Study
A Study entry documents key information about research projects, including methodologies, participants, and ethical considerations. Properly maintaining study records ensures that data is compliant with research standards, traceable, and usable across various scientific fields. This section explains how to create and maintain a valid study entry using the required fields, templates, and example data provided.
Why You Should Contribute Study Entries¶
Contributing study entries ensures that critical research details such as methodology, investigators, and related datasets are documented and accessible. This fosters transparency, collaboration, and reproducibility in research. A well-maintained study entry also helps stakeholders understand the scope, purpose, and outcomes of research efforts, enabling better data integration and analysis across projects.
Who Should Be Contributing Study Entries?¶
-
Principal Investigators (PIs) – Provide clear documentation of your studies to enhance visibility and demonstrate research contributions for funding agencies and collaborators.
-
Research Coordinators and Project Leads – Ensure proper record-keeping of studies under your supervision, supporting compliance, reporting, and resource allocation.
-
Data Managers – Create study entries to link related datasets, publications, and tools, improving data provenance and facilitating cross-references within research ecosystems.
-
Consortium Participants – Contribute study information to showcase collaborative research efforts and track joint achievements.
-
Funding Agencies and Grant Monitors – Monitor study progress by ensuring that all funded research is accurately documented and accessible.
-
Ethics and Compliance Officers – Maintain study entries to verify that all necessary de-identification methods, IRB protocols, and data use policies are in place.
Download Template¶
To streamline the process, download the study entry template for standardized data entry.
Example Data Entry¶
The table below includes sample values to demonstrate proper attribute usage.
| Attribute | Example Value |
|---|---|
| Study | Biology |
| Study Name | Effects of Diet and Exercise on Obesity |
| Study Description | Analysis of Cardiovascular Response during Exercise |
| Investigator | Dr. Jane Doe, PhD in Nutrition Science, University of Texas |
| Study_id | STUDY_2024_OBESITY_EXERCISE |
| Study Number of Participants | 5000 |
| Study Number of Samples | 120 |
| Study Deidentification Method Type | Manual |
| Study Deidentification Method Description | Personal identifiers such as names and dates were removed, and randomization techniques were applied. |
| Study Deidentification Method Software | Safe Harbor Privacy Software |
| Study dbGaP Accession Id | phs000424.v7.p2 |
| Study Project Identifier | syn12345678 |
| Data Use Codes | DUO:0000021, DUO:0000019, DUO:0000006 |
Data Use Ontology (DUO) Implementation¶
MC2 Center uses the Data Use Ontology (DUO) to record the consent permissions and use restrictions that apply to data and materials. DUO terms are defined once, in the shared vocabulary (modules/shared/annotationProperty.csv and modules/shared/duo.csv). Full definitions for every term are on the Shared Standard Terms page.
Which attribute records DUO codes depends on the template:
| Template | Attribute | Controlled list and companion fields? |
|---|---|---|
| Study, File View, and the file-level assay templates (Imaging, Sequencing, NanoString GeoMx, Visium) | Data Use Codes |
Yes |
| DataDSP | DSP Data Use Codes |
Yes |
| Dataset View | Dataset Data Use Codes |
No |
| DataCatalog | dataCatalogDataUseModifiers |
No |
All four are multi-select, string-list attributes. Most values are real DUO term CURIEs (e.g. DUO:0000006, DUO:0000021), plus a Pending Annotation placeholder for records that have not yet been reviewed for data use restrictions. The Dataset View and DataCatalog attributes have no controlled list, so they never add companion fields; each value must still look like a DUO code (DUO:0000042, DUOPlus3) or be Pending Annotation.
DUOPlus terms: Sage Bionetworks extensions to DUO¶
DUO does not have terms for a few governance concepts this model needs to track (deidentification method, data tier, license, etc.), so Sage Bionetworks defined seven extension terms, DUOPlus1 through DUOPlus7, that this model uses alongside the real DUO terms:
| DUOPlus Term | Governance Concept | Companion Field |
|---|---|---|
| DUOPlus1 | Source geography | sourceGeography |
| DUOPlus2 | Study population | populationType |
| DUOPlus3 | Data deidentification | deidentificationType |
| DUOPlus4 | Data permission | dataPermission |
| DUOPlus5 | Data tier | dataTier |
| DUOPlus6 | License | License |
| DUOPlus7 | Attribution | attribution |
How conditionally required fields are surfaced¶
Most DUO terms (e.g. DUO:0000042/General Research Use, DUO:0000006/Health or Medical or Biomedical Research) are self-contained labels — selecting one doesn't require anything else. A subset of terms, however, indicate that additional detail must be provided alongside the code. For these terms, the model links the code to a companion field: a separate attribute where the contributor records that detail. In the templates whose DUO attribute uses the controlled list (see the table above), selecting the code makes its companion field conditionally required; all other companion fields remain optional.
