drosophila gap genes","name":"Gap_Genes","size":9,"type":"Gene"},{"description":"All segmentation genes","name":"Segmentation_Genes","size":45,"type":"Gene"}]},"schema":{"properties":{"lists":{"items":{"properties":{"description":{"type":"string"},"name":{"type":"string"},"size":{"type":"integer"},"type":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"Lists containing the object"}},"summary":"Find lists containing an object","tags":["list"]}},"/schema":{"get":{"description":"Get schema definitions for the API, including available schemas for\nqueries, templates, and other API components.\n","operationId":"getSchema","parameters":[{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"schemas":[{"description":"XML Schema for PathQuery format","name":"query.xsd","url":"/schema/query.xsd"},{"description":"XML Schema for template queries","name":"template.xsd","url":"/schema/template.xsd"}]},"schema":{"properties":{"schemas":{"items":{"properties":{"description":{"type":"string"},"name":{"type":"string"},"url":{"type":"string"}},"type":"object"},"type":"array"}},"type":"object"}}},"description":"Available schemas"}},"summary":"Get API schema information","tags":["model"]}},"/template/upload":{"post":{"description":"Upload a new template query for reuse. Templates are pre-configured\nqueries with parameters that can be easily executed with different values.\n","operationId":"templateUpload","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"example":{"description":"Find all genes in a specified pathway","name":"Genes_In_Pathway","query":{"from":"Gene","select":["symbol","primaryIdentifier","pathways.name"],"where":[{"description":"Pathway name","editable":true,"op":"=","path":"pathways.name","value":""},{"op":"=","path":"organism.name","value":"Drosophila melanogaster"}]},"title":"Genes in a specific pathway"},"schema":{"type":"object"}},"application/xml":{"example":"<template name=\"Genes_In_Pathway\" title=\"Genes in a specific pathway\">\n  <query model=\"genomic\" view=\"Gene.symbol Gene.primaryIdentifier Gene.pathways.name\">\n    <constraint path=\"Gene.pathways.name\" op=\"=\" value=\"\" editable=\"true\" description=\"Pathway name\"/>\n    <constraint path=\"Gene.organism.name\" op=\"=\" value=\"Drosophila melanogaster\"/>\n  </query>\n</template>\n","schema":{"format":"xml","type":"string"}}},"required":true},"responses":{"200":{"content":{"application/json":{"example":{"templateName":"Genes_In_Pathway","wasSuccessful":true},"schema":{"properties":{"templateName":{"type":"string"},"wasSuccessful":{"type":"boolean"}},"type":"object"}}},"description":"Template uploaded successfully"}},"security":[{"tokenAuth":[]}],"summary":"Upload a template","tags":["template"]}},"/user":{"get":{"description":"Get detailed information about the authenticated user's account,\nincluding profile, preferences, and usage statistics.\n","operationId":"getUserInfo","parameters":[{"in":"query","name":"token","required":true,"schema":{"type":"string"}},{"in":"query","name":"format","schema":{"default":"json","enum":["json","xml"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"example":{"user":{"email":"researcher@university.edu","id":123456,"isGuest":false,"isSuperuser":false,"lists":42,"profile":{"interests":["genomics","development","evolution"],"organization":"University Research Lab"},"queries":156,"templates":8,"username":"researcher@university.edu"}},"schema":{"properties":{"user":{"properties":{"email":{"type":"string"},"id":{"type":"integer"},"isGuest":{"type":"boolean"},"isSuperuser":{"type":"boolean"},"lists":{"type":"integer"},"profile":{"type":"object"},"queries":{"type":"integer"},"templates":{"type":"integer"},"username":{"type":"string"}},"type":"object"}},"type":"object"}}},"description":"User account information"}},"security":[{"tokenAuth":[]}],"summary":"Get user account information","tags":["user"]}}},"security":[{},{"tokenAuth":[]}],"servers":[{"description":"FlyMine production server","url":"https://www.flymine.org/flymine/service"}],"tags":[{"description":"Query operations for retrieving genomic data","name":"query"},{"description":"Pre-configured query templates","name":"template"},{"description":"List management operations","name":"list"},{"description":"Search operations","name":"search"},{"description":"Data export in specialized formats","name":"export"},{"description":"Genomic interval operations","name":"genomic-regions"},{"description":"User account and authentication","name":"user"},{"description":"Data model operations","name":"model"},{"description":"Data visualization widgets","name":"widget"},{"description":"Identifier resolution services","name":"id-resolution"}],"x-externalResources":[{"x-description":"FlyMine homepage","x-type":"website","x-url":"https://www.flymine.org/flymine/"},{"x-description":"InterMine web services documentation","x-type":"documentation","x-url":"http://intermine.org/im-docs/docs/web-services/"},{"x-description":"FlyMine source code 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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"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information.","type":"boolean"},"callback":{"description":"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.","format":"uri","nullable":false,"pattern":"^https?://","type":"string"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["callback","message"],"type":"object","x-body-name":"request_body"},"AsyncQueryResponse":{"additionalProperties":true,"description":"The