IDC User Guide
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Limited access content
As discussed in this community forum post, TCIA made the decision to pull a subset of data from public access collections to limited access. At the moment, we still keep those files that used to be public in IDC before the decision made by TCIA, and the metadata for those files is still accessible in our BigQuery tables, but you cannot download those “Limited” access files referenced by
gcs_url from IDC.As discussed in this post the issue will manifest itself in an error accessing
gcs_url that corresponds to a non-public file:1
AccessDeniedException: 403 <user email> does not have storage.objects.list
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access to the Google Cloud Storage bucket.
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bigquery-public-data.idc_current.dicom_all table has a column named access , which takes values Public or Limited that define if the file corresponding to the instance can be accessed. For all practical purposes, if you interact with the IDC BigQuery tables, you should make sure you exclude “Limited” access items using the following clause in your query:1
SELECT
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...
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FROM
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`bigquery-public-data.idc_current.dicom_all`
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WHERE
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access <> "Limited"
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In a future release of IDC we will by default exclude limited access items from what you select in the portal, so the portal selection should be more intuitive. But if you access the data via BigQuery queries you will need to know that “Limited” are not accessible and account for this in your query.
Storage Buckets
Storage Buckets are basic containers in Google Cloud that provide storage for data objects (you can read more about the relevant terms in the Google Cloud Storage documentation here).
All IDC DICOM file data for all IDC data versions and all of the collections hosted by IDC are maintained in Google Cloud Storage (GCS). Currently all DICOM files are maintained in GCS buckets that allow for free egress within or out of the cloud, enabled through the partnership of IDC with Google Public Datasets Program.
The object namespace is flat, where every object name is composed of a standard format CRDC UUID and with the ".dcm" file extension, e.g.
905c82fd-b1b7-4610-8808-b0c8466b4dee.dcm. For example, that instance can be accessed using gsutil as gs://idc-open/905c82fd-b1b7-4610-8808-b0c8466b4dee.dcmEgress of IDC data out of the cloud is free, since IDC data is participating in Google Public Datasets Program!
Typically, the user would not interact with the storage buckets to select and copy files (unless the intent is to copy the entire content hosted by IDC). Instead, one should use either the IDC Portal or IDC BigQuery tables containing file metadata, to identify items of interest and define a cohort. The cohort manifest generated by the IDC Portal can include both the Google Storage URLs for the corresponding files in the bucket, and the CRDC UUIDs, which can be resolved to the Google Storage URLs to access the files.
Assuming you have a list of GCS URLs in a file
gcs_paths.txt, you can download the corresponding items using the command below, substituting $PROJECT_ID with the valid GCP Project ID (see the complete example in this notebook):1
$ cat gcs_paths.txt | gsutil -m cp -I .
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BigQuery Tables
Google BigQuery (BQ) is a massively-parallel analytics engine ideal for working with tabular data. Data stored in BQ can be accessed using standard SQL queries.
The flat address space of IDC DICOM objects in GCS storage is accompanied by BigQuery tables that allow the researcher to reconstruct the DICOM hierarchy as it exists for any given version. There are also several BQ tables and views in which we keep copies of the metadata exposed via the TCIA interface at the time a version was captured and other pertinent information.
There is an instance of each of the following tables and views per IDC version. The set of tables and views corresponding to an IDC version are collected in a single BQ dataset per IDC version,
bigquery-public-data.idc_<idc_version_number> where bigquery-public-data is the project in which the dataset is hosted. As an example, the BQ tables for IDC version 4 are in the bigquery-public-data.idc_v4dataset.In addition to the per-version datasets, the
bigquery-public-data.idc-current dataset consists of a set of BQ views. There is a view for each table or view in the BQ data set corresponding to the current IDC release. Each such view in bigquery-public-data.idc-current is named identically to some table or view in the bigquery-public-data.idc_<idc_version_number> dataset of the current IDC release and can be used to access that table or view.Several Google BigQuery (BQ) tables support searches against metadata extracted from the data files. Additional BQ tables define the composition of each IDC data version.
