Abstract
Every month, numerous publications appear that include neuroanatomic volumetric observations. The current and past literature that includes volumetric measurements is vast, but variable with respect to specific species, structures, and subject characteristics (such as gender, age, pathology, etc.). In this report we introduce the Internet Brain Volume Database (IBVD), www.nitrc.org/projects/ibvd, a site devoted to facilitating access to and utilization of neuroanatomic volumetric observations as published in the literature. We review the design and functionality of the site. The IBVD is the first database dedicated to integrating, exposing and sharing brain volumetric observations across species and disease. It offers valuable functionality for quality assurance assessment of results as well as support for meta-analysis across large segments of the published literature that are obscured from traditional text-based search engines.
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Acknowledgements
This work was supported in part by grant NS34189 (PI Kennedy) as part of the Human Brain Project, MH083320 (Co PIs Kennedy and Frazier) and NS064354 (PI Gao). Thanks for tireless data entry efforts are owed to Julianne Steele, Aliya Dincer and Thomas Buckley. Marilyn Albert and Bruce Fischl provided access to individual data from their published work. Robert Williams provided group and individual mouse brain volumes from the Mouse Brain Library (MBL—http://www.mbl.org/).
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Appendix
Appendix
In this appendix we review the details of the various database tables.
Publication: Data sources. In most cases, publications are journal articles, but they may be other sources of data, such as on-line databases.
ID | Integer | IBVD unique identifier for this publication. |
Title | Text | Name of data source. Typically the title of the journal article, but this may be the name of a special data source (e.g. “Mouse Brain Library”). |
Journal | Text | Journal name. |
Date | Text | Date of publication. |
Volume | Text | Journal volume/number. |
Pages | Text | Page range for journal article. |
URL | Text | URL for this publication or data source. |
Author: Journal article authors.
Author name | Text | The name of an author |
Credited | Integer | An ordinal giving the position of the author in the list of authors. The first author will have credited = 1, second author credited = 2, etc. |
Group: Subject groups. Groups are reported on in publications. The groups can be associated with a reference for the volume measurement methods employed (manual techniques for measurement, algorithms, software packages, etc) by reference to the most representative publication.
ID | Integer | IBVD unique identifier for this subject group. |
Method ID | Integer | IBVD Publication ID for publication(s) indicating methodology employed for this group. |
Species | Text | Species of subjects in this group. |
Species qualifier | Text | Subspecies of subjects in this group, for instance mouse strain. |
Diagnosis | Text | Diagnosis of subjects in this group. |
Vivoness | Text | Whether the volume measurement was done in vivo, in vitro, or ex vivo. |
Number of subjects | Integer | Number of subjects in this group. |
N male | Integer | Number of male subjects in this group. |
N female | Integer | Number of female subjects in this group. |
N left handed | Integer | Number of left handed subjects in this group. |
N right handed | Integer | Number of right handed subjects in this group. |
Mean age | Float | Mean age, in years, of subjects in this group. |
Age std dev | Float | Standard deviation of ages, in years, of subjects in this group. |
Age min | Float | Minimum age, in years, of subjects in this group. |
Age max | Float | Maximum age, in years, of subjects in this group. |
URL | Text | URL for this group (for on-line data sources or publications sharing data on-line). |
Group volume: Reported volumes for subject groups.
ID | Integer | IBVD unique identifier for this reported volume. |
Structure | Text | Structure being measured. |
Hemisphere | Text | Hemisphere of the structure being measured (left, right, or total). |
Mean volume | Float | Mean of volumes in this subject group. |
Volume std dev | Float | Standard deviation of volumes in this subject group. |
Units | Text | Units (ml, cc, etc) of the volume measurement. |
Derived flag | Boolean | Whether this volume was derived from reported individual volumes. False for volumes directly reported in publications. |
Adjusted flag | Boolean | Whether the reported measurement is stated to be ‘adjusted’ (for total brain volume, for example). |
URL | Text | URL for this volume (for on-line data sources or publications sharing data on-line). |
Extra group demographics: Reported demographics for subject groups. Basic demographic information is stored in the group table; this table provides extensibility for storing demographics.
ID | Integer | IBVD unique identifier for this extra demographic value. |
Label | Text | The value being reported, for instance “Body Mass Index” or “Education Level.” |
Qualifier | Text | Type of value being reported. This is unset for a direct measurement, but may indicate a mean, standard deviation, minimum, or maximum. In this way, an education level, say, of 12 +− 3 years may be stored. |
Value | Text | The stored value. |
Units | Text | Units of the stored value. |
Individual: Individual subject demographic data. Individual subjects can be reported in association with a group.
ID | Integer | IBVD unique identifier for this subject. |
Age | Float | Age, in years, of this subject. |
Gender | Text | Gender of this subject. |
Handedness | Text | Handedness of this subject. |
Local code | Text | The source’s identifier for this subject. This is used for identifying a subject in an on-line database. |
Species | Text | Species of the subject. |
Species qualifier | Text | Subspecies of the subject, for instance mouse strain. |
Vivoness | Text | Whether the volume measurements for this subject were done in vivo, in vitro, or ex vivo. |
URL | Text | URL for this subject (for on-line data sources or publications sharing data on-line). |
Individual volume: Reported volumes for individual subjects. The individual volume record can report a volume measurement method (manual techniques for measurement, algorithms, software packages, etc) by reference to the most representative publication.
ID | Integer | IBVD unique identifier for this reported volume. |
Method ID | Integer | IBVD Publication ID for publication(s) indicating methodology employed for this individual. |
Structure | Text | Structure being measured. |
Hemisphere | Text | Hemisphere of the structure being measured (left, right, or total). |
Volume | Float | Reported volume. |
Units | Text | Units (ml, cc, etc) of the volume measurement. |
Derived flag | Boolean | Whether this volume was derived from other volumes. False for volumes directly reported in publications. |
Adjusted flag | Boolean | Whether the reported measurement is stated to be ‘adjusted’ (for total brain volume, for example). |
URL | Text | URL for this volume (for on-line data sources or publications sharing data on-line). |
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Kennedy, D.N., Hodge, S.M., Gao, Y. et al. The Internet Brain Volume Database: A Public Resource for Storage and Retrieval of Volumetric Data. Neuroinform 10, 129–140 (2012). https://doi.org/10.1007/s12021-011-9130-1
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DOI: https://doi.org/10.1007/s12021-011-9130-1