AsyncQueryResponse object contains a payload that must be returned from a submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the result of the async_query submission.","example":"Async_query has been queued","nullable":true,"type":"string"},"job_id":{"description":"An identifier for the submitted job that can be used with /async_query_status to receive an update on the status of the job.","example":"rXEOAosN3L","nullable":false,"type":"string"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"type":"object"},"AsyncQueryStatusResponse":{"additionalProperties":true,"description":"The AsyncQueryStatusResponse object contains a payload that describes the current status of a previously submitted async_query.","properties":{"description":{"description":"A brief human-readable description of the current state or summary of the problem if the status is Failed.","example":"Callback URL returned 500","nullable":false,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first. The most recent entry should be last. Its timestamp will be compared against the current time to see if there is still activity.","items":{"$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":"CURIE identifier for this node","example":["OMIM:603903"],"items":{"$ref":"#/components/schemas/CURIE"},"minItems":1,"nullable":true,"type":"array"},"set_interpretation":{"description":"Indicates how multiple CURIEs in the ids property MUST be interpreted. BATCH indicates that the query is intended to be a batch query and each CURIE is treated independently. ALL means that all specified CURIES MUST appear in each Result. MANY means that member CURIEs MUST form one or more sets in the Results, and sets with more members are generally considered more desirable that sets with fewer members. If this property is missing or null, the default is BATCH.","enum":["BATCH","ALL","MANY"],"nullable":true,"type":"string"}},"type":"object"},"Qualifier":{"additionalProperties":false,"description":"An additional nuance attached to an assertion","properties":{"qualifier_type_id":{"$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.","type":"boolean"},"log_level":{"description":"The least critical level of logs to return","nullable":true,"oneOf":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$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":{"$ref":"#/components/schemas/QNode"},"description":"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.","type":"object"}},"required":["nodes","edges"],"type":"object"},"ResourceRoleEnum":{"description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.  This enumeration is found in Biolink Model, but is repeated here for convenience.","enum":["primary_knowledge_source","aggregator_knowledge_source","supporting_data_source"],"type":"string"},"Response":{"additionalProperties":true,"description":"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.","properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","nullable":true,"type":"string"},"description":{"description":"A brief human-readable description of the outcome","example":"Success. 42 results found.","nullable":true,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":0,"nullable":false,"type":"array"},"message":{"description":"Contains the knowledge of the response (query graph, knowledge graph, and results).","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"schema_version":{"description":"Version label of the TRAPI schema used in this document","example":"1.4.0","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable","example":"Success","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps that were executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object"},"Result":{"additionalProperties":true,"description":"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and a list of Analysis objects.","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"minItems":0,"nullable":false,"type":"array"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"minItems":1,"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.","nullable":false,"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"},"nullable":true,"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":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"}},"required":["resource_id","resource_role"],"type":"object"}}},"externalDocs":{"description":"Documentation for the NCATS Biomedical Translator Reasoners web services","url":"https://github.com/NCATSTranslator/ReasonerAPI"},"info":{"contact":{"email":"brett.smith@isbscience.org"},"description":"SPOKE KP for TRAPI 1.5 - an NIH NCATS Knowledge Provider exposing UCSF's SPOKE","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://spoke.rbvi.ucsf.edu/license.html","title":"SPOKE KP for TRAPI 1.5","version":"1.5.0","x-translator":{"biolink-version":"4.1.4","component":"KP","externalDocs":{"description":"Repository","url":"https://github.com/suihuanglab/spoke-kp"},"infores":"infores:spoke","team":["imProving Agent"]},"x-trapi":{"asyncquery":false,"batch_size_limit":200,"operations":["lookup"],"rate_limit":20,"test_data_location":{"default":{"url":"https://github.com/suihuanglab/spoke-kp/tree/main/test-data"}},"version":"1.5.0"}},"openapi":"3.0.1","paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$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"]}},"/query":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n00\": {\n          \"ids\": [\"DOID:1681\"],\n          \"categories\": [\"biolink:Disease\"]\n        },\n        \"n01\": {\n          \"categories\": [\"biolink:Gene\"]\n        }\n      },\n      \"edges\": {\n        \"e00\": {\n          \"subject\": \"n00\",\n          \"object\": \"n01\"\n        }\n      }\n    }\n  }\n}","schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"]}},"/asyncquery":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n00\": {\n          \"ids\": [\"DOID:1681\"],\n          \"categories\": [\"biolink:Disease\"]\n        },\n        \"n01\": {\n          \"categories\": [\"biolink:Gene\"]\n        }\n      },\n      \"edges\": {\n        \"e00\": {\n          \"subject\": \"n00\",\n          \"object\": \"n01\"\n        }\n      }\n    }\n  }\n}","schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","example":"rXEOAosN3L","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"ITRB Production server","url":"https://spokekp.transltr.io/api/v1.5/","x-maturity":"production"},{"description":"ITRB Test server","url":"https://spokekp.test.transltr.io/api/v1.5/","x-maturity":"testing"},{"description":"ITRB CI server","url":"https://spokekp.ci.transltr.io/api/v1.5/","x-maturity":"staging"},{"description":"dev","url":"https://spokekp.healthdatascience.cloud/api/v1.5/","x-maturity":"development"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Initiate a query with a callback to receive the response","name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]},{"components":{"requestBodies":{"resource_createData":{"content":{"application/json":{"schema":{"properties":{"bag_url":{"description":"","type":"string"},"coverages":{"description":"","type":"string"},"creator":{"description":"","type":"string"},"date_created":{"description":"","type":"string"},"date_last_updated":{"description":"","type":"string"},"discoverable":{"description":"","type":"boolean"},"immutable":{"description":"","type":"boolean"},"public":{"description":"","type":"boolean"},"published":{"description":"","type":"boolean"},"resource_id":{"description":"","type":"string"},"resource_map_url":{"description":"","type":"string"},"resource_title":{"description":"","type":"string"},"resource_type":{"description":"","type":"string"},"resource_url":{"description":"","type":"string"},"science_metadata_url":{"description":"","type":"string"},"shareable":{"description":"","type":"boolean"}},"required":["resource_type","resource_title","resource_id","creator","date_created","date_last_updated","public","discoverable","shareable","immutable","published","bag_url","science_metadata_url","resource_map_url","resource_url"],"type":"object"}}}}},"securitySchemes":{"basic":{"scheme":"basic","type":"http"}}},"info":{"contact":{"email":"hongyi@renci.org","name":"Hong Yi"},"description":"A web interface and web service API for sharing data and running workflows on data in a cloud-agnostic environment.","termsOfService":"https://helx.commonsshare.org/terms-of-use/","title":"CommonsShare API","version":"0.1.2"},"openapi":"3.0.0","paths":{"/django_irods/rest_download/{path}":{"get":{"description":"download a resource bag or file\n:param request:\n:param path:\n:param args:\n:param kwargs:\n:return:","operationId":"rest_download_read","parameters":[{"description":"","in":"path","name":"path","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"download a resource bag or file","tags":["django_irods"]}},"/dosapi/dataobjects/":{"get":{"description":"Get a list of data objects based on the following filter query parameters\n\nREST URL: dosapi/dataobjects/\nHTTP method: GET\n\nSupported query parameters (all are optional):\n\n:type   owner: str\n:type   from_date:  str (e.g., 2015-04-01)\n:type   to_date:    str (e.g., 2015-05-01)\n:param  owner: (optional) - to get a list of resources owned by a specified username\n:param  from_date: (optional) - to get a list of resources created on or after this date\n:param  to_date: (optional) - to get a list of resources created on or before this date\n:rtype:  json string\n:return:  a paginated list of resources with data for resource id, title, resource type,\ncreator, public, date created, date last updated, resource bag url path, and science\nmetadata url path\n\nexample return JSON format for GET /dosapi/dataobjects/:\n\n{   \"count\":n\n\"next\": link to next page\n\"previous\": link to previous page\n\"results\":[\n{\"resource_id\": resource id,\n\"date_last_updated\": date resource last updated,\n\"public\": true or false,\n\"resource_url\": link to resource landing HTML page,\n]\n}","operationId":"dataobjects_list","parameters":[{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a list of data objects based on the following filter query parameters","tags":["dosapi"]}},"/dosapi/dataobjects/{id}/":{"get":{"description":"Get a dataobject in json format\n:param request:\n:param pk:\n:return:","operationId":"dataobjects_read","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a dataobject in json format","tags":["dosapi"]}},"/hsapi/_internal/data-store-move-to-folder/":{"post":{"description":"Move a list of files and/or folders to another folder in a resource file hierarchy.\n\n:param request: a REST request\n:param pk: the short_id of a resource to modify, from REST URL.\n\nIt is invoked by an AJAX call and returns a json object that has the relative paths of\nthe target files or folders to which files have been moved. The AJAX request must be a POST\nrequest with input data passed in for source_paths and target_path where source_paths\nand target_path are the relative paths for the source and target file or folder in the\nres_id file directory.