NDA Help Center

Collection - General Tab

Fields available for edit on the top portion of the page include:

  • Collection Title
  • Investigators
  • Collection Description
  • Collection Phase
  • Funding Source
  • Clinical Trials

Collection Status: The visibility status of an NDA Collection.  Collection Status can be Shared or Private.  Collections in Shared status are visible to all users and can be searched in the NDA Query Tool. Private Collections are not visible to NDA users.  The Status of an NDA Collection only affects the visibility of information about the Collection (metadata) and does not relate to the status of the record-level research data in the NDA Collection.

Collection Phase: The current status of a research project submitting data to an NDA Collection, based on the timing of the award and/or the data that have been submitted.
 

  • Pre-Enrollment: The default entry made when the NDA Collection is created.
     
  • Enrolling: Data have been submitted to the NDA Collection or the NDA Data Expected initial submission date has been reached for at least one data structure category in the NDA Collection.
     
  • Data Analysis: Subject level data collection for the research project is completed and has been submitted to the NDA Collection.  The NDA Collection owner or the NDA Help Desk may set this phase when they’ve confirmed data submission is complete and submitted subject counts match at least 90% of the target enrollment numbers in the NDA Data Expected. Data submission reminders will be turned off for the NDA Collection.
     
  • Funding Completed: The NIH grant award (or awards) associated with the NDA Collection has reached its end date. NDA Collections in Funding Completed phase are assigned a subphase to indicate the status of data submission.
     
    • The Data Expected Subphase indicates that NDA expects more data will be submitted
    • The Closeout Subphase indicates the data submission is complete.
    • The Sharing Not Met Subphase indicates that data submission was not completed as expected. 

Blinded Clinical Trial Status:

  • This status is set by a Collection Owner and indicates the research project is a double blinded clinical trial.  When selected, the public view of Data Expected will show the Data Expected items and the Submission Dates, but the targeted enrollment and subjects submitted counts will not be displayed.
     
  • Targeted enrollment and subjects submitted counts are visible only to NDA Administrators and to the NDA Collection or as the NDA Collection Owner.
     
  • When an NDA Collection that is flagged Blinded Clinical Trial reaches the maximum data sharing date for that Data Repository (see https://nda.nih.gov/about/sharing-regimen.html), the embargo on Data Expected information is released.
     

Funding Source

The organization(s) responsible for providing the funding is listed here. 

Supporting Documentation

Users with Submission privileges, as well as Collection Owners, Program  Officers, and those with Administrator privileges, may upload and attach supporting documentation. By default, supporting documentation is shared to the general public, however, the option is also available to limit this information to qualified researchers only. 

Grant Information 

Identifiable details are displayed about the Project of which the Collection was derived from. You may click in the Project Number to view a full report of the Project captured by the NIH. 

Clinical Trials

Any data that is collected to support or further the research of clinical studies will be available here. Collection Owners and those with Administrator privileges may add new clinical trials. 

Frequently Asked Questions

  • When a Collection is created by NDA staff and marked as Shared, an email notification will automatically be sent to the PI(s) of the grant(s) associated with the Collection to notify them.

  • During Collection creation, NDA staff determine the appropriate Permission Group based on the type of data to be submitted, the type of access that will be available to data access users, and the information provided by the Program Officer during grant award.

  • The NDA system does not allow for a single grant to be associated with more than one Collection; therefore, a single grant will not be listed in the Grant Information section of a Collection for more than one Collection.

  • In general, each Collection is associated with only one grant; however, multiple grants may be associated if the grant has multiple competing segments for the same grant number or if multiple different grants are all working on the same project and it makes sense to hold the data in one Collection (e.g., Cooperative Agreements).

Glossary

  • Number of human subjects enrolled in an NIH-funded clinical research study. The data is provided in annual progress reports.

  • A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users. 

  • Generally, the Collection Owner is the contact PI listed on a grant. Only one NDA user is listed as the Collection owner. Most automated emails are primarily sent to the Collection Owner.

  • The Collection Phase provides information on data submission as opposed to grant/project completion so while the Collection phase and grant/project phase may be closely related they are often different.  Collection users with Administrative Privileges are encouraged to edit the Collection Phase.  The Program Officer as listed in eRA (for NIH funded grants) may also edit this field. Changes must be saved by clicking the Save button at the bottom of the page.  This field is sortable alphabetically in ascending or descending order. Collection Phase options include: 

    • Pre-Enrollment:  A grant/project has started, but has not yet enrolled subjects.
    • Enrolling:  A grant/project has begun enrolling subjects.  Data submission is likely ongoing at this point.
    • Data Analysis:  A grant/project has completed enrolling subjects and has completed all data submissions.
    • Funding Completed:  A grant/project has reached the project end date.
  • The Collection State indicates whether the Collection is viewable and searchable.  Collections can be either Private, Shared, or an Ongoing Study.  A Collection that is shared does not necessarily have shared data as the Collection State and state of data are independent of each other.  This field can be edited by Collection users with Administrative Privileges and the Program Officer as listed in eRA (for NIH funded grants). Changes must be saved by clicking the Save button at the bottom of the page.

  • An editable field with the title of the Collection, which is often the title of the grant associated with the Collection.

  • Data Use Limitations (DULs) describe the appropriate secondary use of a dataset and are based on the original informed consent of a research participant. NDA only accepts consent-based data use limitations defined by the NIH Office of Science Policy.

  • Provides the grant number(s) for the grant(s) associated with the Collection.  The field is a hyperlink so clicking on the Grant number will direct the user to the grant information in the NIH Research Portfolio Online Reporting Tools (RePORT) page.

  • A virtual container and organization structure for data and associated documentation from one grant or one large project/consortium. It contains tools for tracking data submission and allows investigators to define a wide array of other elements that provide context for the data, including all general information regarding the data and source project, experimental parameters used to collect any event-based data contained in the Collection, methods, and other supporting documentation. They also allow investigators to link underlying data to an NDA Study, defining populations and subpopulations specific to research aims. 

  • NDA Collections may be organized by scientific similarity into NIH Research Initiatives, to facilitate query tool user experience. NIH Research Initiatives map to one or multiple Funding Opportunity Announcements. 

  • Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.

  • Number of human subject participants to be enrolled in an NIH-funded clinical research study. The data is provided in competing applications and annual progress reports.

  • Various documents and materials to enable efficient use of the data by investigators unfamiliar with the project and may include the research protocol, questionnaires, and study manuals.  

  • The total number of unique subjects for whom data have been shared and are available for users with permission to access data.

NDA Help Center

Collection - Shared Data Tab

This tab provides a quick overview of the Data Structure title, Data Type, and Number of Subjects that are currently Shared for the Collection. The information presented in this tab is automatically generated by NDA and cannot be edited. If no information is visible on this tab, this would indicate the Collection does not have shared data or the data is private.

The shared data is available to other researchers who have permission to access data in the Collection's designated Permission Group(s). Use the Download button to get all shared data from the Collection to the Filter Cart.

 

Frequently Asked Questions

  • To see what data your project have submitted are being used by a study, simply go the Associated Studies tab of your collection.  Alternatively, you may review an NDA Study Attribution Report available on the General tab.  

  • Often it becomes more difficult to organize and format data electronically after the project has been completed and the information needed to create a GUID may not be available; however, you may still contact a program staff member at the appropriate funding institution for more information.

  • Unlike completed projects where researchers may not have the information needed to create a GUID and/or where the effort needed to organize and format data becomes prohibitive, ongoing projects have more of an opportunity to overcome these challenges.  Please contact a program staff member at the appropriate funding institution for more information.

Glossary

  • A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points.  Data structures that have been defined in the NDA Data Dictionary are available at https://ndar.nih.gov/data_dictionary.html. 

  • A grouping of data by similar characteristics such as Clinical Assessments, Omics, or Neurosignal data.

