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BIRN-INCF Derived Data Project

Name: BIRN-INCF Derived Data Project
Description: The Derived Data Working Group is focused on understanding, addressing and solving the known difficulties of sharing and combining data across multiple sites after post-processing and/or data analysis. This WG is working closely with researchers at UC Irvine, Columbia, Duke, MIT, MRN and INCF on these goals:

-Develop provenance and derived data extraction scripts for common neuroimaging analysis software and pipelines -Extend tools and specifications for international community requirements -Create/curate an initial neuroimaging terminology and ontology for derived data and common neuroimaging concepts -Augment/improve derived data import and query functionality for multi-site derived data federations

Neuroimaging data often involves many aspects of image and signal processing on the raw data which takes considerable time and expertise. Making such derived data available in a structured and well documented way is of interest to the international neuroimaging community. The availability of large multi-site datasets such as the Function BIRN schizophrenia datasets and the 1000 Functional Connectomes Project data provides researchers with well-documented and structured raw data. The addition of a similarly well-documented and structured form for derived data is the focus of this working group. Although the Function BIRN had made strides in developing the XCEDE XML schema for the structured storage and interchange of neuroimaging derived data, being able to extract both the derived results and the provenance of what happened to the data during the analytical manipulations directly from the software and pipelines performing the computations is missing. Without this piece, documenting derived data provenance and results becomes a burden on the researchers who are more interested in addressing scientific hypotheses than in documenting who the result was obtained for other users.

To address the needs for providing derived data to the public community we have formed the derived data working group. This group brings together researchers with extensive experience with neuroimaging studies and specifically with large-scale data analysis and management using the more prevalent software packages in the field, e.g. SPM and FSL. This working group leverages the experience of the group both within BIRN and in communication with other researchers through the INCF to identify information needed for a provenance description to be useful. Face-to-face meetings to discuss needs and possible approaches were held in 2011 and 2012 at UC Irvine in January, at OHBM in June 2011, at the INCF Standards for Data Sharing task force meeting in September, and a fourth meeting in November at the annual meeting for the Society for Neuroscience.

Once these details are established and there is consensus among the community, we will address the format for which this information will be stored. Initially we are focusing on XML schemas that integrate with the existing XCEDE XML schema (W3C Prov model) which describes neuroimaging data sets in general. After identifying the needed pieces of information and their storage format we will both work with the developers of the software packages to integrate the provenance schemas into their distributions or where not possible, write scripts to extract the information. All products of the derived data group are open-source and freely available to the community through the BIRN public wiki and INCF GitHub repositories.
Is part of: BIRN
Super-category: Project role
*Id: nlx_149615
Publication link: https://wiki.birncommunity.org/display/NEWBIRNCC/Derived+Data+WG
Link to OWL / RDF: Download this content as OWL/RDF

Categories related to BIRN-INCF Derived Data Project

Accessory Code, Acquisition, Acquisition Contrast, Acquisition Date, Acquisition Datetime, Acquisition Device Type Code Sequence, Acquisition Duration, Acquisition Matrix, Acquisition Number, Acquisition Start Condition, Acquisition Start Condition Data, Acquisition Termination Condition, Acquisition Termination Condition Data, Acquisition Time, Acquisition Time Synchronized, Acquisitions in Series, Acquisitions in Study, Active Source Diameter, Active Source Length, Actual Human Performers Sequence, Additional Patient History, Administration Route Code Sequence, Admission ID, Admitting Date, Admitting Diagnoses Code Sequence, Admitting Diagnoses Description, Admitting Time, Air Kerma Rate Reference Date, Air Kerma Rate Reference Time, Allow Lossy Compression, Allow Media Splitting, Alternate Representation Sequence, Anatomic Region Modifier Sequence, Anatomic Region Sequence, Anatomic Structure, Anatomic Structure Space or Region Sequence, Anchor Point, Anchor Point Annotation Units, Anchor Point Visibility, Angio Flag, Angle Number, Angular Position, Angular Step, Angular View Vector, Annotation Flag, Annotation Group Number, Annotation Sequence, Anode Target Material, Applicable Frame Range, Applicable Safety Standard Agency … further results

Categories with role BIRN-INCF Derived Data Project

Acquisitions in Series, Annotation Sequence have the role BIRN-INCF Derived Data Project


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Facts about BIRN-INCF Derived Data ProjectRDF feed
CurationStatusuncurated  +
DefinitionThe Derived Data Working Group is focused The Derived Data Working Group is focused on understanding, addressing and solving the known difficulties of sharing and combining data across multiple sites after post-processing and/or data analysis. This WG is working closely with researchers at UC Irvine, Columbia, Duke, MIT, MRN and INCF on these goals:

-Develop provenance and derived data extraction scripts for common neuroimaging analysis software and pipelines -Extend tools and specifications for international community requirements -Create/curate an initial neuroimaging terminology and ontology for derived data and common neuroimaging concepts -Augment/improve derived data import and query functionality for multi-site derived data federations

Neuroimaging data often involves many aspects of image and signal processing on the raw data which takes considerable time and expertise. Making such derived data available in a structured and well documented way is of interest to the international neuroimaging community. The availability of large multi-site datasets such as the Function BIRN schizophrenia datasets and the 1000 Functional Connectomes Project data provides researchers with well-documented and structured raw data. The addition of a similarly well-documented and structured form for derived data is the focus of this working group. Although the Function BIRN had made strides in developing the XCEDE XML schema for the structured storage and interchange of neuroimaging derived data, being able to extract both the derived results and the provenance of what happened to the data during the analytical manipulations directly from the software and pipelines performing the computations is missing. Without this piece, documenting derived data provenance and results becomes a burden on the researchers who are more interested in addressing scientific hypotheses than in documenting who the result was obtained for other users.

To address the needs for providing derived data to the public community we have formed the derived data working group. This group brings together researchers with extensive experience with neuroimaging studies and specifically with large-scale data analysis and management using the more prevalent software packages in the field, e.g. SPM and FSL. This working group leverages the experience of the group both within BIRN and in communication with other researchers through the INCF to identify information needed for a provenance description to be useful. Face-to-face meetings to discuss needs and possible approaches were held in 2011 and 2012 at UC Irvine in January, at OHBM in June 2011, at the INCF Standards for Data Sharing task force meeting in September, and a fourth meeting in November at the annual meeting for the Society for Neuroscience.

Once these details are established and there is consensus among the community, we will address the format for which this information will be stored. Initially we are focusing on XML schemas that integrate with the existing XCEDE XML schema (W3C Prov model) which describes neuroimaging data sets in general. After identifying the needed pieces of information and their storage format we will both work with the developers of the software packages to integrate the provenance schemas into their distributions or where not possible, write scripts to extract the information. All products of the derived data group are open-source and freely available to the community through the BIRN public wiki and INCF GitHub repositories.
public wiki and INCF GitHub repositories.
Idnlx_149615  +
Is part ofBIRN  +
LabelBIRN-INCF Derived Data Project  +
ModifiedDate14 August 2012  +
PublicationLinkhttps://wiki.birncommunity.org/display/NEWBIRNCC/Derived+Data+WG  +
SuperCategoryProject role  +