\n\nThis routine is **specifically** targeted at validating requests from the UI.\nThus it is much more limiting than a general purpose REST responder.","operationId":"_internal_data-store-move-to-folder_create","responses":{"201":{"description":"Created"}},"summary":"Move a list of files and/or folders to another folder in a resource file hierarchy.","tags":["hsapi"]}},"/hsapi/_internal/data-store-rename-file-or-folder/":{"post":{"description":"Rename one file or folder in a resource file hierarchy.  It is invoked by an AJAX call\n\n:param request: a REST request\n:param pk: the short_id of a resource to modify, from REST URL.\n\nThis is invoked by an AJAX call in the UI. It returns a json object that has the\nrelative path of the target file or folder that has been renamed. The AJAX request\nmust be a POST request with input data for source_path and target_path, where source_path\nand target_path are the relative paths for the source and target file or folder.\n\nThis routine is **specifically** targeted at validating requests from the UI.\nThus it is much more limiting than a general purpose REST responder.","operationId":"_internal_data-store-rename-file-or-folder_create","responses":{"201":{"description":"Created"}},"summary":"Rename one file or folder in a resource file hierarchy.  It is invoked by an AJAX call","tags":["hsapi"]}},"/hsapi/_internal/{shortkey}/rest-download-refts-resource-bag/":{"get":{"description":"Download a reference time series resource bag\n:param request:\n:param shortkey: resource uuid\n:param args:\n:param kwargs:\n:return:","operationId":"_internal_rest-download-refts-resource-bag_list","parameters":[{"description":"","in":"path","name":"shortkey","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Download a reference time series resource bag","tags":["hsapi"]}},"/hsapi/dictionary/universities/":{"get":{"description":"Return a list of all vocabulary items\n:return:","operationId":"dictionary_universities_list","responses":{"200":{"description":"OK"}},"summary":"Return a list of all vocabulary items","tags":["hsapi"]}},"/hsapi/resource/":{"get":{"description":"List existing resources\n:param request:\n:return:","operationId":"resource_list","parameters":[{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"List existing resources","tags":["hsapi"]},"post":{"description":"Create a new resource\n:param request:\n:return:","operationId":"resource_create","requestBody":{"$ref":"#/components/requestBodies/resource_createData"},"responses":{"201":{"description":"Created"}},"summary":"Create a new resource","tags":["hsapi"]}},"/hsapi/resource/accessRules/{id}/":{"put":{"description":"Update access rules for a resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_accessRules_update","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Update access rules for a resource","tags":["hsapi"]}},"/hsapi/resource/types/":{"get":{"description":"Get a list of resource types\n\nREST URL: hsapi/resourceTypes\nHTTP method: GET\n\nexample return JSON format for GET /hsapi/resourceTypes (note response will consist of only\none page):\n\n[\n{\n\"resource_type\": \"GenericResource\"\n},\n{\n\"resource_type\": \"RasterResource\"\n},\n{\n\"resource_type\": \"RefTimeSeries\"\n},\n{\n\"resource_type\": \"TimeSeriesResource\"\n},\n{\n\"resource_type\": \"NetcdfResource\"\n},\n{\n\"resource_type\": \"ModelProgramResource\"\n},\n{\n\"resource_type\": \"ModelInstanceResource\"\n},\n{\n\"resource_type\": \"ToolResource\"\n},\n{\n\"resource_type\": \"SWATModelInstanceResource\"\n}\n]","operationId":"resource_types_list","parameters":[{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a list of resource types","tags":["hsapi"]}},"/hsapi/resource/{id}/":{"delete":{"description":"Delete a resource\n:param request:\n:param pk:\n:return:","operationId":"resource_delete","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"204":{"description":"No Content"}},"summary":"Delete a resource","tags":["hsapi"]},"get":{"description":"Get a resource in zipped BDBag format\n:param request:\n:param pk:\n:return:","operationId":"resource_read","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a resource in zipped BDBag format","tags":["hsapi"]},"put":{"description":"Update a resource bag (to be implemented)\n:param request:\n:param pk:\n:return:","operationId":"resource_update","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"$ref":"#/components/requestBodies/resource_createData"},"responses":{"200":{"description":"OK"}},"summary":"Update a resource bag (to be implemented)","tags":["hsapi"]}},"/hsapi/resource/{id}/access/":{"delete":{"description":"Delete access permission for a resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_access_delete","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"204":{"description":"No Content"}},"summary":"Delete access permission for a resource","tags":["hsapi"]},"get":{"description":"Retrieve access permission for a resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_access_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve access permission for a resource","tags":["hsapi"]},"put":{"description":"Update access permission for a resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_access_update","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"privilege":{"description":"","type":"string"}},"required":["privilege"],"type":"object"}}}},"responses":{"200":{"description":"OK"}},"summary":"Update access permission for a resource","tags":["hsapi"]}},"/hsapi/resource/{id}/copy/":{"post":{"description":"Copy a resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_copy_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Copy a resource","tags":["hsapi"]}},"/hsapi/resource/{id}/file_list/":{"get":{"description":"Get a listing of files within a resource.