BODB Insert SED

The current version of BODB allows the user to insert generic or brain imaging Summary of Experimental Data (SED) in addition to BOP and Model entries. The summary could be any facts, hypotheses or experimental settings and results in a particular domain from one or several publications. A form for populating BODB with SEDs will be described here that is shown after clicking on the “Summary of Experimental Data” link in the Insert page. Click on the “Save Draft” button to save a draft of the present SED to the BODB database. The SED draft will also be available to edit at a later time and will be listed in the Workspace for convenience.

The input form for Summary of Experimental Data entries.

The input form for Summary of Experimental Data entries.


Type

Currently there are two types of SEDs in BODB: generic and brain imaging. Generic summary data could be a description of experimental data using any technique, while brain imaging summary data describes neuroimaging data such as that obtained from fMRI or PET experiments. Selecting “brain imaging” will display the form shown in the Brain Imaging Data section.

Generic Summary Data

Title

The name of the SED entry.

Brief Description

A brief description of the SED. We provide a text input area but in general the entry should be much shorter (say 200 words) since a full description can be entered in the “Narrative” field.

Narrative

A full length description of the SED. The narrative must be detailed enough to provide rigorous constraints for the design and/or testing of models.

Tags

A list of keywords associated with this SED entry.

Figures

Clicking on the “Show” link in the “Figures” section will expand the Figures section, displaying figures linked to the current entry and allowing the user to add new figures. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Figures section.

The expanded Figures section

The expanded Figures section

To add a new figure, click on the “Add new” link. This will open up the Add Figure window. Clicking the “Edit” link next to an existing figure will open the Edit Figure window, while clicking “Delete” will delete the figure and remove it from the SED.

Related Brain Regions

Brain region(s) that relate to the present SED. Clicking on the “Show” link in the “Related Brain Regions” section will expand the Related Brain Regions section, displaying the Brain Regions linked to the current entry. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Related Brain Regions section.

The expanded Related Brain Regions section

The expanded Related Brain Regions section

In order to add an existing Brain Region to the current SED, clicking on the “Search” link will open the Brain Region Search window. Clicking “Select” next to one of the search results will add that Brain Region to the current SED entry. Clicking “Remove” next to a linked Brain Region will remove it from the current SED entry.

References

References to articles, books chapters, etc., relevant to this SED. Clicking on the “Show” link in the “References” section will expand the References section, displaying Literature linked to the current entry and allowing the user to add new Literature entries. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the References section.

The expanded References section

The expanded References section

To link an existing Literature entry to the current SED, click on the “Search” link. This will open the Literature Search window where “Select” link next to any search result can be clicked to link it to the current SED entry. To add a new Literature entry, click on the “Add new” link. This will open up the Insert Literature window. Clicking the “Edit” link next to an existing Literature entry will open the Edit Literature window, while clicking “Remove” will remove the Literature entry from the SED.

Brain Imaging Summary Data

BODB is intended to serve also as an experimental-data repository. In addition to the generic SED entry form, it provides an explicit storage and user interface for tables of brain imaging data based on Talairach coordinates. Although brain imaging data are often supplied in table format, different articles may differ in the number, labeling and layout of columns, and differ in the freeform description of the experimental conditions of that table. Moreover, article data files are in various formats such as PDF, HTML and Microsoft Word. Therefore, it is difficult to provide a tool that automatically reads the data file, excerpts the whole table and its description, then marshals and puts these data into BODB properly. Our solution for importing the table is to provide a structured input form for pasting the table’s description and data, and specifying metadata (column configuration). The structure of the input form and the metadata will assist the user populate the table data correctly.

Title

The name of the SED entry.

Brief Description

A brief description of the SED. We provide a text input area but in general the entry should be much shorter (say 200 words) since a full description can be entered in the “Narrative” field.

Narrative

A full length description of the SED. The narrative must be detailed enough to provide rigorous constraints for the design and/or testing of models.

Tags

A list of keywords associated with this SED entry.

Method

The imaging method used (currently “PET” or “fMRI”)

Control Condition

A description of the control condition (if applicable) that the activity in the experimental condition is being compared to.

Experimental Condition

A description of the task in the experimental condition.

Coordinate System

The system that the coordinates are reported in (MNI or Talairach). Coordinates in the MNI system will converted to Talairach coordinates for visualization in the Talairach Applet.

Core Column Header

The mandatory “core” columns for brain-imaging data consists of “Brain Region”, “Hemisphere”, the “X Y Z” Talairach coordinates, “rCBF” and “T”. The user has to specify these columns corresponding to the columns and their order of the present table.

Extra Header

The user can specify optional “extra” columns by inserting the column names, separating each one with a Tab character, and ordering by the column sequence in the present table.

Data

The user has to paste the data into the text area.

Figures

Clicking on the “Show” link in the “Figures” section will expand the Figures section, displaying figures linked to the current entry and allowing the user to add new figures. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Figures section.

The expanded Figures section

The expanded Figures section

To add a new figure, click on the “Add new” link. This will open up the Add Figure window. Clicking the “Edit” link next to an existing figure will open the Edit Figure window, while clicking “Delete” will delete the figure and remove it from the SED.

Related Brain Regions

Brain region(s) that relate to the present SED. Clicking on the “Show” link in the “Related Brain Regions” section will expand the Related Brain Regions section, displaying the Brain Regions linked to the current entry. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the Related Brain Regions section.

The expanded Related Brain Regions section

The expanded Related Brain Regions section

In order to add an existing Brain Region to the current SED, clicking on the “Search” link will open the Brain Region Search window. Clicking “Select” next to one of the search results will add that Brain Region to the current SED entry. Clicking “Remove” next to a linked Brain Region will remove it from the current SED entry.

References

References to articles, books chapters, etc., relevant to this SED. Clicking on the “Show” link in the “References” section will expand the References section, displaying Literature linked to the current entry and allowing the user to add new Literature entries. After expansion, the “Show” link will turn into a “Hide” link that can be used to collapse the References section.

The expanded References section

The expanded References section

 To link an existing Literature entry to the current SED, click on the “Search” link. This will open the Literature Search window where “Select” link next to any search result can be clicked to link it to the current SED entry. To add a new Literature entry, click on the “Add new” link. This will open up the Insert Literature window. Clicking the “Edit” link next to an existing Literature entry will open the Edit Literature window, while clicking “Remove” will remove the Literature entry from the SED.