| AC | Allele Count; Number of times we see each alternate allele in the sample genotypes. Note that a “1/1” would count as 2 for the first alternate allele. |
| AF | Allele Frequency; Rate that the alternate alleles are seen in the genotypes. This is equivalent to AC/AN. |
| AN | Allele Number; Total number of alleles seen. Usually, this will be the number of samples times two, since humans are diploid organisms. |
| AoU | All of Us Research Program |
| Applications (Apps) | Apps is a general term to refer to any cloud-hosted software applications available within the Researcher Workbench. There are a variety of applications available. |
| Array | A data structure consisting of a collection of elements (values or variables), each identified by at least one array index or key. An array is stored such that the position of each element can be computed from its index tuple by a mathematical formula |
| ATC | Anatomical Therapeutic Chemical; classification scheme for drug data |
| Available Fields | Lists all fields present within the program data model with relevant metadata, including a description, the data provenance, and whether the field was impacted by privacy methods |
| CDM | Common Data Model |
| CDR | Curated Data Repository |
| Cleaning & Conformance | Details cleaning and conformance rules run between CDR_base and CDR to shape data to adhere to clean norms and expectations. |
| Cloud Resource | A cloud resource is any computing component or service provided by a cloud platform that can be provisioned, managed, and consumed on demand. These resources typically include compute (virtual machines, containers, etc), storage (workbench bucket, persistent disk, object storage), and platform services (APIs, orchestration services). It is a broad term to describe resources that can be added or created via cloud storage or services. In the Researcher Workbench, under the “Resources” tab of a workspace, there are two main types of cloud resources: referenced or controlled resources. |
| Cohort | Selected group of participants you are interested in researching; created through Cohort Builder tool |
| Command-line interface (CLI) | A command-line interface (CLI) is a text-based interface that uses defined commands to execute user actions. Using the command line requires more computational knowledge than a graphical user interface (GUI) - such as JupyterLab. You can leverage the CLI from Linux or from a variety of virtual machines, including apps in the Researcher Workbench itself. The "Workbench CLI” package is pre-installed in all app images offered by the workbench. |
| Concepts | Information in a patient’s medical record including diagnosed conditions (“conditions”), prescribed medications (“drugs”), or recorded physical measurements (“measurements”) |
| Concept Generalizations | Details all concepts (rows) which are generalized in the data model with relevant metadata, including the Concept ID, the data provenance, a description of the generalization applied, and the expected generalization output |
| Concept Set | A saved collection of concepts from a particular domain (conditions, drugs, or measurements) to use for analysis |
| Concept Suppressions | Details all concepts (rows) which are suppressed (removed) from the data model with relevant metadata, including the Concept ID and the data provenance |
| Controlled Resources | A controlled resource is a cloud resource created within a specific workspace, such as a cloud storage bucket or bucket object. It is specific to that workspace and is deleted if the workspace or resource inside the workspace is deleted. To use it in another workspace, a reference to the original controlled resource must be created. |
| Core Participant | A participant who has consented to providing EHR data has completed the 3 main surveys |
| CPT Codes | Current Procedural Terminology; a list of descriptive terms and identifying numeric codes used by physicians and health care professionals for the billing of medical services and procedures |
| Cram Files |
Cram files, based on short-reads, are the input to sequencing-based variant calling pipelines and are used to call short variants (SNPs and Indels) and copy number variants. |
| Data Catalog | This is a catalog of data collections you have access to. In the Researcher Workbench, your @researchallofus.org username will allow you access to data in Registered Tier or Controlled Tier data collections. |
| Data Collection | Curated datasets that are published in the Verily Workbench catalog. All of Us Research Program data collections are synonymous with the Curated Data Repository (CDR). There are two data collections available in the Researcher Workbench: “All of Us Registered Tier” and “All of Us Controlled Tier.” |
| Data Collection Policies | Restrictions that may be attached to workspaces and data collections and dictate how the data can be accessed and used, chiefly for the purposes of privacy and legal compliance. There are several data collection policies that are attached to the All of Us Data Collections and workspaces, such as perimeter policy, region policy, group policy, network policy, and “Researcher Use Statement Questions.” |
| Data Explorer | The Data Explorer is a point-and-click interface within the Researcher Workbench that enables users to build datasets using All of Us Data Collections. |
| DRC | Data and Research Center |
| DV | Direct Volunteer; a participant who did not register through an HPO location |
| EHR | Electronic health record |
| Exchange | This is a data collection catalog available in the Researcher Workbench where researchers find and access additional biomedical data available on the Verily Pre platform. |
| FHIR | Fast Healthcare Interoperability Resources |