\n:param request:\n:param pk: Primary key of the resource (i.e. resource short ID)\n:return:","operationId":"resource_file_list_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a listing of files within a resource.","tags":["hsapi"]},"post":{"description":"Add a file to a resource.\n:param request:\n:param pk: Primary key of the resource (i.e. resource short ID)\n:return:","operationId":"resource_file_list_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"content_type":{"description":"","type":"string"},"size":{"description":"","type":"integer"},"url":{"description":"","type":"string"}},"required":["url","size","content_type"],"type":"object"}}}},"responses":{"201":{"description":"Created"}},"summary":"Add a file to a resource.","tags":["hsapi"]}},"/hsapi/resource/{id}/files/":{"get":{"description":"Get a listing of files within a resource.\n:param request:\n:param pk: Primary key of the resource (i.e. resource short ID)\n:return:","operationId":"resource_files_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a listing of files within a resource.","tags":["hsapi"]}},"/hsapi/resource/{id}/files/{pathname}/":{"delete":{"description":"Delete a resource file\n:param request:\n:param pk:\n:param pathname:\n:return:","operationId":"resource_files_delete","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"204":{"description":"No Content"}},"summary":"Delete a resource file","tags":["hsapi"]},"get":{"description":"Retrieve a resource file\n:param request:\n:param pk:\n:param pathname:\n:return:","operationId":"resource_files_read","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve a resource file","tags":["hsapi"]},"post":{"description":"Add a file to a resource.\n:param request:\n:param pk: Primary key of the resource (i.e. resource short ID)\n:param pathname: the path to the containing folder in the folder hierarchy\n:return:\n\nLeaving out pathname in the URI calls a different class function in ResourceFileListCreate\nthat stores in the root directory instead.","operationId":"resource_files_create","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Add a file to a resource.","tags":["hsapi"]},"put":{"description":"Retrieve, add, update or delete a resource file\n\nREST URL: hsapi/resource/{pk}/files/{filename}\nHTTP method: GET\n\n:type pk: str\n:type filename: str\n:param pk: resource id\n:param filename: name of the file to retrieve/download\n:return: resource file data\n:rtype: file data bytes\n\nREST URL: POST hsapi/resource/{pk}/files/","operationId":"resource_files_update","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve, add, update or delete a resource file","tags":["hsapi"]}},"/hsapi/resource/{id}/flag/":{"post":{"description":"Set resource flag\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_flag_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Set resource flag","tags":["hsapi"]}},"/hsapi/resource/{id}/folders/{pathname}/":{"delete":{"description":"Delete a folder.","operationId":"resource_folders_delete","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"204":{"description":"No Content"}},"summary":"Delete a folder.","tags":["hsapi"]},"get":{"description":"list a given folder","operationId":"resource_folders_read","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"list a given folder","tags":["hsapi"]},"put":{"description":"create a given folder if not present and allowed","operationId":"resource_folders_update","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"create a given folder if not present and allowed","tags":["hsapi"]}},"/hsapi/resource/{id}/functions/move-or-rename/":{"post":{"description":"Move or rename a resource file or folder\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_functions_move-or-rename_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Move or rename a resource file or folder","tags":["hsapi"]}},"/hsapi/resource/{id}/functions/set-file-type/{file_path}/{hs_file_type}/":{"post":{"description":"Set file type as specified by *hs_file_type* using the file given by *file_path*\n\n:param request: an instance of HttpRequest object\n:param pk: id of the composite resource in which this file type needs to be set\n:param file_path: relative file path of the file which needs to be set to the specified file\ntype. If the absolute file path is [resource-id]/data/some-folder/some-file.txt then\nfile_path needs to be set as: some-folder/some-file.txt\n:param hs_file_type: type of file to be set (e.g, NetCDF, GeoRaster, GeoFeature etc)\n:return:","operationId":"resource_functions_set-file-type_create","parameters":[{"description":"","in":"path","name":"file_path","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"hs_file_type","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Set file type as specified by *hs_file_type* using the file given by *file_path*","tags":["hsapi"]}},"/hsapi/resource/{id}/functions/unzip/{pathname}/":{"post":{"description":"Public version of data_store_folder_unzip, incorporating path variables\n\n:param request:\n:param pk: resource uuid\n:param pathname: path to the zip file to be unzipped\n:return