  • The term 'Shared' generally means available to others; however, there are some slightly different meanings based on what is Shared.  A Shared NDA Collection or NDA Study is viewable and searchable publicly regardless of the user's role or whether the user has an NDA account.  A Shared Collection or NDA Study does not necessarily mean that data submitted to the Collection or used in the NDA Study have been shared as this is independently determined.  Data are shared according the schedule defined in a Collection's Data Expected Tab and/or in accordance with data sharing expectations in the NDA Data Sharing Terms and Conditions.  Additionally, Supporting Documentation uploaded to a Collection may be shared independent of whether data are shared, but will only be viewable and accessible if the Collection is Shared.

NDA Help Center

fMRi

fMRI stands for functional magnetic resonance imaging. fMRI tests measure blood flow, providing detailed functional images of the brain or body. 

Acquisition
The Acquisition parameters needed for an experiment include the following:

The name of the experiment is required. Please be concise and specific as possible.
Following experiment name, selection boxes are provided for the Equipment, Software, or other items specific to the experiment type. At least one selection is required for each. If NDAR does not have the appropriate listing, select Add New to add the information provided. Following the selection boxes, provide additional information may be required depending on the experiment type. Any required items are denoted by an asterisk (*).

Block/Event Design
At least one block/event is required. Note that any fields denoted with an asterisk (*) are required. All data must be devoid of personally identifiable data, including the contents of any files attached to the experiment.

Note: To simplify the definition of multiple events, we provide an Import from XML function. This function supports importing data from all three experiment sections (Acquisition, Block/Event Design, and Post Processing), at this time files cannot be uploaded from XML A test format is provided here and our XML Schema Definition (xsd) can be found here.

Post Processing
If you have completed any post-processing on your data, please choose 'Yes' for Has Postprocessing? If not, select 'No'. Depending on this selection the remaining post-processing fields will be enabled (some of which will be required). If you are initially providing data you can select 'No', then return to the experiment to add post-processing steps at a later date when the data are being provided.

Please provide information about post-processing manipulations, i.e. artifact detection algorithms, segmentation used for post data collection, items denoted with an asterisk (*) are required.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Submissions Tab

Users with permission to access Shared data in the Collection’s assigned Permission Group may use this tab. 

Here, you can:

  • Review your uploads to your Collection, monitor their status, and download them individually to verify their contents.
  • Download individual datasets as a secondary user of the data approved for access.
  • Identify and download datasets containing errors identified by NDA's QA/QC process for review and resolution.
  • Report suspected or discovered Personally Identifiable Information in a submission via the Actions column.

Frequently Asked Questions

Glossary

  • The default view of Datasets within a Collection's Submission tab.

  • A Submission Loading Status on a Collection's Submission Tab that indicates that an issue has prevented the successful loading of the submission.  Users should contact the NDA Help Desk for assistance at NDAHelp@mail.nih.gov.

  • The NDA has two Submission Cycles per year - January 15 and July 15.

  • An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.  

  • The unique and sequentially assigned ID for a submission (e.g. a discrete upload via the Validation and Upload Tool), which may contain any number of datafiles, Data Structures and/or Data Types, regardless of the Submission Loading Status. A single submission may be divided into multiple Datasets, which are based on Data Type.

  • The total number of unique subjects for whom data have been shared and are available for users with permission to access data.

  • The total number of unique subjects for whom data have been submitted, which includes data in both a Private State and a Shared State.

NDA Help Center

Collection - Publications Tab

The number of Publications is displayed in parentheses next to the tab name. Clicking on any of the Publication Titles will open the Publication in a new internet browsing tab. 

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may mark a publication as either Relevant or Not Relevant in the Status column. 

 

Frequently Asked Questions

  • Publications are considered relevant to a collection when the data shared is directly related to the project or collection.

  • PubMed, an online library containing journals, articles, and medical research. Sponsored by NiH and National Library of Medicine (NLM). 

Glossary

  • A link to the Create an NDA Study page that can be clicked to start creating an NDA Study with information such as the title, journal and authors automatically populated.

  • Indicates that the publication has not yet been reviewed and/or marked as Relevant or Not Relevant so it has not been determined whether an NDA Study is expected.

  • A publication that is not based on data related to the aims of the grant/project associated with the Collection or not based on any data such as a review article and, therefore, an NDA Study is not expected to be created.

  • PubMed provides citation information for biomedical and life sciences publications and is managed by the U.S. National Institutes of Health's National Library of Medicine.

  • The PUBMed ID is the unique ID number for the publication as recorded in the PubMed database.  

  • A publication that is based on data related to the aims of the grant/project associated with the Collection and, therefore, an NDA Study is expected to be created.

NDA Help Center

EEG

EEG stands for electroencencephalogram and is a test used to measure electrical activity in the brain.

Acquisition
The Acquisition parameters needed for an experiment include the following:

Name of the experiment is required. Please be concise and specific as possible.
Following experiment name, selection boxes are provided for the Equipment, Software, or other items specific to experiment type. At least one selection is required for each. If NDAR does not have the appropriate listing, select Add New to add the information provided. Following the selection boxes, provide additional information may be required depending on experiment type. Any required items are denoted by an asterisk (*).

Block/Event Design
At least one block/event is required. Note that any fields denoted with an asterisk (*) are required. All data must be devoid of personally identifiable data, including the contents of any files attached to the experiment.

Note: To simplify definition of multiple events, we provide an Import from XML function. This function supports importing data from all three experiment sections (Acquisition, Block/Event Design, and Post Processing), at this time files cannot be uploaded from XML A test format is provided here and our XML Schema Definition (xsd) can be found here.

Post Processing
If you have completed any post processing on your data, please choose 'Yes' for Has Postprocessing? If not, select 'No'. Depending on this selection the remaining post processing fields will be enabled (some of which will be required). If you are initially providing data you can select 'No', then return to the experiment to add post processing steps at a later date when the data are being provided.

Please provide information about post-processing manipulations, i.e. artifact detection algorithms, segmentation used for post data collection, items denoted with an asterisk (*) are required.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Data Expected

The Data Expected tab displays the list of all data that NDA expects to receive in association with the Collection as defined by the contributing researcher, as well as the dates for the expected initial upload of the data, and when it is first expected to be shared, or with the research community. Above the primary table of Data Expected, any publications determined to be relevant to the data within the Collection are also displayed - members of the contributing research group can use these to define NDA Studies, connecting those papers to underlying data in NDA.

The tab is used both as a reference for those accessing shared data, providing information on what is expected and when it will be shared, and as the primary tracking mechanism for contributing projects. It is used by both contributing primary researchers, secondary researchers, and NIH Program and Grants Management staff.

Contributing researchers just getting started on their project will need to define this list by adding all of the items they are collecting under their grant and setting their schedule according to the NDA Data Sharing Regimen. If you fall into this category, you can begin by clicking "add new Data Expected" and selecting which data structures you will be using, saving the page after each change, or requesting new structures by adding and naming a new item, providing any materials NDA Data Dictionary Curators can use to help define your structure. For more information see the tutorial on creating Data Expected.

If you are a contributing researcher creating this list for the first time, or making changes to the list as your project progress, please note the following:

  • Although items you add to the list and changes you make are displayed, they are not committed to the system until you Save the entire page using the "Save" button at the bottom of your screen. Please Save after every change to ensure none of your work is lost.
  • If you attempt to add a new structure, the title you provide must be unique - if another structure exists with the same name your change will fail.
  • Adding a new structure to this list is the only way to request the creation of a new Data Dictionary definition.

 

Frequently Asked Questions

  • An NDA Data Structure is comprised of multiple Data Elements to make up an electronic definition of an assessment, measure, questionnaire, etc will have a corresponding Data Structure.

  • The NDA Data Dictionary is comprised of electronic definitions known as Data Structures.

Glossary

  • Data specific to the primary aims of the research being conducted (e.g. outcome measures, other dependent variables, observations, laboratory results, analyzed images, volumetric data, etc.) including processed images.

  • Items listed on the Data Expected list in the Collection which may be an individual and discrete Data Structure, Data Structure Category, or Data Structure Group.

  • A defined organization and group of Data Elements to represent an electronic definition of a measure, assessment, questionnaire, or collection of data points.  Data structures that have been defined in the NDA Data Dictionary are available at https://ndar.nih.gov/data_dictionary.html. 

