Caret:Operations/StudyMetadata

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Contents

Study Metadata

Study Metadata Editor

Image:CaretStudyMetaDataEditorDialog.jpg

Use the study editor to enter study information. After entering study information, data types such as foci, paint, metric, and shape, are linked to studies. When data that is linked to studies is identified within Caret, information about the linked study is printed.

The PubMed ID is the "key" for studies and uniquely identifies each study. When data is linked to a study, the PubMed ID is used in the link to identify the appropriate study. If the PubMed ID in the link is a Project ID, Caret will locate the appropriate study using the Project ID.

The PubMed identifier is typically assigned to a journal article that has been entered in www.pubmed.gov. If the study's journal article has been entered and a PubMed identifier is available, enter the identifier into the PubMed field and press the Fetch from PubMed button in the Study Operations section to automatically transfer data form PubMed and place the data into their respective fields.

If a PubMed ID is not available, the PubMed ID defaults to the Project ID. When the PubMed ID becomes available, the PubMed ID field should be updated. The Project ID is generated by Caret and should not be modified by the user.

If the user will be projecting foci to the PALS atlas, the foci must be linked to studies with valid stereotaxic spaces.

Study Selection Group

This group contains controls for selecting loaded studies. The top control lists the index of the selected study and the arrows are used to step to other studies.

  • First Selects the first study in the study metadata file.
  • Last Selects the last study in the study metadata file.
  • Choose by Author Provides a list of authors, sorted alphabetically, for selecting a study.
  • Choose by Name Provides a list of study names, sorted alphabetically, for selecting a study.
  • Choose by Title Provides a list of study titles, sorted alphabetically, for selecting a study.

File Operations Group

  • Add New Study Add a new study.
  • Delete Unlinked Studies Deletes all studies that are not linked by foci, metric, paint, shape, or vocabulary data.
  • Delete By Name Allows deletion of studies by the studies' names.
  • Fetch All PMIDs For each study that has a valid PubMed ID, fill in some of the studies entries with data provided from the PubMed database.

Study Operations Group

  • Add Figure Add a figure section to the current study.
  • Add Page Ref Add a page reference to the current study.
  • Add Provenance Add a provenance entry to the current study.
  • Add Table Add a table section to the current study.
  • Delete Study Delete the current study.
  • Fetch from PubMed Contact PubMed for information about the study, using the study's PubMed ID, and enter the information into the study. Information available from PubMed typically includes the title, authors, citation, DOI-URL, Medical Subject Headings, and the Comment.

Study Metadata Group

This group contains the information describing the study. Enter data into each catagory for which you have data. As data values are entered, they are automatically loaded into the current study so there is no need for an “Apply” button. After entering study metadata, be sure to save the Study Metadata File using the File Menu→Save Data File menu item.

