Requestors who receive tissues or biospecimens from the NNTC or CHARTER enter an agreement to submit data generated from the samples they receive to the NNTC-DCC. The data submitted by requestors is documented and curated by the NNTC DCC. This process includes the development of data dictionary and methods documents, as well as harmonizing participant IDs across research and clinical studies. One benefit of this process is that the ID variables used to identify unique participants are harmonized across the CHARTER Research Study data, the NNTC Experimental data resource and the NNTC Clinical data resource. As of 2016, the NNTC-DCC began requesting CHARTER requestors submit data generated from the samples they have received. These efforts are aimed at making harmonized data generated from participants in the NNTC and CHARTER studies available for request shaping and post hoc analysis.
The NNTC-CHARTER Experimental Data Query Tool is a web-based utility that allows researchers to quickly search experimental data generated from NNTC biospecimens, including tissues, and CHARTER biospecimens. The data for the Query Tool are collected from CHARTER and NNTC requestors, who are asked to share their published (and in some cases, unpublished) raw data with the NNTC-DCC at the conclusion of their work with the samples. This effort is aimed at providing high quality data for post-hoc analysis, to allow researchers to select cases based on experimental values, and to prevent redundancy in testing.
The Query Tool allows researchers to query data types against NNTC/CHARTER participants. The results from the Query Tool indicate the data types available for each NNTC/CHARTER participant. The measured data values for each participant are not presented in the Query Tool. Requestors who would like to access the measured lab values are asked to send the results of their query to the NNTC-DCC and the data will be transferred to them.
The presence of records returned by the Experimental Data Query tool indicates whether an NNTC and/or CHARTER participant’s biospecimens were utilized in a particular research study. Generally speaking, this indicates data will be available for that participant and variable. However, in some cases, data may be missing for particular variables and/or participants within a study because data could not be generated for that biospecimen (e.g. insufficient signal was detected or insufficient sample was collected for analysis). These study specific missing data mechanisms are summarized formally in the experimental data sent to requestors.
Data present in the database can be filtered using the Query Tool along multiple variables to help researchers identify studies of interest. The Query Tool variables are summarized below:
Biofluids and components:
Please keep the following in mind when using the Query Tool:
The gene search tool integrates with the Expression Omnibus (GEO) to search for GEO datasets that including NNTC participants for expression of selected genes of interest. NNTC Experimental data for these studies can be accessed for specific studies using the Publication Search tool and browsed for using the Experimental Data Query tool. The data files are generally structured to match the GSM profile ID in GEO with the central NNTC participant ID. This participant ID is harmonized across all NNTC Experimental Studies, the NNTC Data Query tool, and the CHARTER Data Query tool.
To use the Gene Search tool, select genes of interest using the “Gene Name” box. Gene names are standardized using Gene Nomenclature Committee conventions. The results of your search will be a popup window return of a GEO search across all of the NNTC-DCC experimental datasets currently on GEO that include the selected genes of interest.
The Publication Search tool allows users to browse the study specific data collected in the NNTC-DCC central database and download study specific resources for studies of interest. The publication study search tool can be used to browse experimental studies in the database using keywords from the title, the PubMed ID assigned by NCBI, and author name.
To use the Publication Search tool, enter the PubMed ID, title keyword, or author’s last name into the corresponding search box. The return will include all studies matching the search criteria. If data is available, the “download” link will return a .rar archive including the study data, a study specific data dictionary, and a description of the study methods supplied with the data submission.
The cohort browser allows users to browse all the experimental data available for selected NNTC/CHARTER participants using a unified participant ID. The search results will detail all of the experimental data available for the submitted list of participant IDs.
Please format your query as a list of NNTC IDs of interest. Please delimit your list with commas (e.g. 03601, 02230, 03165, 03738, 04905, 03343, 03304, 03388, 04349, 04945). Leading “0” values are not required for the cohort browser tool (i.e. the query above may also be formatted as 3601, 2230, 3165, 3738, 4905, 3343, 3304, 3388, 4349, 4945)