  • An NDA term describing the affiliation of a Data Structure to a Category, which may be disease/disorder or diagnosis related (Depression, ADHD, Psychosis), specific to data type (MRI, eye tracking, omics), or type of data (physical exam, IQ).

  • A Data Item listed on the Data Expected tab of a Collection that indicates a group of Data Structures (e.g., ADOS or SCID) for which data may be submitted instead of a specific Data Structure identified by version, module, edition, etc. For example, the ADOS Data Structure Category includes every ADOS Data Structure such as ADOS Module 1, ADOS Module 2, ADOS Module 1 - 2nd Edition, etc. The SCID Data Structure Group includes every SCID Data Structure such as SCID Mania, SCID V Mania, SCID PTSD, SCID-V Diagnosis, and more. 

  • A new Data Structure category, Evaluated Data is analyzed data resulting from the use of computational pipelines in the Cloud and can be uploaded directly back to a miNDAR database.  Evaluated Data is expected to be listed as a Data Item in the Collection's Data Expected Tab.

  • Imaging+ is an NDA term which encompasses all imaging related data including, but not limited to, images (DTI, MRI, PET, Structural, Spectroscopy, etc.) as well as neurosignal data (EEG, fMRI, MEG, EGG, eye tracking, etc.) and Evaluated Data.

  • Initial Submission and Initial Share dates should be populated according to the NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data will be shared with authorized users upon publication (via an NDA Study) or 1-2 years after the grant end date specified on the first Notice of Award, as defined in the applicable Data Sharing Terms and Conditions.

  • Initial Submission and Initial Share dates should be populated according to these NDA Data Sharing Terms and Conditions. Any modifications to these will go through the approval processes outlined above. Data for all subjects is not expected on the Initial Submission Date and modifications may be made as necessary based on the project's conduct.

  • An NDA created Data Structure used to convey basic information about the subject such as demographics, pedigree (links family GUIDs), diagnosis/phenotype, and sample location that are critical to allow for easier querying of shared data.

  • The NDA has two Submission Cycles per year - January 15 and July 15.

  • An interface to notify NDA that data may not be submitted during the upcoming/current submission cycle.  

NDA Help Center

Collection - Permissions Tab

Collection Owners, Program Officers, and users with Administrator privileges may view this tab.

The available permission groups include:

  • Query: This read-only access is generally for NIH Program Officers
  • Submission: This will grant read access and allow the user to upload data and create experiment definitions. This is for the typical contributing personnel member.
  • Administrator: In addition to the access provided to Query and Submission users, Admins can also edit the Collection itself, create or edit the Data Expected list, and edit user permissions. This access is for the PI, data managers, and anyone they wish to delegate this to.

The PI has a special designation as the Collection Owner in addition to administrator access.

Frequently Asked Questions

  • Collection Owners and Admins may assign Collection Privileges to anyone.

  • Yes, you can assign various Privileges to other users with an NDA account.

  • If you are the Collection Owner or have Admin privileges, you can view and make changes to the list of individuals who have access to the Collection on the Collection's Permissions tab.  Information on users who have access to data Shared in your Collection because they were granted access to a Permission Group is not available.

  • Staff/collaborators who are working submitting data to the Collection, checking the quality of the data, and/or analyzing data should have access for the duration of the project until all data have been submitted, NDA Studies have been created for data used in publications, and/or a collaborative relationship with the user exists.  

  • The individual listed as an Investigator on the General tab of the NDA Collection will generally be able to provide a user access to the NDA Collection.  Additional users may also have this ability if granted Administrator access to an NDA Collection; however, these users are not viewable unless your account has access to the NDA Collection.  Given this, it is best to contact the Investigator to request access to the Collection.

  • Privileges that can be assigned to a user include:
    Submission allows a user to submit data to Collection
    Query allows the user to download data from Collection even when in a Private state
    Admin is both the Submission and Query Privilege + the ability to give privileges to other users.

  • You may have staff who are working on the submission of data or other activities associated with data sharing such as the definition of the Data Expected list or NDA Experiment creation.  Also, many projects have multiple performance sites and wish to share data among the site PIs.  Submitting to the NDA facilitates access by all investigators working on a project even before data have been shared with other users.  You can control who gets access to data while in a Private state.

Glossary

  • A privilege provided to a user associated with an NDA Collection or NDA Study whereby that user can perform a full range of actions including providing privileges to other users. 

  • Access to shared record-level data in NDA is provisioned at the level of a Permission Group. NDA Permission Groups consist of one or multiple NDA Collections that contain data with the same subject consents.

NDA Help Center

Eye Tracking

EyeTracking tests follow the movement of the eye. The visual trajectory or focus can help determine predictions and assist in diagnoses. 

Acquisition
The Acquisition parameters needed for an experiment include the following:

The name of the experiment is required. Please be concise and specific as possible.
Following experiment name, selection boxes are provided for the Equipment, Software, or other items specific to the experiment type. At least one selection is required for each. If NDAR does not have the appropriate listing, select Add New to add the information provided. Following the selection boxes, provide additional information may be required depending on the experiment type. Any required items are denoted by an asterisk (*).

Block/Event Design
At least one block/event is required. Note that any fields denoted with an asterisk (*) are required. All data must be devoid of personally identifiable data, including the contents of any files attached to the experiment.

Note: To simplify the definition of multiple events, we provide an Import from XML function. This function supports importing data from all three experiment sections (Acquisition, Block/Event Design, and Post Processing), at this time files cannot be uploaded from XML A test format is provided here and our XML Schema Definition (xsd) can be found here.

Post Processing
If you have completed any post-processing on your data, please choose 'Yes' for Has Postprocessing? If not, select 'No'. Depending on this selection the remaining post-processing fields will be enabled (some of which will be required). If you are initially providing data you can select 'No', then return to the experiment to add post-processing steps at a later date when the data are being provided.

Please provide information about post-processing manipulations, i.e. artifact detection algorithms, segmentation used for post data collection, items denoted with an asterisk (*) are required.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Collection - Experiments Tab

The number of Experiments included is displayed in parentheses next to the tab name. You may download all experiments associated with the Collection via the Download button. You may view individual experiments by clicking the Experiment Name and add them to the Filter Cart via the Add to Cart button.

Collection Owners, Program Officers, and users with Submission or Administrative Privileges for the Collection may create or edit an Experiment.

Please note: The creation of an NDA Experiment does not necessarily mean that data collected, according to the defined Experiment, has been submitted or shared.

Frequently Asked Questions

  • Yes -see the “Copy” button in the bottom left when viewing an experiment. There are two actions that can be performed via this button:

    1. Copy the experiment with intent for modifications.  
    2. Associate the experiment to the collection. No modifications can be made to the experiment.

     

Glossary

  • An Experiment must be Approved before data using the associated Experiment_ID may be uploaded.

  • The ID number automatically generated by NDA which must be included in the appropriate file when uploading data to link the Experiment Definition to the subject record.

NDA Help Center

Omics

Omics is a collective group of technologies, related to a field of study in Biology such as Genomics or proteomics. 

Experiment Parameters

To define an Omics experiment, provide a meaningful name and select a single molecule. The standard molecules are listed. However, if you are doing proteomic or environmental experiments, simply “Add New” and the new selection will be created. Only one value for molecule is permitted.

Next the technology (box 2) associated with the molecule will be presented along with its application. Again, only one selection is possible. If you wish to see all of NDAR’s options for any one box, Select “Show All”.

Platform

Continue to select the Platform (box 3).

Extraction

Next, the Extraction Protocol (box 4) and Kits (box 5) are presented based upon the Molecule selected and the Processing Protocol (box 6) and Kits (box 7) are presented based upon the Molecule and Technology Application (Box 1 and 2)

Processing

Note that for each of these (boxes 4, 5, 6, and 7) multiple selections are possible.

Additional Information

Lastly, the Software (box 8) and Equipment (box 9) is expected.

 

Once saved, the experiment will be associated with the Collection and by using the returned Experiment_ID, the NDA makes it possible to associate the experiment meta data directly with the data from the experiment.

Frequently Asked Questions

Glossary

  • This button will add all selections to the Filter Cart. 