| Field Generalizations | Details all fields (columns) which are generalized in the data model with relevant metadata, including a field description, the data provenance, a description of the generalization applied, and the expected generalization output |
| Field Suppressions | Details all fields (columns) which are suppressed (set to null) in the data model with relevant metadata, including a description and the data provenance |
| GATK | Genome Analysis Toolkit - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more |
| Git Repository | A git repository is a version-controlled directory that stores project files and their change history. Typically, repositories are hosted on platforms such as GitHub. You can add Git repositories to your Researcher Workbench workspace as references. When you create a cloud app for analysis, it will clone your repository to the app. |
| Group Policy | A group policy limits workspace access and data sharing to users of the selected groups. The All of Us data collections group policy only allows users with the affiliated @researchallofus.org usernames to access a workspace that has an All of Us data collection in it. To collaborate on a workspace, all users must be approved for access to the data collection attached to the workspace. For example, only users who have access to Controlled Tier data can access workspaces with the All of Us Controlled Tier data collection in it. Users are automatically added to the All of Us data collections once they complete applicable data access requirements. Users are not allowed to add both Registered and Controlled Tier data collections to the workspace, meaning you are only able to add Registered Tier or Controlled Tier data collections to a given workspace. |
| GQ | Genotype Quality; The phred-scaled confidence that genotypes are correct. A higher score indicates a higher confidence. For more information on interpreting phred-scaled values, please see this article. |
| GT | Genotype; GT field specifies the alleles carried by the sample, encoded by a 0 for the REF allele, 1 for the first ALT allele, 2 for the second ALT allele, etc. Since humans are diploid organisms, we expect two alleles (e.g. “0/1”). |
| Hail | Hail is an open-source Python library that simplifies genomic data analysis. It provides powerful, easy-to-use data science tools that can be used to interrogate even biobank-scale genomic data. For more information about Hail, see this tutorial. |
| HPO | Health provider organization |
| ICD Codes | International Classification of Diseases; used in the United States to classify diseases, illnesses, or injuries |
| indel | Insertion/Deletion Polymorphism; a type of genetic variation in which a specific nucleotide sequence is present (insertion) or absent (deletion). |
| JupyterLab | JupyterLab is an open-source web application that provides an interactive environment for notebooks, code, and data. In the Researcher Workbench, selecting “JupyterLab” will create a standard Google Compute Engine (GCE) instance. |
| JupyterLab Spark cluster | This is a JupyterLab extension on dataproc cluster service on Google Cloud Platform. In the Researcher Workbench, selecting “JupyterLab Spark cluster” will create a dataproc cluster environment. |
| JupyterLab (NVIDIA NeMo) | NVIDIA NeMo is a NVIDIA software suite leveraging a GPU-accelerated environment for large-scale generative AI tasks, such as training, customization, and deployment of your custom AI, LLMs, and multimodal models. In the Researcher Workbench, selecting “JupyterLab (NVIDIA NeMo)” will create a Compute Engine (GCE) instance with resourced GPUs for AI development. |
| JupyterLab (NVIDIA Parabricks and CUDA-X Data Science) | NVIDIA Parabricks and CUDA-X Data Science is an NVIDIA software and libraries suite that leverages GPU-accelerated environments for secondary and tertiary genomics analysis. Leveraging this environment allows for large scale genomic and multi-omics analyses much faster than on a CPU-only environment. In the Researcher Workbench, selecting “JupyterLab (NVIDIA Parabricks and CUDA-X Data Science)” will create a Compute Engine (GCE) instance with resourced GPUs tailored for genomics analysis. |
| Kernel | A “computational engine” operating within notebooks; executes codes within notebook |
| LOINC | Logical Observation Identifiers Names and Codes; it is used by health care provider organizations to code laboratory test orders and results. For example, 2345-7 is the code used for the amount of glucose measured in blood during a blood test |
| Medical Concepts | Medical concepts describe information in a patient’s medical record, such as a condition they have, a doctor’s diagnosis, a prescription they are taking, or a procedure or measurement the doctor performed |
| Network Policy | A network policy is a type of policy that disables direct internet access for virtual machines (VMs) that run batch jobs. For example, you will be unable to access certain SSH commands or externally access the VM through the internet. |
| NIH | National Institutes of Health |
| Notebook | A notebook resides within JupyterLab and provides an interface for writing and running code in languages such as R, Python, and SQL. It lets you work within a single file for tasks like cleaning and transforming data, exploring datasets, and building machine learning models, while also supporting visualizations and narrative text. |
| OHDSI | Observational Health Data Sciences and Informatics |
| OMOP | Observational Medical Outcomes Partnership |
| Participant | Individual who has registered for the program, but not necessarily provided consent or completed surveys |