We maintain several additional tables that curate metadata non-DICOM metadata (e.g., attribution of a given item to a specific collection and DOI, collection-level metadata, etc).
bigquery-public-data.idc_v<idc_version_number>.auxiliary_metadata(also available via thebigquery-public-data.idc_current.auxiliary_metadataview.) This table defines the contents of the corresponding IDC version. There is a row for each instance in the version. Collection attributes:tcia_api_collection_id:The ID, as accepted by the TCIA API, of the original data collection containing this instanceidc_webapp_collection_id:The ID, as accepted by the IDC web app, of the original data collection containing this instancecollection_timestamp:Datetime when the IDC data in the collection was last revisedsource_doi:A DOI of the TCIA wiki page corresponding to the original data collection or analysis results that is the source of this instancecollection_hash: The md5 hash of the sortedpatient_hashesof all patients in the collection containing this instancecollection_init_idc_version:The IDC version in which the collection containing this instance first appearedcollection_revised_idc_version:The IDC version in which the collection containing this instance was most recently revised
Patient attributes:submitter_case_id:The submitter’s (of data to TCIA) ID of the patient containing this instance. This is the DICOM PatientIDidc_case_id:IDC generated UUID that uniquely identifies the patient containing this instanceThis is needed because DICOM PatientIDs are not required to be globally uniquepatient_hash: the md5 hash of the sortedstudy_hashesof all studies in the patient containing this instancepatient_init_idc_version:The IDC version in which the patient containing this instance first appearedpatient_revised_idc_version:The IDC version in which the patient containing this instance was most recently revised
Study attributes:StudyInstanceUID:DICOM UID of the study containing this instancestudy_uuid:IDC assigned UUID that identifies a version of the study containing this instance.study_instances:The number instances in the study containing this instancestudy_hash: the md5 hash of the sortedseries_hashesof all series in study containing this instancestudy_init_idc_version:The IDC version in which the study containing this instance first appearedstudy_revised_idc_version:The IDC version in which the study containing this instance was most recently revised
Series attributes:SeriesInstanceUID:DICOM UID of the series containing this instanceseries_uuid:IDC assigned UUID that identifies a version of the series containing this instancesource_doi:A DOI of the TCIA wiki page corresponding to the original data collection or analysis results that is the source of this instanceseries_instances:The number of instances in the series containing this instanceseries_hash: the md5 hash of the sortedinstance_hashesof all instance in the series containing this instanceseries_init_idc_version:The IDC version in which the series containing this instance first appearedseries_revised_idc_version:The IDC version in which the series containing this instance was most recently revised
Instance attributes:SOPInstanceUID:DICOM UID of this instance.instance_uuid:IDC assigned UUID that identifies a version of this instance.gcs_url:The GCS URL of a file containing the version of this instance that is identified by theinstance_uuidinstance_hash: the md5 hash of the version of this instance that is identified by theinstance_uuidinstance_size:the size, in bytes, of this version of the instance that is identified by theinstance_uuidinstance_init_idc_version:The IDC version in which this instance first appearedinstance_revised_idc_version:The IDC version in which this instance was most recently revisedlicense_url:The URL of a web page that describes the license governing this instancelicense_long_name:A long form name of the license governing this instancelicense_short_name:A short form name of the license governing this instance
bigquery-public-data.idc_v<idc_version_number>.dicom_metadata(also available viabigquery-public-data.idc_current.dicom_metadataview for the current version of IDC data) DICOM metadata for each instance in the corresponding IDC version. IDC utilizes the standard capabilities of the Google Healthcare API to extract all of the DICOM metadata from the hosted collections into a single BQ table. Conventions of how DICOM attributes of various types are converted into BQ form are covered in the Understanding the BigQuery DICOM schema Google Healthcare API documentation article. IDC users can access this table to conduct detailed exploration of the metadata content, and build cohorts using fine-grained controls not accessible from the IDC portal. The schema is too large to document here. Refer to the BQ table and the above referenced documentation.
Due to the existing limitations of Google Healthcare API, not all of the DICOM attributes are extracted and are available in BigQuery tables. Specifically:
- sequences that have more than 15 levels of nesting are not extracted (see https://cloud.google.com/bigquery/docs/nested-repeated) - we believe this limitation does not affect the data stored in IDC
- sequences that contain around 1MiB of data are dropped from BigQuery export and RetrieveMetadata output currently. 1MiB is not an exact limit, but it can be used as a rough estimate of whether or not the API will drop the tag (this limitation was not documented as of writing this) - we know that some of the instances in IDC will be affected by this limitation. The fix for this limitation is targeted for sometime in 2021, according to the communication with Google Healthcare support.