  • This button will allow you to copy all of the Experiment details as a template for a new experiment. 

  • Adds all data from the current selections in a Collection or NDA Study to the Filter Cart.

  • This button will allow you to return to the Experiments tab. 

NDA Help Center

Filter Cart

Viewable at the top right of NDA pages, the Filter Cart is a temporary holder for filters and data they select. Filters are added to the Workspace first, before being submitted to The Filter Cart. Data selected by filters in the Filter Cart can be added to a Data Package or an NDA Study from the Data Packaging Page, by clicking the 'Create Data Package / Add Data to Study' button.

The filter cart supports combining multiple filters together, and depending on filter type will use "AND" or "OR"  when combining filters.

Multiple selections from the same filter type will result in those selections being applied with an ‘OR’ condition. For example, if you add an NDA Collection Filter with selections for both collections 2112 and 2563 to an empty Workspace, the subjects from NDA Collection 2112 ‘OR’ NDA Collection 2563 will be added to your Workspace even if a subject is in both NDA Collections. You can then add other NDA Collections to your Workspace which further extends the ‘OR’ condition.

If a different filter type is added to your Workspace, or a filter has already been submitted to the Filter Cart, the operation then performs a logical ‘AND’ operation. This means that given the subjects returned from the first filter, only those subjects that matched the first filter are returned by the second filter (i.e., subjects that satisfied both filters).

When combining other filters with the GUID filter, please note the GUID filter should be added last. Otherwise, preselected data may be lost. For example, a predefined filter from Featured Datasets may select a subset of data available for a subject. When combined with a GUID filter for the same subject, the filter cart will contain all data available from that subject, data structure, and dataset; this may be more data than was selected in the predefined filter for that subject. Again, you should add the GUID Filter as the last filter to your cart. This ensures 'AND' logic between filters and will limit results to the subjects, data structures, and datasets already included in your filter cart.

Note that only the subjects specific to your filter will be added to your Filter Cart and only on data shared with the research community. Other data for those same subjects may exist (i.e., within another NDA Collection, associated with a data structure that was not requested in the query, etc.). So, users should select ‘Find all Subjects Data’ to identify all data for those specific subjects. 

Additional Tips:

  • You may query the data without an account, but to gain access you will need to create an NDA user account and apply for access.  Most data access requires that you or your lab are sponsored by an NIH recognized institution with Federal Wide Assurance (FWA).  Without access, you will not be able to obtain individual-level data. 

    Once you have selected data of interest you can:
  • Create a data package - This allows you to specify format for access/download
  • Assign to Study Cohort - Associate the data to an NDA Study allowing for a DOI to be generated and the data to be linked directly to a finding, publication, or data release. 
  • Find All Subject Data - Depending on filter types being used, not all data associated with a subject will be selected.  Data may be restricted by data structure, NDA Collection, or outcome variables (e.g., NDA Study). ‘Find All Data’ expands the fliter criteria by replacing all filters in your Filter Cart with a single Query by GUID filter for all subjects selected by those filters.

    Please Note:
  • When running a query, it may take a moment to populate the Filter Cart. Queries happen in the background so you can define other queries during this time. 
  • When you add your first filter, all data associated with your query will be added to the Filter Cart (e.g., a Concept, an NDA Collection, a Data Structure/Element, etc.). As you add additional filters, they will also display in the Filter Cart. Only the name of filter will be shown in the Filter Cart, not the underlying structures. 
  • Information about the contents of the Filter Cart can be seen by clicking "Edit”.
  • Once your results appear in the Filter Cart, you can create a data package or assign subjects to a study by selecting the 'Package/Assign to Study' option. You can also 'Edit' or 'Clear' filters.
     

Frequently Asked Questions

  • The Filter Cart currently employs basic AND/OR Boolean logic. A single filter may contain multiple selections for that filter type, e.g., a single NDA Study filter might contain NDA Study 1 and NDA Study 2. A subject that is in EITHER 1 OR 2 will be returned.  Adding multiple filters to the cart, regardless of type, will AND the result of each filter.  If NDA Study 1 and NDA Study 2 are added as individual filters, data for a subject will only be selected if the subject is included in  BOTH 1 AND 2.

    When combining other filters with the GUID filter, please note the GUID filter should be added last. Otherwise, preselected data may be lost. For example, a predefined filter from Featured Datasets may select a subset of data available for a subject. When combined with a GUID filter for the same subject, the filter cart will contain all data available from that subject, data structure, and dataset; this may be more data than was selected in the predefined filter for that subject. Again, you should add the GUID Filter as the last filter to your cart. This ensures 'AND' logic between filters and will limit results to the subjects, data structures, and datasets already included in your filter cart.

  • Viewable at the top right of NDA pages, the Filter Cart is a temporary holder of data identified by the user, through querying or browsing, as being of some potential interest. The Filter Cart is where you send the data from your Workspace after it has been filtered.

  • After filters are added to the Filter Cart, users have options to ‘Create a Package’ for download, ‘Associate to Study Cohort’, or ‘Find All Subject Data’. Selecting ‘Find All Subject Data’ identifies and pulls all data for the subjects into the Filter Cart. Choosing ‘Create a Package’ allows users to package and name their query information for download. Choosing ‘Associate to Study Cohort’ gives users the opportunity to choose the Study Cohort they wish to associate this data.

Glossary

  • Once your filter cart contains the subjects of interest, select Create Data Package/Assign to Data Study which will provide options for accessing item level data and/or assigning to a study.  

  • Once queries have been added to your workspace, the next step is to Submit the Filters in the workspace to the Filter Cart.  This process runs the queries selected, saving the results within a filter cart attached to your account.  

  • The Workspace within the General Query Tool is a holding area where you can review your pending filters prior to adding them to Filter Cart. Therefore, the first step in accessing data is to select one or more items and move it into the Workspace. 

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Collection - Associated Studies

Clicking on the Study Title will open the study details in a new internet browser tab. The Abstract is available for viewing, providing the background explanation of the study, as provided by the Collection Owner. 

Primary v. Secondary Analysis: The Data Usage column will have one of these two choices. An associated study that is listed as being used for Primary Analysis indicates at least some and potentially all of the data used was originally collected by the creator of the NDA Study. Secondary Analysis indicates the Study owner was not involved in the collection of data, and may be used as supporting data. 

Private v. Shared State: Studies that remain private indicate the associated study is only available to users who are able to access the collection. A shared study is accessible to the general public. 

Frequently Asked Questions

  • Studies are associated to the Collection automatically when the data is defined in the Study. 

Glossary

  • A tab in a Collection that lists the NDA Studies that have been created using data from that Collection including both Primary and Secondary Analysis NDA Studies.

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1 Numbers reported are subjects by age
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Format should be in the following format: Activity Code, Institute Abbreviation, and Serial Number. Grant Type, Support Year, and Suffix should be excluded. For example, grant 1R01MH123456-01A1 should be entered R01MH123456

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Collection - Use Existing Experiment

To associate an experiment to the current collection, just select an axperiment from the table below then click the associate experiment button to persist your changes (saving the collection is not required). Note that once an experiment has been associated to two or more collections, the experiment will not longer be editable.

The table search feature is case insensitive and targets the experiment id, experiment name and experiment type columns. The experiment id is searched only when the search term entered is a number, and filtered using a startsWith comparison. When the search term is not numeric the experiment name is used to filter the results.