  • File Index The index of the study in the Study Metadata File. The indices start at one.
  • Project ID This is a unique identifier that is generated for each study. It consists of the four-digit year, two-digit month, two-digit day, two-digit hour, two-digit minutes, three-digit-milliseconds, and a random five-digit number. This value cannot be altered by the user.
  • PubMed ID The PubMed ID (www.pubmed.gov) assigned to the study. If a PubMed ID is not available, use the Project ID until the PubMed ID becomes available. If a PubMed ID is available for the study, press the Fetch from PubMed in the Study Operations section after entering the PubMed ID which will fill in some of the other data fields. Pressing the Link button displays the PubMed web page for the study in the web browser.
  • Name Enter a short name for the study. We suggest the first author's last name followed by an underscore, an acronym for the journal's name, and a two-digit year.
  • Title The title of the study.
  • Authors Authors of the study.
  • Citation Journal title, publication date, volume, and page numbers.
  • DOI-URL The Digital Object Identifier (see www.doi.org).
  • Species The species examined in the study. Press the Species button to select a species.
  • Stereotaxic Space The stereotaxic space of the neuroimaging data. Pressing the Stereotaxic Space provides a list of common stereotaxic spaces from which a space may be selected.
  • Stereo Space Details Additional information about the stereotaxic space.
  • Data Format The format of the data in the study. Essentially, the type of Caret data file used for the study's data. Pressing the Add button provides a list of data formats. If more that one data format is entered, separate them with semicolons.
  • Data Type Type or methodology of the study. Presing the Add button provides a list of data types. If more than one data type is entered, separate them with semicolons.
  • Keywords Keywords from the study. Separate multiple keywords with semicolons.
  • Medical Subject Headings See http://www.nlm.nih.gov/mesh. Separate multiple entries with semicolons.
  • Part Scheme Abbrev An abbreviation for the partitioning scheme such as an authors initials and a two-digit year of the study.
  • Part Scheme Name The full name for the partitioning scheme.
  • Quality
  • Comment A description of the study, perhaps the abstract.
  • Last Saved Contains the date and time the study was last saved. This value cannot be altered by the user.
  • MSL ID Filled in by the SuMS Database. This value cannot be altered by the user.
  • Parent ID Filled in by the SuMS Database. This value cannot be altered by the user.
  • Core Data Completed Filled in by the SuMS Database. This value cannot be altered by the user.
  • Completed Filled in by the SuMS Database. This value cannot be altered by the user.
  • Public Access Filled in by the SuMS Database. This value cannot be altered by the user.

Figure Group

  • Number
  • Legend

Figure Panel Group

  • Identifier
  • Description
  • Task Description
  • Task Baseline
  • Test Attributes

Page Reference Group

  • Number
  • Header
  • Comment
  • Size Units
  • Voxel Size
  • Statistic
  • Stat Description

Provenance Group

  • Name
  • Date
  • Comment

Sub Header Group

  • Number
  • Name
  • Short Name
  • Task Description
  • Task Baseline
  • Test Attributes

Table Group

  • Number
  • Header
  • Footer
  • Size Units
  • Voxel Size
  • Statistic
  • Stat Description

Linking to Study Metadata

Image:CaretStudyMetaDataLinkDialog.jpg

To create a link, press the Add button, scroll through the list of studies and check the box is the Select Study column for the desired study. Next, choose the type of link which involves linking only to the study or a specific figure, page, or table in the study. If the data comes from multiple studies, press the Add button to create a link to a new study.

Study Link Section

Link Each datum may link to multiple studies. Use the arrows to sequence through the current study metadata links.

Add Press this button to add a new study metadata link.

Delete Delete the selected link to study metadata.


Study Selection

Scroll through the list of studies and check the box in the Select Study column to select a study.

Link Type

Link to Study Link only to the study.

Link to Figure In Study Link to a specific figure (and optional panel) in the study.

Link to Page Reference Link to a specific page (and optional subheader) in the study.

Link to Table in Study Link to a table (and optional subheader) in the study.

Page Number Enter an optional page number.

Linking Foci to Study Metadata

On the Map Stereotaxic Focus Dialog, press the Study Metadata button to launch the Link to Study Metadata Dialog. Be sure to press the Apply button to apply the new link to the focus.

Linking Metric Data to Study Metadata

On the Display Control Dialog, select Page Selection: Metric and then select the Selection sub-page. Press the “M” button in the row corresponding to the metric column for which you would like to link to study data. The study information will be displayed when a node is identified and the column is the selected metric column.

Linking Paint Data to Study Metadata

On the Display Control Dialog, select Page Selection: Paint and then select the Selection sub-page. Press the “M” button in the row corresponding to the paint column for which you would like to link to study data. The study information will be displayed when a node is identified and the column is the selected paint column.

Linking Surface Shape Data to Study Metadata

On the Display Control Dialog, select Page Selection: Surface Shape and then select the Selection sub-page. Press the “M” button in the row corresponding to the surface shape column for which you would like to link to study data. The study information will be displayed when a node is identified and the column is the selected surface shape column.

Linking Vocabulary to Study Metadata

On the Vocabulary Editor Dialog, press the Study Metadata button to launch the Link to Study Metadata Dialog. Be sure to press the Apply button to apply the new link to the vocabulary entry.

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