HttpResponse:","operationId":"resource_functions_unzip_create","parameters":[{"description":"","in":"path","name":"pathname","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Public version of data_store_folder_unzip, incorporating path variables","tags":["hsapi"]}},"/hsapi/resource/{id}/functions/zip/":{"post":{"description":"Zip a folder in a resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_functions_zip_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Zip a folder in a resource","tags":["hsapi"]}},"/hsapi/resource/{id}/map/":{"get":{"description":"Retrieve resource map\n\nREST URL: hsapi/resource/{pk}/map\nHTTP method: GET\n\n:type pk: str\n:param pk: id of the resource\n:return: resource map as XML document\n:rtype: str\n:raises:","operationId":"resource_map_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve resource map","tags":["hsapi"]}},"/hsapi/resource/{id}/scimeta/":{"get":{"description":"Retrieve resource science metadata\n:param request:\n:param pk:\n:return:","operationId":"resource_scimeta_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve resource science metadata","tags":["hsapi"]},"put":{"description":"Update resource science metadata based on resourcemetadata.xml uploaded\n:param request:\n:param pk:\n:return:","operationId":"resource_scimeta_update","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Update resource science metadata based on resourcemetadata.xml uploaded","tags":["hsapi"]}},"/hsapi/resource/{id}/scimeta/custom/":{"post":{"description":"Create resource custom science metadata\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_scimeta_custom_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Create resource custom science metadata","tags":["hsapi"]}},"/hsapi/resource/{id}/scimeta/elements/":{"get":{"description":"Retrieve resource science (Dublin Core) metadata\n:param request:\n:param pk:\n:return:","operationId":"resource_scimeta_elements_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve resource science (Dublin Core) metadata","tags":["hsapi"]},"put":{"description":"Update resource science (Dublin Core) metadata\n:param request:\n:param pk:\n:return:","operationId":"resource_scimeta_elements_update","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"requestBody":{"content":{"application/json":{"schema":{"properties":{"contributors":{"description":"","items":{"type":"string"},"type":"array"},"coverages":{"description":"","items":{"type":"string"},"type":"array"},"creators":{"description":"","items":{"type":"string"},"type":"array"},"dates":{"description":"","items":{"type":"string"},"type":"array"},"description":{"description":"","type":"string"},"formats":{"description":"","items":{"type":"string"},"type":"array"},"funding_agencies":{"description":"","items":{"type":"string"},"type":"array"},"identifiers":{"description":"","items":{"type":"string"},"type":"array"},"language":{"description":"","type":"string"},"publisher":{"description":"","type":"string"},"relations":{"description":"","items":{"type":"string"},"type":"array"},"rights":{"description":"","type":"string"},"sources":{"description":"","items":{"type":"string"},"type":"array"},"subjects":{"description":"","items":{"type":"string"},"type":"array"},"title":{"description":"","type":"string"},"type":{"description":"","type":"string"}},"type":"object"}}}},"responses":{"200":{"description":"OK"}},"summary":"Update resource science (Dublin Core) metadata","tags":["hsapi"]}},"/hsapi/resource/{id}/sysmeta/":{"get":{"description":"Get resource system metadata, as well as URLs to the bag and science metadata","operationId":"resource_sysmeta_list","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Get resource system metadata, as well as URLs to the bag and science metadata","tags":["hsapi"]}},"/hsapi/resource/{id}/version/":{"post":{"description":"Create a new version of the resource\n:param request:\n:param pk: resource uuid\n:return:","operationId":"resource_version_create","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"201":{"description":"Created"}},"summary":"Create a new version of the resource","tags":["hsapi"]}},"/hsapi/resourceList/":{"get":{"description":"Get a list of resources based on the following filter query parameters","operationId":"resourceList_list","parameters":[{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a list of resources based on the following filter query parameters","tags":["hsapi"]}},"/hsapi/resourceTypes/":{"get":{"description":"Get a list of resource types\n\nREST URL: hsapi/resourceTypes\nHTTP method: GET\n\nexample return JSON format for GET /hsapi/resourceTypes (note response will consist of only\none page):\n\n[\n{\n\"resource_type\": \"GenericResource\"\n},\n{\n\"resource_type\": \"RasterResource\"\n},\n{\n\"resource_type\": \"RefTimeSeries\"\n},\n{\n\"resource_type\": \"TimeSeriesResource\"\n},\n{\n\"resource_type\": \"NetcdfResource\"\n},\n{\n\"resource_type\": \"ModelProgramResource\"\n},\n{\n\"resource_type\": \"ModelInstanceResource\"\n},\n{\n\"resource_type\": \"ToolResource\"\n},\n{\n\"resource_type\": \"SWATModelInstanceResource\"\n}\n]","operationId":"resourceTypes_list","parameters":[{"description":"A page number within the paginated result set.","in":"query","name":"page","required":false,"schema":{"type":"integer"}}],"responses":{"200":{"description":"OK"}},"summary":"Get a list of resource types","tags":["hsapi"]}},"/hsapi/scimeta/{id}/":{"get":{"description":"Retrieve resource science metadata\n:param request:\n:param