SelectExperiment IdExperiment NameExperiment Type
  • Select One
  • EEG
  • EGG
  • Eye Tracking
  • Omics
  • fMRI
Created On
1858GNG Anger, Gender, Happy Tasks- EEGEEG10/15/2021
1857PVDM, imaging sessionEye Tracking10/14/2021
1856PVDM, imaging sessionfMRI10/13/2021
1855PVDM, behavioral sessionEye Tracking10/13/2021
1854Cerebellar Dysfunction in Autism: resting state fMRIfMRI10/13/2021
1851Reappraisal Emotion Regulation Task - V2fMRI09/22/2021
1850Reappraisal Emotion Regulation Task - V1fMRI09/22/2021
1849Stop-Signal Arrows - Randomization BfMRI09/22/2021
1848Stop-Signal Arrows - Randomization AfMRI09/22/2021
1847NPU Threat Countdown Short - V2fMRI09/22/2021
1846NPU Threat Countdown Short - V1fMRI09/22/2021
1836Alcohol Cue ReactivityEEG09/02/2021
1835Doors Reward ParadigmEEG08/30/2021
1834Flanker ArrowsEEG08/30/2021
1833Transcriptomic data of Clozapine-treated Ngn2-induced Human Excitatory NeuronsOmics08/20/2021
1830Illumina Global Screening ArrayOmics08/02/2021
1829Single-cell multiome sequencing: ATAC-seqOmics07/26/2021
1828Single-cell multiome sequencing - RNA-seqOmics07/26/2021
1827scATACseqOmics07/26/2021
1826scRNAseqOmics07/26/2021
1825Fetal Resting-state fMRI Brain MasksfMRI07/23/2021
1824Apex of Cognitive ControlfMRI07/22/2021
1823Face adaptationEye Tracking07/21/2021
1822Presaccadic AttentionEye Tracking07/21/2021
1821templefMRI07/19/2021
1820parvizi_eeg_145EEG07/16/2021
1819parvizi_eeg_166EEG07/16/2021
1818parvizi_eeg_164EEG07/16/2021
1817parvizi_eeg_165EEG07/16/2021
1816parvizi_eeg_162EEG07/16/2021
1815parvizi_eeg_161EEG07/16/2021
1814eeg_parvizi_160EEG07/16/2021
1813parvizi_eeg_159EEG07/16/2021
1812Singleton distractor rejectionEEG07/16/2021
1810InterlayerfMRI07/15/2021
1809Alpha, BOLD, experience, and expectancy during associative learningEEG07/14/2021
1808Alpha, BOLD, experience, and expectancy during associative learningfMRI07/14/2021
1807Correlating concurrent EEG/BOLD in occipital cortex while presenting Gabor patch steadily increasing in contrastEEG07/14/2021
1806Correlating concurrent EEG/BOLD in occipital cortex while presenting Gabor patch steadily increasing in contrastfMRI07/14/2021
1805Resting StatefMRI07/13/2021
1804Hierarchical task control fMRI07/13/2021
1803FXC_EEG_IncentivizedStroopEEG07/13/2021
1802FXC_fMRI_IncentivizedStroopfMRI07/13/2021
1801ER Resting-State ScanfMRI07/12/2021
1799Offset ResponseEEG07/07/2021
1798VEPEEG07/06/2021
1797The Parametric Go-No-Go TaskfMRI07/02/2021
1796oppPEfMRI07/01/2021
1795D3 - MIDT TaskfMRI06/30/2021
1794D3 - Effort TaskfMRI06/30/2021
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Collection Summary Collection Charts
Collection Title Collection Investigators Collection Description
Fetal Programming of the Newborn and Infant Human Brain
Claudia Buss and Pathik D. Wadhwa 
We propose to conduct a prospective, longitudinal, follow-up study in a population-based cohort of children born to mothers who will participate in an NIH-funded study of biological and behavioral processes in pregnancy. We will have extensive characterization in this child cohort over the course of their intrauterine life and birth with all the prenatal measures required to address the above questions, including serial measures of the maternal-placental fetal endocrine and immune/inflammatory milieu, clinical measures of obstetric complications, laboratory results of clinical/diagnostic tests, measures of maternal sociodemographic, behavioral, and psychosocial characteristics, measures of the birth phenotype, and banked samples of maternal biologic tissue and extracted maternal and child DNA samples. We will recruit a sample of 120-140 children from this cohort at birth and follow them up until 12 months age. We propose two major study assessments at T1= 2-4 weeks and T2= 12 months age. Our primary study outcomes, brain morphology (size of the hippocampus, amygdala and prefrontal cortex) will be derived from serial MRI scans, and white matter integrity (fractional anisotropy along major white matter tracts: corpus callosum genu and splenium tracts and uncinate fasciculus) will be derived from serial DTI scans. For all predictor variables (CRH, cortisol, IL-6 and TNF-alpha), the area under the curve (AUC) will be estimated using General Additive Models(GAM) via cubic B-splines, which will be used as the predictors for measures of brain morphology and white matter integrity. In order to determine if there are particular time points during pregnancy that represent sensitive periods in predicting size of HC, AG and PFC, polynomial distributed lag models will be employed. Infants mental and motor development will be assessed at concurrent time points (at T1 and T2) with the Bayley Scales of Infant Development. Mediation models will be applied to test whether alterations in the brain associated with MPF parameters account for the association between the same MPF parameters and BSID performance.demographics, DTI, T1, and T2 brain images for healthy 0 to 4 week old infants.
NIMH Data Archive
NIMH Data Archive
Funding Completed
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$1,825,473.00
391
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NIH - Extramural None

QA-notification.txt Other Quality Assurance Notification Qualified Researchers

R01MH091351-01 FETAL PROGRAMMING OF THE NEWBORN AND INFANT HUMAN BRAIN 12/01/2010 11/30/2015 140 142 UNIVERSITY OF CALIFORNIA-IRVINE $1,825,473.00

IDNameCreated DateStatusType
1133resting fMRI12/20/2018ApprovedfMRI

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Shared Data

Data structures with the number of subjects submitted and shared are provided.

Assays Form Clinical Assessments 204
Bayley-III Scales of Infant Development Clinical Assessments 119
Blood Sample Collection Clinical Assessments 153
Clinical Lab Tests Part II Clinical Assessments 218
Cortisol Samples Questionnaire Clinical Assessments 209
Home Observation for Measurement of the Environment Inventory Clinical Assessments 128
Image Imaging 118
Research Subject Clinical Assessments 108
Test of Infant Motor Performance Clinical Assessments 115
Wechsler Adult Intelligence Scale Fourth Edition [part 1] Clinical Assessments 191

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Publications

Publications relevant to NDA data are listed below. Most displayed publications have been associated with the grant within Pubmed. Use the "+ New Publication" button to add new publications. Publications relevant/not relevant to data expected are categorized. Relevant publications are then linked to the underlying data by selecting the Create Study link. Study provides the ability to define cohorts, assign subjects, define outcome measures and lists the study type, data analysis and results. Analyzed data and results are expected in this way.