This conditional relationship is declared directly in modules/shared/annotationProperty.csv: each of these DUO/DUOPlus terms also appears there as its own Attribute row, and that row's DependsOn column names the companion field it requires. When the model is compiled to JSON Schema, each of these rows becomes an if/then rule on the DUO attribute — e.g. DataUseCodes containing DUO:0000026 requires UserSpecificRestriction to be filled in. json_schemas/Study.json has 14 such rules, one for each term below except DUOPlus6: Study always includes License, so it needs no rule.
| DUO Term | Meaning | Companion Field (conditionally required) |
|---|---|---|
| DUO:0000007 | Disease-specific research | diseaseSpecificResearch (MONDO ID) |
| DUO:0000012 | Research-specific restrictions | researchSpecificRestrictions |
| DUO:0000020 | Collaboration required | collaborationRequired (PI contact email) |
| DUO:0000022 | Geographical restriction | geographicalRestriction (country code) |
| DUO:0000024 | Publication moratorium | publicationMoratorium (end date) |
| DUO:0000025 | Time limit on use | timeLimitOnUse (number of months) |
| DUO:0000026 | User-specific restriction | userSpecificRestriction |
| DUO:0000028 | Institution-specific restriction | institutionSpecificRestriction (ROR ID) |
| DUOPlus1–DUOPlus7 | Sage Bionetworks DUOPlus governance extensions (see table above) | sourceGeography, populationType, deidentificationType, dataPermission, dataTier, License, attribution |
For example, a Study entry with Data Use Codes set to DUO:0000024, DUO:0000022 must also provide values for publicationMoratorium (the moratorium end date) and geographicalRestriction (the applicable country code(s)) — but can leave every other companion field blank, since none of the other DUO/DUOPlus terms were selected.
Full Field Reference¶
Below is the full field reference table with attributes and their descriptions.
| Attribute | Description | Required | Column Type | Format | Regex Pattern | Standard Terms | CDE | Examples |
|---|---|---|---|---|---|---|---|---|
| Study_id | Unique row identifier, used as a primary key for record updates. | True | string | None | None | None | CA261717-CancerResearch-7-2024 | |
| GrantView Key | Unique GrantView_id foreign key(s) that group the resource with other components, as part of the same grant-associated collection. Please provide multiple values as a comma-separated list. | False | string | None | (CA\d{6}|Affiliated/Non-Grant Associated) | None | ||
| ProjectView Key | Unique ProjectView_id foreign key(s) that group the resource with other components, as part of the same grant-associated studies. Please provide multiple values as a comma-separated list. | False | string | None | None | None | ||
| Study dbGaP Accession Id | A stable unique alphanumeric identifier assigned to a study and any objects by the database of Genotypes and Phenotypes (dbGaP). Required for controlled access data being submitted to CDS/CRDC. | False | string | None | None | None | CDE:11524544, CRDC_CDE:11524544 | phs000424.v7.p2 |
| Study Name | Name of the study | True | string | None | None | None | CDE:11459810, CRDC_CDE:11459810 | Effects of Diet and Exercise on Cancer |
| Study Description | Description of the study, including the types of experimental assays, model systems, types of analysis, description of cohort, associated vulnerable populations, special categories of data, rare diseases, etc. Maps to DUOplus2. | True | string | None | None | None | CDE:03444002 | Analysis of Cancerous Cell Response during Exercise |
| Investigator | Investigator(s) associated with this record. Provide either the investigator's free-text name or a PersonView_id reference (see PersonView Key) -- both forms are acceptable. Multiple values permitted, comma separated. | True | string_list | None | None | None | ||
| PersonView Key | Unique PersonView_id foreign key(s) that group the resource with other components, as part of the same person-associated studies. Please provide multiple values as a comma-separated list. | False | string | None | None | None | ||
| Study Number of Participants | The number of participant instances associated with systematic investigation into a subject. | True | number | None | None | None | CDE:11555662 | 5000 |
| Study Number of Samples | The number of specimens associated with systematic investigation into a subject. | True | number | None | None | None | CDE:11555663 | 120 |
| Study Deidentification Method Type | General description of the de-identification method. Maps to DUOplus3. | True | string | None | None | View | CDE:14576319 | Manual |
| Study Deidentification Method Description | Description of the process of removing potentially identifying data or data elements to render data into a form that does not identify individuals and where identification is not likely to take place. | False | string | None | None | None | All personal identifiable information such as names, addresses, and identification numbers were removed from the data. The dates were also shifted to a random point in the future to preserve the temporal relationships but without revealing the actual dates. The datasets were further reviewed and verified by a privacy officer to ensure all participants' identity is completely unidentifiable. | |
| Study Deidentification Method Software | Software that was used to de-identify the data (if used) | False | string | None | None | None | Safe Harbor Method Software | |
| Study Index Date | The reference event associated with timepoints in this study. One of Diagnosis Date, Enrollment Date, Collection Date, or Birth Date. | False | string | None | None | View | Diagnosis Date | |
| Study Project Identifier | The Synapse Project identifier (synID) with which this Study is related. | False | string_list | None | syn[0-9]+ | None | syn12345678 | |
| Data Use Codes | DUO code - A data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used. Available DUO code definitions can be found here: https://mc2-center.github.io/data-models/valid_values/shared/#attribute-data-use-codes | False | string_list | None | None | View | CDE:0002001 | |
| Study Short Name | The acronym or abbreviated form of the title for a research data collection (e.g. GLIOMA01). | False | string | None | None | None | CRDC_CDE:11459812 | |
| License | The license(s) applied to this item, if applicable. Multiple values permitted, comma separated. Studies with data submitted to CDS are required to provide a license (maps to DUOplus6). | False | string_list | None | None | View | CDE:14902606 |
Test¶
..include :: test.md