bigquery-public-data.idc_v<idc_version_number>.original_collections_metadata(also available via thebigquery-public-data.idc_current.original_collections_metadataview) This table is comprised of IDC data Collection-level metadata for the original TCIA data collections hosted by IDC, for the most part corresponding to the content available in this table at TCIA. One row per collection:tcia_api_collection_id:The collection ID as is accepted by the TCIA APtcia_wiki_collection_id:The collection ID as on the TCIA wiki pageidc_webapp_collection_id:The collection ID as accepted by the IDC web appProgram:The program to which this collection belongsUpdated:Moser recent update date reported by TCIAStatus:Collection status" Ongoing or completeAccess:Collection access conditions: Limited or PublicImageType:Enumeration of image types/modalities in the collectionSubjects:Number of subjects in the collectionDOI:DOI that can be resolved at doi.org to the TCIA wiki page for this collectionCancerType:TCIA assigned cancer type of this collectionSupportingData:Type(s) of additional data availableSpecies:Species of collection subjectsLocation:Body location that was studiedDescription:TCIA description of the collection (HTML format)license_url:The URL of a web page that describes the license governing this collectionlicense_long_name:A long form name of the license governing this collectionlicense_short_name:A short form name of the license governing this collection
bigquery-public-data.idc_v<idc_version_number>.analysis_results_metadata(also available via thebigquery-public-data.idc_current.analysis_results_metadataview for the current version of IDC data) Metadata for the TCIA analysis results hosted by IDC, for the most part corresponding to the content available in this table at TCIA. One row per analysis result:ID:Results IDTitle:Descriptive titleDOI:DOI that can be resolved at doi.org to the TCIA wiki page for this analysis resultCancerType:TCIA assigned cancer type of this analysis resultLocation:Body location that was studiedSubjects:Number of subjects in the analysis resultCollections:Original collections studiedAnalysisArtifactsonTCIA:Type(s) of analysis artifacts generatedUpdated:Data when results were last updatedlicense_url:The URL of a web page that describes the license governing this collectionlicense_long_name:A long form name of the license governing this collectionlicense_short_name:A short form name of the license governing this collection
cancer-idc.idc_v<version_number>.version_metadata(also available via the canceridc-data.idc-current.version_metadata view for the current version of IDC data). Metadata for each IDC version, one row per row:- idc_version: IDC version number
- version_hash: MD5 hash of hashes of collections in this version
- version_timestamp: Version creation timestamp
The following BigQuery views (virtual tables defined by queries) extract specific subsets of metadata, or combine attributes across different tables, for convenience of the users
bigquery-public-data.idc_v<idc_version_number>.dicom_all(also available viabigquery-public-data.idc_current.dicom_allview for the current version of IDC data) DICOM metadata together with selected auxiliary and collection metadatabigquery-public-data.idc_v<idc_version_number>.segmentations(also available viabigquery-public-data.idc_current.segmentationsview for the current version of IDC data) Attributes of the segments stored in DICOM Segmentation objectsbigquery-public-data.idc_v<idc_version_number>.measurement_groups(also available viabigquery-public-data.idc_current.measurement_groupsview for the current version of IDC data) Measurement group sequences extracted from the DICOM SR TID1500 objectsbigquery-public-data.idc_v<idc_version_number>.qualitative_measurements(also available viabigquery-public-data.idc_current.qualitative_measurementsview for the current version of IDC data) Coded evaluation results extracted from the DICOM SR TID1500 objectsbigquery-public-data.idc_v<idc_version_number>.quantitative_measurements(also available viabigquery-public-data.idc_current.quantitative_measurementsview for the current version of IDC data) Quantitative evaluation results extracted from the DICOM SR TID1500 objects
The following tables contain TCGA-specific metadata:
tcga_biospecimen_rel9:biospecimen metadatatcga_clinical_rel9:clinical metadata
Collection-specific BigQuery tables
Some of the collections are accompanied by BigQuery tables that have not been harmonized to a single data model. Those tables are available within the BigQuery dataset corresponding to a given release, and will have the name prefix corresponding to the short name of the collection. The list below discusses those collection-specific tables.
NLST
IDC hosts a subset of the NLST clinical data, which was cleared for public sharing. If you need the full clinical data, please visit the Cancer Data Access System (CDAS) system.
The following tables contain NLST specific metadata. The detailed schema of those tables is available from the TCIA NLST collection page.
DICOM Stores
IDC utilizes a single Google Healthcare DICOM store to host all of the instances in the current IDC version. That store, however, is primarily intended to support visualization of the data using OHIF Viewer. At this time, we do not support access of the hosted data via DICOMWeb interface by the IDC users. See more details in the discussion here, and please comment about your use case if you have a need to access data via the DICOMweb interface.
BigQuery tables external to IDC
In addition to the DICOM data, some of the image-related data hosted by IDC is stored in additional tables. These include the following:
- BigQuery TCGA clinical data:
isb-cgc:TCGA_bioclin_v0.clinical_v1. Note that this table is hosted under the ISB-CGC Google project, as documented here, and its location may change in the future!