PubMed IDStudyTitleJournalAuthorsDateStatus
33766778Create StudyNeuroanatomical Correlates Underlying the Association Between Maternal Interleukin 6 Concentration During Pregnancy and Offspring Fluid Reasoning Performance in Early Childhood.Biological psychiatry. Cognitive neuroscience and neuroimagingRasmussen, Jerod M; Graham, Alice M; Gyllenhammer, Lauren E; Entringer, Sonja; Chow, Daniel S; O'Connor, Thomas G; Fair, Damien A; Wadhwa, Pathik D; Buss, ClaudiaMarch 23, 2021Not Determined
33313841Create StudyPlacental Corticotrophin-Releasing Hormone is a Modulator of Fetal Liver Blood Perfusion.The Journal of clinical endocrinology and metabolismIkenoue, Satoru; Waffarn, Feizal; Ohashi, Masanao; Tanaka, Mamoru; Gillen, Daniel L; Buss, Claudia; Entringer, Sonja; Wadhwa, Pathik DMarch 8, 2021Not Determined
33040973Create StudyNeonatal hippocampal volume moderates the effects of early postnatal enrichment on cognitive development.Developmental cognitive neuroscienceOverfeld, Judith; Entringer, Sonja; Rasmussen, Jerod M; Heim, Christine M; Styner, Martin A; Gilmore, John H; Wadhwa, Pathik D; Buss, ClaudiaOctober 1, 2020Not Determined
32807730Create StudyNeonatal brain volume as a marker of differential susceptibility to parenting quality and its association with neurodevelopment across early childhood.Developmental cognitive neuroscienceNolvi, Saara; Rasmussen, Jerod M; Graham, Alice M; Gilmore, John H; Styner, Martin; Fair, Damien A; Entringer, Sonja; Wadhwa, Pathik D; Buss, ClaudiaOctober 1, 2020Not Determined
32240906Create StudyIntergenerational transmission of the effects of maternal exposure to childhood maltreatment on offspring obesity risk: A fetal programming perspective.PsychoneuroendocrinologyLindsay, Karen L; Entringer, Sonja; Buss, Claudia; Wadhwa, Pathik DJune 2020Not Determined
31983868Create StudyEntropy-based Correspondence Improvement of Interpolated Skeletal Models.Computer vision and image understanding : CVIUTu L, Vicory J, Elhabian S, Paniagua B, Prieto JC, Damon JN, Whitaker R, Styner M, Pizer SMOctober 2016Not Determined
31920593Create StudyNeonatal White Matter Maturation Is Associated With Infant Language Development.Frontiers in human neuroscienceSket, Georgina M; Overfeld, Judith; Styner, Martin; Gilmore, John H; Entringer, Sonja; Wadhwa, Pathik D; Rasmussen, Jerod M; Buss, ClaudiaJanuary 2019Not Determined
31402834Create StudyFitting Skeletal Object Models Using Spherical Harmonics Based Template Warping.IEEE signal processing lettersTu, Liyun; Yang, Dan; Vicory, Jared; Zhang, Xiaohong; Pizer, Stephen M; Styner, MartinDecember 2015Not Determined
30858011Create StudyA Role of Oxytocin Receptor Gene Brain Tissue Expression Quantitative Trait Locus rs237895 in the Intergenerational Transmission of the Effects of Maternal Childhood Maltreatment.Journal of the American Academy of Child and Adolescent PsychiatryToepfer, Philipp; O'Donnell, Kieran J; Entringer, Sonja; Heim, Christine M; Lin, David T S; MacIsaac, Julia L; Kobor, Michael S; Meaney, Michael J; Provençal, Nadine; Binder, Elisabeth B; Wadhwa, Pathik D; Buss, ClaudiaDecember 2019Not Determined
30690225Create StudyDynamic DNA methylation changes in the maternal oxytocin gene locus (OXT) during pregnancy predict postpartum maternal intrusiveness.PsychoneuroendocrinologyToepfer, Philipp; O'Donnell, Kieran J; Entringer, Sonja; Garg, Elika; Heim, Christine M; Lin, David T S; MacIsaac, Julia L; Kobor, Michael S; Meaney, Michael J; Provençal, Nadine; Binder, Elisabeth B; Wadhwa, Pathik D; Buss, ClaudiaMay 2019Not Determined
30581123Create StudyNewborn amygdala connectivity and early emerging fear.Developmental cognitive neuroscienceThomas, Elina; Buss, Claudia; Rasmussen, Jerod M; Entringer, Sonja; Ramirez, Julian S B; Marr, Mollie; Rudolph, Marc D; Gilmore, John H; Styner, Martin; Wadhwa, Pathik D; Fair, Damien A; Graham, Alice MJune 2019Not Determined
30122286Create StudyMaternal Cortisol Concentrations During Pregnancy and Sex-Specific Associations With Neonatal Amygdala Connectivity and Emerging Internalizing Behaviors.Biological psychiatryGraham, Alice M; Rasmussen, Jerod M; Entringer, Sonja; Ben Ward, Elizabeth; Rudolph, Marc D; Gilmore, John H; Styner, Martin; Wadhwa, Pathik D; Fair, Damien A; Buss, ClaudiaJanuary 2019Not Determined
29714050Create StudyMaternal Metabolomic Profile and Fetal Programming of Offspring Adiposity: Identification of Potentially Protective Lipid Metabolites.Molecular nutrition & food researchHellmuth, Christian; Lindsay, Karen L; Uhl, Olaf; Buss, Claudia; Wadhwa, Pathik D; Koletzko, Berthold; Entringer, SonjaJanuary 2019Not Determined
29654875Create StudyMaternal Interleukin-6 concentration during pregnancy is associated with variation in frontolimbic white matter and cognitive development in early life.NeuroImageRasmussen, Jerod M; Graham, Alice M; Entringer, Sonja; Gilmore, John H; Styner, Martin; Fair, Damien A; Wadhwa, Pathik D; Buss, ClaudiaJanuary 2019Not Determined
29632361Create StudyMaternal IL-6 during pregnancy can be estimated from newborn brain connectivity and predicts future working memory in offspring.Nature neuroscienceRudolph, Marc D; Graham, Alice M; Feczko, Eric; Miranda-Dominguez, Oscar; Rasmussen, Jerod M; Nardos, Rahel; Entringer, Sonja; Wadhwa, Pathik D; Buss, Claudia; Fair, Damien AMay 2018Not Determined
29332985Create StudyCIVILITY: Cloud based Interactive Visualization of Tractography Brain Connectome.Proceedings of SPIE--the International Society for Optical EngineeringPuechmaille, Danaële; Styner, Martin; Prieto, Juan CMarch 2017Not Determined
29332984Create StudyWhite Matter Fiber-based Analysis of T1w/T2w Ratio Map.Proceedings of SPIE--the International Society for Optical EngineeringChen, Haiwei; Budin, Francois; Noel, Jean; Prieto, Juan Carlos; Gilmore, John; Rasmussen, Jerod; Wadhwa, Pathik D; Entringer, Sonja; Buss, Claudia; Styner, MartinFebruary 2017Not Determined
28945591Create StudySkeletal Shape Correspondence Through Entropy.IEEE transactions on medical imagingTu, Liyun; Styner, Martin; Vicory, Jared; Elhabian, Shireen; Wang, Rui; Hong, Junpyo; Paniagua, Beatriz; Prieto, Juan C; Yang, Dan; Whitaker, Ross; Pizer, Stephen MJanuary 2018Not Determined
28842114Create StudyIntergenerational Effect of Maternal Exposure to Childhood Maltreatment on Newborn Brain Anatomy.Biological psychiatryMoog, Nora K; Entringer, Sonja; Rasmussen, Jerod M; Styner, Martin; Gilmore, John H; Kathmann, Norbert; Heim, Christine M; Wadhwa, Pathik D; Buss, ClaudiaJanuary 2018Not Determined
28755549Create StudyChildhood maltreatment is associated with increased risk of subclinical hypothyroidism in pregnancy.PsychoneuroendocrinologyMoog NK, Heim CM, Entringer S, Kathmann N, Wadhwa PD, Buss COctober 2017Relevant
28754515Create StudyMaternal Systemic Interleukin-6 During Pregnancy Is Associated With Newborn Amygdala Phenotypes and Subsequent Behavior at 2 Years of Age.Biological psychiatryGraham, Alice M; Rasmussen, Jerod M; Rudolph, Marc D; Heim, Christine M; Gilmore, John H; Styner, Martin; Potkin, Steven G; Entringer, Sonja; Wadhwa, Pathik D; Fair, Damien A; Buss, ClaudiaJanuary 2018Relevant
28723888Create StudyAssociation between supraclavicular brown adipose tissue composition at birth and adiposity gain from birth to 6 months age.Pediatric researchEntringer S, Rasmussen J, Cooper DM, Ikenoue S, Waffarn F, Potkin SG, Wadhwa PD, Buss CJuly 2017Relevant
28487552Create StudyNewborn insula gray matter volume is prospectively associated with early life adiposity gain.International journal of obesity (2005)Rasmussen JM, Entringer S, Kruggel F, Cooper DM, Styner M, Gilmore JH, Potkin SG, Wadhwa PD, Buss CMay 2017Relevant
28433734Create StudyProspective association of fetal liver blood flow at 30 weeks gestation with newborn adiposity.American journal of obstetrics and gynecologyIkenoue S, Waffarn F, Ohashi M, Sumiyoshi K, Ikenoue C, Buss C, Gillen DL, Simhan HN, Entringer S, Wadhwa PDAugust 2017Relevant
28433086Create StudyIntergenerational Transmission of Maternal Childhood Maltreatment Exposure: Implications for Fetal Brain Development.Journal of the American Academy of Child and Adolescent PsychiatryBuss, Claudia; Entringer, Sonja; Moog, Nora K; Toepfer, Philipp; Fair, Damien A; Simhan, Hyagriv N; Heim, Christine M; Wadhwa, Pathik DMay 2017Not Relevant
28334351Create StudyEffects of Antenatal Maternal Depressive Symptoms and Socio-Economic Status on Neonatal Brain Development are Modulated by Genetic Risk.Cerebral cortex (New York, N.Y. : 1991)Qiu A, Shen M, Buss C, Chong YS, Kwek K, Saw SM, Gluckman PD, Wadhwa PD, Entringer S, Styner M, Karnani N, Heim CM, O'Donnell KJ, Holbrook JD, Fortier MV, Meaney MJ, May 2017Not Determined
28135691Create StudyAssessment of acculturation in minority health research.Social science & medicine (1982)Fox, Molly; Thayer, Zaneta; Wadhwa, Pathik DMarch 2017Not Relevant
28027955Create StudyOxytocin pathways in the intergenerational transmission of maternal early life stress.Neuroscience and biobehavioral reviewsToepfer, Philipp; Heim, Christine; Entringer, Sonja; Binder, Elisabeth; Wadhwa, Pathik; Buss, ClaudiaFebruary 2017Not Relevant
27988340Create StudyA novel maturation index based on neonatal diffusion tensor imaging reflects typical perinatal white matter development in humans.International journal of developmental neuroscience : the official journal of the International Society for Developmental NeuroscienceRasmussen, Jerod M; Kruggel, Frithjof; Gilmore, John H; Styner, Martin; Entringer, Sonja; Consing, Kirsten N Z; Potkin, Steven G; Wadhwa, Pathik D; Buss, ClaudiaFebruary 2017Not Determined
27900852Create StudyAssociation of ultrasound-based measures of fetal body composition with newborn adiposity.Pediatric obesityIkenoue, S; Waffarn, F; Sumiyoshi, K; Ohashi, M; Ikenoue, C; Buss, C; Gillen, D L; Simhan, H N; Entringer, S; Wadhwa, P DAugust 2017Not Determined
27235635Create StudyCorrespondence between hair cortisol concentrations and 30-day integrated daily salivary and weekly urinary cortisol measures.PsychoneuroendocrinologyShort SJ, Stalder T, Marceau K, Entringer S, Moog NK, Shirtcliff EA, Wadhwa PD, Buss CSeptember 2016Not Determined
27065227Create StudyAutotract: Automatic cleaning and tracking of fibers.Proceedings of SPIE--the International Society for Optical EngineeringPrieto, Juan C; Yang, Jean Y; Budin, François; Styner, MartinFebruary 27, 2016Not Relevant
26716698Create StudyLongitudinal Metabolomic Profiling of Amino Acids and Lipids across Healthy Pregnancy.PloS oneLindsay, Karen L; Hellmuth, Christian; Uhl, Olaf; Buss, Claudia; Wadhwa, Pathik D; Koletzko, Berthold; Entringer, Sonja2015Not Determined
26612964Create StudyEarly Postnatal Myelin Content Estimate of White Matter via T1w/T2w Ratio.Proceedings of SPIE--the International Society for Optical EngineeringLee, Kevin; Cherel, Marie; Budin, Francois; Gilmore, John; Consing, Kirsten Zaldarriaga; Rasmussen, Jerod; Wadhwa, Pathik D; Entringer, Sonja; Glasser, Matthew F; Van Essen, David C; Buss, Claudia; Styner, Martin2015Not Determined
26499255Create StudyImplications of newborn amygdala connectivity for fear and cognitive development at 6-months-of-age.Developmental cognitive neuroscienceGraham, Alice M; Buss, Claudia; Rasmussen, Jerod M; Rudolph, Marc D; Demeter, Damion V; Gilmore, John H; Styner, Martin; Entringer, Sonja; Wadhwa, Pathik D; Fair, Damien AApril 2016Not Determined
26434624Create StudyInfluence of maternal thyroid hormones during gestation on fetal brain development.NeuroscienceMoog NK, Entringer S, Heim C, Wadhwa PD, Kathmann N, Buss COctober 3, 2015Not Determined
26372770Create StudyPrenatal stress, development, health and disease risk: A psychobiological perspective-2015 Curt Richter Award Paper.PsychoneuroendocrinologyEntringer S, Buss C, Wadhwa PDDecember 2015Not Determined
26089584Create StudyAutomatic Tissue Segmentation of Neonate Brain MR Images with Subject-specific Atlases.Proceedings of SPIE--the International Society for Optical EngineeringCherel, Marie; Budin, Francois; Prastawa, Marcel; Gerig, Guido; Lee, Kevin; Buss, Claudia; Lyall, Amanda; Consing, Kirsten Zaldarriaga; Styner, MartinFebruary 21, 2015Not Determined
26028804Create StudySkeletal shape correspondence via entropy minimization.Proceedings of SPIE--the International Society for Optical EngineeringTu, Liyun; Styner, Martin; Vicory, Jared; Paniagua, Beatriz; Prieto, Juan Carlos; Yang, Dan; Pizer, Stephen M2015Not Determined
25905831Create StudyIntergenerational transmission of the effects of acculturation on health in Hispanic Americans: a fetal programming perspective.American journal of public healthFox M, Entringer S, Buss C, DeHaene J, Wadhwa PDJuly 2015Not Determined
24205024Create StudyBrown adipose tissue quantification in human neonates using water-fat separated MRI.PloS oneRasmussen, Jerod M; Entringer, Sonja; Nguyen, Annie; van Erp, Theo G M; Burns, Joshua; Guijarro, Ana; Oveisi, Fariba; Swanson, James M; Piomelli, Daniele; Wadhwa, Pathik D; Buss, Claudia; Potkin, Steven G2013Not Determined
24119939Create StudyMaternal positive affect over the course of pregnancy is associated with the length of gestation and reduced risk of preterm delivery.Journal of psychosomatic researchVoellmin A, Entringer S, Moog N, Wadhwa PD, Buss COctober 2013Not Determined
23047922Create StudyFetal programming of brain development: intrauterine stress and susceptibility to psychopathology.Science signalingBuss C, Entringer S, Wadhwa PDOctober 9, 2012Not Determined
22719848Create StudyImpaired executive function mediates the association between maternal pre-pregnancy body mass index and child ADHD symptoms.PloS oneBuss, Claudia; Entringer, Sonja; Davis, Elysia Poggi; Hobel, Calvin J; Swanson, James M; Wadhwa, Pathik D; Sandman, Curt A2012Not Determined
22529357Create StudyMaternal cortisol over the course of pregnancy and subsequent child amygdala and hippocampus volumes and affective problems.Proceedings of the National Academy of Sciences of the United States of AmericaBuss C, Davis EP, Shahbaba B, Pruessner JC, Head K, Sandman CAMay 15, 2012Not Determined
21995526Create StudyMaternal pregnancy-specific anxiety is associated with child executive function at 6-9 years age.Stress (Amsterdam, Netherlands)Buss C, Davis EP, Hobel CJ, Sandman CANovember 2011Not Determined
21890014Create StudyThe contribution of maternal stress to preterm birth: issues and considerations.Clinics in perinatologyWadhwa PD, Entringer S, Buss C, Lu MCSeptember 2011Not Determined