pk:\n:return:","operationId":"scimeta_read","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Retrieve resource science metadata","tags":["hsapi"]},"put":{"description":"Update resource science metadata based on resourcemetadata.xml uploaded\n:param request:\n:param pk:\n:return:","operationId":"scimeta_update","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Update resource science metadata based on resourcemetadata.xml uploaded","tags":["hsapi"]}},"/hsapi/sysmeta/{id}/":{"get":{"description":"Get resource system metadata, as well as URLs to the bag and science metadata","operationId":"sysmeta_read","parameters":[{"description":"","in":"path","name":"id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"Get resource system metadata, as well as URLs to the bag and science metadata","tags":["hsapi"]}},"/hsapi/user/":{"get":{"description":"Retrieve user info list\n:param request:\n:return:","operationId":"user_list","responses":{"200":{"description":"OK"}},"summary":"Retrieve user info list","tags":["hsapi"]}},"/hsapi/userInfo/":{"get":{"description":"Retrieve user info list\n:param request:\n:return:","operationId":"userInfo_list","responses":{"200":{"description":"OK"}},"summary":"Retrieve user info list","tags":["hsapi"]}},"/resource/{shortkey}/data/{var}/":{"get":{"description":"maps the file URIs in resourcemap document to django_irods download view function\n:param request:\n:param shortkey: resource uuid\n:return:","operationId":"data_read","parameters":[{"description":"","in":"path","name":"var","required":true,"schema":{"type":"string"}},{"description":"","in":"path","name":"shortkey","required":true,"schema":{"type":"string"}}],"responses":{"200":{"description":"OK"}},"summary":"maps the file URIs in resourcemap document to django_irods download view function","tags":["resource"]}}},"servers":[{"url":"https://helx.commonsshare.org/"}],"tags":[{"name":"NIHdatacommons"},{"name":"Helx"},{"name":"CommonsShare"},{"name":"Portals"},{"name":"WebServices"}]},{"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"},"AsyncQuery":{"additionalProperties":true,"description":"The AsyncQuery class is effectively the same as the Query class but it requires a callback property.","properties":{"bypass_cache":{"default":false,"description":"Set to true in order to request that the agent obtain fresh information from its sources in all cases where it has a viable choice between requesting fresh information in real time and using cached information. The agent receiving this flag MUST also include it in TRAPI sent to downstream sources (e.g., ARS -> ARAs -> KPs).","type":"boolean"},"callback":{"description":"Upon completion, this server will send a POST request to the callback URL with `Content-Type: application/json` header and request body containing a JSON-encoded `Response` object. The server MAY POST `Response` objects before work is fully complete to provide interim results with a Response.status value of 'Running'. If a POST operation to the callback URL does not succeed, the server SHOULD retry the POST at least once.","format":"uri","nullable":false,"pattern":"^https?://","type":"string"},"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. 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.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$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.","example":"rXEOAosN3L","nullable":false,"type":"string"},"status":{"description":"One of a standardized set of short codes: e.g. Accepted, QueryNotTraversable, KPsNotAvailable","example":"Accepted","nullable":true,"type":"string"}},"required":["job_id"],"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":[{"$ref":"#/components/schemas/LogLevel"}]},"message":{"description":"The query Message is a serialization of the user request. Content of the Message object depends on the intended TRAPI operation. For example, the fill operation requires a non-empty query_graph field as part of the Message, whereas other operations, e.g. overlay, require non-empty results and knowledge_graph fields.","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"submitter":{"description":"Any string for self-identifying the submitter of a query. The purpose of this optional field is to aid in the tracking of the source of queries for development and issue resolution.","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps to be executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object","x-body-name":"request_body"},"QueryGraph":{"additionalProperties":true,"description":"A graph representing a biomedical question. It serves as a template for each result (answer), where each bound knowledge graph node/edge is expected to obey the constraints of the associated query graph element.","properties":{"edges":{"additionalProperties":{"$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":{"$ref":"#/components/schemas/QNode"},"description":"The node specifications. The keys of this map are unique node identifiers and the corresponding values include the constraints on bound nodes.","type":"object"}},"required":["nodes","edges"],"type":"object"},"ResourceRoleEnum":{"description":"The role played by the InformationResource in serving as a source for an Edge. Note that a given Edge should have one and only one 'primary' source, and may have any number of 'aggregator' or 'supporting data' sources.  