| Perimeter Policy | A perimeter policy restricts data movement - such as copy, transfer, and retrieval of data - to the cloud boundaries. It limits copy, transfer, and retrieval of data. In the Researcher Workbench, data collections and workspaces can be placed within a perimeter to enforce these limits. The All of Us Research Program requires workspaces using All of Us data collections (Registered Tier and Controlled Tier) to be restricted within a perimeter, and each workspace can belong to only one perimeter. A workspace perimeter is automatically and permanently assigned when you add an All of Us data collection to your workspace. |
| PDR | Program Data Repository |
| PL | Phred-scaled Likelihood - Genotype likelihood for a variant can be calculated by dividing Genotype Quality (GQ) by the Reference Genotype Quality (RGQ) |
| PLINK | An open-source Whole Genome-Association Study tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage |
| Pods | Pods connect workspaces with the cloud billing. Billing pods are created to connect to the GCP billing account, and workspace costs are charged to the billing pod. One pod can be used for many workspaces, and you can invite other users to be part of your pod. Note, All of Us researchers have a pod_manager role which allows you to create your own billing pod and link to your designated GCP billing account. A billing pod can only be connected to one GCP billing account. |
| PPI | Participant Provided Information |
| PPSC | Participant & Partner Services Center; provides websites for participants to enroll in All of Us, provide data, and receive updates |
| R analysis environment | This is a compute engine instance used to launch the RStudio interface |
| RBR | Represented in Biomedical Research |
| RDR | Raw Data Repository |
| Region Policy | A region policy is a type of policy that limits which regions of a platform may be used to create cloud resources and apps. The Researcher Workbench uses Google Cloud Platform (GCP) and will utilize regions within GCP. All of Us data collections and workspaces are restricted and automatically assigned to the region us-central1(Iowa). When you create a workspace in the Workbench, it will automatically keep cloud resources and apps created in the workspace within this region. This is the same region restriction that exists in the legacy Researcher Workbench. |
| Researcher Use Statement Questions | The All of Us Data User Code of Conduct (DUCC) requires researchers to provide transparency into their study plans for each workspace. Before you can create a workspace, you must provide a thorough, meaningful description of your research project and study plans in the “Workspace Description Form.” |
| RGQ | Reference Genotype Quality; the phred-scaled confidence that the reference genotypes are correct. A higher score indicates a higher confidence. For more information on interpreting phred-scaled values, please see this article. |
| Reference Resource | A referenced resource (or reference) is a pointer to data or elements that exist outside your workspace, allowing you to use them without altering the original source. For example, creating a reference to a BigQuery dataset lets you analyze it in your workspace while keeping the source intact. References can be safely deleted or duplicated across workspaces without affecting the original resource, provided you maintain access to the source. |
| RxNorm | Naming system for all medications available in the U.S. market; the RxNorm name of each drug is a compilation of its active ingredients, strength, and form |
| SNV | Single-Nucleotide Variants |
| SNOMED | Systematized Nomenclature of Medicine; connects the various terminology, medical codes, synonyms, and definitions used among different electronic health records (EHRs) so that they can be matched up for later reference |
| SNP | Single Nucleotide Polymorphisms; most common type of genetic variation among people |
| Source Vocabulary | The original classification system in a participant’s EHR used for categorization of conditions, diagnoses, and procedures (e.g., ICD-9 and ICD-10CM codes) when it first enters our system. Source vocabularies are retained after being “mapped” to standard vocabularies so that data can still be searched using the original terminology or codes |
| Standard Vocabulary | A classification system that incorporates different source vocabularies into one system by “mapping” multiple terms or codes to a common vocabulary to facilitate and optimize data analysis |
| Table Suppressions | Details all tables which are suppressed (not available) in the data model |
| Tuple | A data structure that stores a specific number of elements. These elements may include integers, characters, strings, or other data types. Tuples provide an efficient way to store multiple values. Since they are static and cannot be modified, tuples generally require less memory than arrays. They are also flexible since they can store multiple data types. |
| UBR | Under-represented in Biomedical Research |
| VCF | Variant Call Format; stores genomic variants in a tabular form (genomic position by sample ID) with a descriptive header. Most genomic tools that run on variants support VCF (e.g. Hail, Variant Effect Predictor (VEP), Genome Analysis Toolkit (GATK)). |
| Verily Pre | Verily Pre is an AI-native precision health data platform from Verily, purpose-built to accelerate biomedical research and deploy AI solutions in healthcare environments. It is what powers the Researcher Workbench. Within Verily Pre, the All of Us Researcher Workbench leverages the Workbench and Exchange. |
| WGS | Whole Genome Sequencing |
| Workflows | This term broadly refers to computational workflows that automate multi-stage data processing, streamlining tasks by executing them autonomously. the Researcher Workbench supports workflows on Cromwell, dsub, and Nextflow, and can be accessed through the "Workflows" section of a workspace. |
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