Relevant Publications
PubMed IDStudyTitleJournalAuthorsDate
28755549Create StudyChildhood maltreatment is associated with increased risk of subclinical hypothyroidism in pregnancy.PsychoneuroendocrinologyMoog NK, Heim CM, Entringer S, Kathmann N, Wadhwa PD, Buss COctober 2017
28754515Create StudyMaternal Systemic Interleukin-6 During Pregnancy Is Associated With Newborn Amygdala Phenotypes and Subsequent Behavior at 2 Years of Age.Biological psychiatryGraham, Alice M; Rasmussen, Jerod M; Rudolph, Marc D; Heim, Christine M; Gilmore, John H; Styner, Martin; Potkin, Steven G; Entringer, Sonja; Wadhwa, Pathik D; Fair, Damien A; Buss, ClaudiaJanuary 2018
28723888Create StudyAssociation between supraclavicular brown adipose tissue composition at birth and adiposity gain from birth to 6 months age.Pediatric researchEntringer S, Rasmussen J, Cooper DM, Ikenoue S, Waffarn F, Potkin SG, Wadhwa PD, Buss CJuly 2017
28487552Create StudyNewborn insula gray matter volume is prospectively associated with early life adiposity gain.International journal of obesity (2005)Rasmussen JM, Entringer S, Kruggel F, Cooper DM, Styner M, Gilmore JH, Potkin SG, Wadhwa PD, Buss CMay 2017
28433734Create StudyProspective association of fetal liver blood flow at 30 weeks gestation with newborn adiposity.American journal of obstetrics and gynecologyIkenoue S, Waffarn F, Ohashi M, Sumiyoshi K, Ikenoue C, Buss C, Gillen DL, Simhan HN, Entringer S, Wadhwa PDAugust 2017

You can use "Add New Data Expected" to add exsiting structures and create your project's list. However, this is also the method you can use to request new structures be created for your project. When adding the Data Expected item, if the structure already exists you can locate it and specify your dates and enrollment. To add a new structure and request it be defined in the Data Dictionary, select Upload Definition and attach the definition or material needed to create it, including manual, codebooks, forms, etc. If you have multiple files, please upload a zipped archive containing them all.