This enumeration is found in Biolink Model, but is repeated here for convenience.","enum":["primary_knowledge_source","aggregator_knowledge_source","supporting_data_source"],"type":"string"},"Response":{"additionalProperties":true,"description":"The Response object contains the main payload when a TRAPI query endpoint interprets and responds to the submitted query successfully (i.e., HTTP Status Code 200). The message property contains the knowledge of the response (query graph, knowledge graph, and results). The status, description, and logs properties provide additional details about the response.","properties":{"biolink_version":{"description":"Version label of the Biolink model used in this document","example":"3.1.2","nullable":true,"type":"string"},"description":{"description":"A brief human-readable description of the outcome","example":"Success. 42 results found.","nullable":true,"type":"string"},"logs":{"description":"A list of LogEntry items, containing errors, warnings, debugging information, etc. List items MUST be in chronological order with earliest first.","items":{"$ref":"#/components/schemas/LogEntry"},"minItems":0,"nullable":false,"type":"array"},"message":{"description":"Contains the knowledge of the response (query graph, knowledge graph, and results).","nullable":false,"oneOf":[{"$ref":"#/components/schemas/Message"}]},"schema_version":{"description":"Version label of the TRAPI schema used in this document","example":"1.4.0","nullable":true,"type":"string"},"status":{"description":"One of a standardized set of short codes, e.g. Success, QueryNotTraversable, KPsNotAvailable","example":"Success","nullable":true,"type":"string"},"workflow":{"description":"List of workflow steps that were executed.","nullable":true,"oneOf":[{"$ref":"https://standards.ncats.io/workflow/1.3.5/schema"}]}},"required":["message"],"type":"object"},"Result":{"additionalProperties":true,"description":"A Result object specifies the nodes and edges in the knowledge graph that satisfy the structure or conditions of a user-submitted query graph. It must contain a NodeBindings object (list of query graph node to knowledge graph node mappings) and a list of Analysis objects.","properties":{"analyses":{"description":"The list of all Analysis components that contribute to the result. See below for Analysis components.","items":{"$ref":"#/components/schemas/Analysis"},"minItems":0,"nullable":false,"type":"array"},"node_bindings":{"additionalProperties":{"items":{"$ref":"#/components/schemas/NodeBinding"},"minItems":1,"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.","nullable":false,"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"},"nullable":true,"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":{"$ref":"#/components/schemas/CURIE"},"nullable":true,"type":"array"}},"required":["resource_id","resource_role"],"type":"object"}}},"externalDocs":{"description":"Documentation for the NCATS Biomedical Translator Reasoners web services","url":"https://github.com/NCATSTranslator/ReasonerAPI"},"info":{"contact":{"email":"qi.wei@isbscience.org","name":"Qi Wei"},"description":"TRAPI 1.5 endpoint for the CATRAX BigGIM DrugResponse Performance Phase KP, an NCATS Biomedical Translator Knowledge Provider","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://github.com/RTXteam/PloverDB/blob/main/LICENSE","title":"CATRAX BigGIM DrugResponse Performance Phase KP - TRAPI 1.5.0","version":"2.7.8","x-translator":{"biolink-version":"4.2.1","component":"KP","externalDocs":{"description":"The values for component and team are restricted according to this external JSON schema. See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-translator/"},"infores":"infores:biothings-multiomics-biggim-drugresponse","team":["Multiomics Provider"]},"x-trapi":{"asyncquery":false,"externalDocs":{"description":"The values for version are restricted according to the regex in this external JSON schema. See schema and examples at url","url":"https://github.com/NCATSTranslator/translator_extensions/blob/\\ production/x-trapi/"},"multicuriequery":false,"operations":["lookup"],"pathfinderquery":false,"test_data_location":{"default":{"url":"https://multiomics.rtx.ai:9990/BigGIM_DrugResponse_PerformancePhase/sri_test_triples"}},"version":"1.5.0"}},"openapi":"3.0.1","paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$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"]}},"/query":{"post":{"description":"","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"]}},"/asyncquery":{"post":{"description":"","requestBody":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing and the Response will be sent to the callback url when complete."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query with a callback to receive the response","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"CTKP TRAPI 1.5 endpoint - development","url":"https://multiomics.rtx.ai:9990/BigGIM_DrugResponse_PerformancePhase","x-maturity":"development"},{"description":"CTKP TRAPI 1.5 endpoint - staging","url":"https://multiomics.ci.transltr.io/BigGIM_DrugResponse_PerformancePhase","x-maturity":"staging"},{"description":"CTKP TRAPI 1.5 endpoint - testing","url":"https://multiomics.test.transltr.io/BigGIM_DrugResponse_PerformancePhase","x-maturity":"testing"},{"description":"CTKP TRAPI 1.5 endpoint - production","url":"https://multiomics.transltr.io/BigGIM_DrugResponse_PerformancePhase","x-maturity":"production"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Initiate a query with a callback to receive the response","name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]}]}