Expected dates should be selected based on the standard Data Sharing Regimen and are restricted to within date ranges based on the project start and end dates.

Data Expected
Data ExpectedTargeted EnrollmentInitial SubmissionSubjects SharedStatus
Test of Infant Motor Performance (TIMP) info icon
1611/30/2015
115
Approved
Medical History info icon
20901/15/2012
209
Approved
Bayley Scales of Infant and Toddler Development, Third Edition (BSID) info icon
1611/30/2015
119
Approved
Wechsler Adult Intelligence Scale info icon
1611/30/2015
191
Approved
Research Subject and Pedigree info icon
1601/15/2012
108
Approved
Clinical Lab Tests info icon
21801/15/2012
218
Approved
Home Observation for Measurement of the Environment Inventory (HOME) info icon
1611/30/2015
128
Approved
Imaging (Structural, fMRI, DTI, PET, microscopy) info icon
1601/15/2012
118
Approved
Blood Sample Collection info icon
15301/15/2012
153
Approved
Structure not yet defined

Collection Owners and those with Collection Administrator permission, may edit a collection. The following is currently available for Edit on this page:

Associated Studies

Studies that have been defined using data from a Collection are important criteria to determine the value of data shared. The number of subjects column displays the counts from this Collection that are included in a Study, out of the total number of subjects in that study. The Data Use column represents whether or not the study is a primary analysis of the data or a secondary analysis. State indicates whether the study is private or shared with the research community.

Study NameAbstractCollection/Study SubjectsData UsageState
Derivation of Brain Structure Volumes from MRI Neuroimages hosted by NDAR using C-PAC pipeline and ANTsAn automated pipeline was developed to reference Neuroimages hosted by the National Database for Autism Research (NDAR) and derive volumes for distinct brain structures using Advanced Normalization Tools (ANTs) and the Configurable-Pipeline for the Analysis of Connectomes (C-PAC) platform. This pipeline utilized the ANTs cortical thickness methodology discuessed in "Large-Scale Evaluation of ANTs and Freesurfer Cortical Tchickness Measurements" [http://www.ncbi.nlm.nih.gov/pubmed/24879923] to extract a cortical thickness volume from T1-weighted anatomical MRI data gathered from the NDAR database. This volume was then registered to an stereotaxic-space anatomical template (OASIS-30 Atropos Template) which was acquired from the Mindboggle Project webpage [http://mindboggle.info/data.html]. After registration, the mean cortical thickness was calculated at 31 ROIs on each hemisphere of the cortex and using the Desikan-Killiany-Tourville (DKT-31) cortical labelling protocol [http://mindboggle.info/faq/labels.html] over the OASIS-30 template. **NOTE: This study is ongoing; additional data my be available in the future.** As a result, each subject that was processed has a cortical thickness volume image and a text file with the mean thickness ROIs (in mm) stored in Amazon Web Services (AWS) Simple Storage Service (S3). Additionally, these results were tabulated in an AWS-hosted database (through NDAR) to enable simple, efficient querying and data access. All of the code used to perform this analysis is publicly available on Github [https://github.com/FCP-INDI/ndar-dev]. Additionally, as a computing platform, we developed an Amazon Machine Image (AMI) that comes fully equipped to run this pipeline on any dataset. Using AWS Elastic Cloud Computing (EC2), users can launch our publicly available AMI ("C-PAC with benchmark", AMI ID: "ami-fee34296", N. Virginia region) and run the ANTs cortical thickness pipeline. The AMI is fully compatible with Sun Grid Engine as well; this enables users to perform many pipeline runs in parallel over a cluster-computing framework.6/1428Secondary AnalysisShared
Derivation of Quality Measures for Structural Images by Neuroimaging PipelinesUsing the National Database for Autism Research cloud platform, MRI data were analyzed using neuroimaging pipelines that included packages available as part of the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) Computational Environment to derive standardized measures of MR image quality. Structural QA was performed according to Haselgrove, et al (http://journal.frontiersin.org/Journal/10.3389/fninf.2014.00052/abstract) to provide values for Signal to Noise (SNR) and Contrast to Noise (CNR) Ratios that can be compared between subjects within NDAR and between other public data releases.10/423Secondary AnalysisShared
Derivation of Brain Structure Volumes from MRI Neuroimages hosted by NDAR using NITRC-CEA draft publication is in progress. GitHub repository with code for working with NDAR Data is available here: https://github.com/chaselgrove/ndar **Note this study is ongoing; additional may be added.**6/356Secondary AnalysisShared
A human craniofacial life-course: cross-sectional morphological covariations during postnatal growth, adolescence, and agingCovariations between anatomical structures are fundamental to craniofacial ontogeny, maturation and aging and yet are rarely studied in such a cognate fashion. Here we offer a comprehensive investigation of the human craniofacial complex using freely available software and MRI datasets representing 575 individuals from 0 to 79 years old. We employ both standard craniometrics methods as well as Procrustes based analyses to capture and document cross-sectional trends. Findings suggest that anatomical structures behave primarily as modules, and manifest integrated patterns of shape change as they compete for space, particularly with relative expansions of the brain during early postnatal life and of the face during puberty. Sexual dimorphism was detected in infancy and intensified during adolescence with gender differences in the magnitude and pattern of morphological covariation as well as of aging. These findings partly support the spatial-packing hypothesis and reveal important insights into phenotypic adjustments to deep-rooted, and presumably genetically defined, trajectories of morphological size and shape change that characterise the normal human craniofacial life-course.5/308Secondary AnalysisShared
A growth curve of the human eye from 0-20 yearsThis study involves the semi automatic segmentation of the eyes of pediatric subjects for volume measurements5/173Secondary AnalysisPrivate
Age attenuates noise and increases symmetry of head movements during sleep resting-state fMRI in healthy neonates, infants, and toddlersNewborns produce spontaneous movements during sleep that are functionally important for their future development. This nuance has been previously studied using animal models and more recently using movement data from sleep resting-state fMRI (rs-fMRI) scans. Age-related trajectory of statistical features of spontaneous movements of the head is under-examined. This study quantitatively mapped a developmental trajectory of spontaneous head movements during an rs-fMRI scan acquired during natural sleep in 91 datasets from healthy children from ~birth to 3 years old, using the Open Science Infancy Research upcycling protocol. The youngest participants studied, 2-3 week-old neonates, showed increased noise-to-signal levels as well as lower symmetry features of their movements; noise-tosignal levels were attenuated and symmetry was increased in the older infants and toddlers (all Spearman’s rank-order correlations, P< 0.05). Thus, statistical features of spontaneous head movements become more symmetrical and less noisy from birth to ~3 years in children. Because spontaneous movements during sleep in early life may trigger new neuronal activity in the cortex, the key outstanding question for in-vivo, non-invasive neuroimaging studies in young children is not “How can we correct head movement better?” but rather: How can we represent all important sources of neuronal activity that shape functional connections in the still-developing human central nervous system?22/86Secondary AnalysisShared
* Data not on individual level
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