Study Curation Core Module

Warning: Future plans ahead

The following description of the Study Curation module is intended as an overview of the BioConnet team's future direction for this system and interface. There are stakeholders to consult, designs to be developed, and open questions to be solved. Please contact the BioConnect team if you have suggestions!

Overview

The Study Curation module is the central point of curation for studies stored or indexed in BioConnect. It provides for creating and updating of ISA documents, viewing the history of changes, and tracking study status as it moves through the curation process.

Study curation system architecture

The Study Curation system is a composite module built on top of the core modules listed on the left including: metadata repository, resource registration, authorization, tasks, events, and authentication.

Creating and editing a study in BioConnect (User Guide)

1. Log into BioConnect using JAX SSO (https://bioconnect.jax.org/). The home page will be displayed as shown in screenshot 1 below:

   Screenshot 1:

2. Launch the Curation dashboard or under Admin tab, select Curation. If the Curation tab is not visible, contact Abigail Miller (Abigail.Ames@jax.org). You need to be added as curator in order to access Admin tab.

   Screenshot 2:

3. To create(enter) a new study, in the top right of the Curation Dashboard, select + Add New Study as shown in screenshot3

   If you are editing a pre-existing study, find the study by entering a term in the search box and select the pencil icon for the selected study , under Actions on the right hand-side of the page as shown in screenshot3.

   Screenshot 3:

4. Add Study Details (Title [mandatory] and Description). Study ID is automatically assigned.

   Screenshot 4

5. Investigation : For investigation, use the dropdown menu to select an existing investigation or select the + to the right of the Investigation box to create a new investigation as shown in screenshot 5.

   If you are creating a new Investigation: Add Title, Description, and Contacts. If the appropriate contact doesn’t appear on the list, select + in the upper right corner of the Add Investigation Contact window and fill in the necessary details as shown in screenshot 6.

   Screenshot 5:

   Screenshot 6 : Add new Investigation

6. Factors : (genotype, strain, sex, etc.). Factors are a controlled vocabulary and can be chosen from the dropdown list. Select one or more study factors that drive the study design. A factor corresponds to an independent variable manipulated by the experimentalist with the intention to affect biological systems in a way that can be measured by an assay. The list of available factors is managed by BioConnect curators, there is an additional admin section for administering controlled terms. Contact the BioConnect team if you need to add new factor terms.

7. Design Descriptors : Add one or more terms describing the nature of the assay variables included in the study (e.g., longitudinal, factorial, time series).

8. Characteristic Categories : Select one or more categories that define the characteristics you will collect for study sources. For example, if you will be recording the strain of the mice in the study, select strain as a characteristic category. All categories will be included in the sources grid below.

9. Protocols : Select all protocols used in the study from the grid by clicking the plus icon. Protocols are an administered controlled term, contact BioConnect curators if you want additional protocols to be added to the existing list.

   Screenshot 7:

   *Assays is next in the list but skip this for now; assays shouldn’t be added until you’ve added your sources. Also, assays are not available until study is saved.

10. Contacts : Add any individual who will be contributing to the study. Each contact has a role within the study. Click the plus icon to add a contact to your study. You will be able to add existing contacts to the study or enter new ones if they don't already exist. As with investigation contacts, you can add a new contact by clicking the plus icon in the top right of the contact window if needed as shown in screenshot 8

    Screenshot 8:

11. Publications : Add any publications associated with the study. Click the plus icon to add a publication. You will be able to add existing publications to the study from Publication table or enter new ones if they don't already exist. You can add one or multiple publications to your study.

    Screenshot 9:

12. Sources : The columns generated in the sources table will match up with your characteristic categories. You can copy and paste your metadata from Excel into the source table. The cell you are copy/pasting into must be blue for the copy/paste to work correctly. If there is a flashing cursor in the cell, your clipboard contents will all paste into that one cell. Make sure to click the empty row underneath before saving. You can drag the columns to reorder them to match up with your own spreadsheets to facilitate easier copy/pasting.

    Note: Once you save the study, the columns in source’s grid will be displayed in alphabetical order.The columns can also be filtered, sorted, and resized much like Excel.

13. Comments: User may include multiple distinct comments for example funding information, grant aims as shown in screenshot 10

    Screenshot 10:

14. Assays : Once your sources are input and saved, you can add assays. Select + next to Assays. This will open a new side-drawer window. Assays do not have titles; they are given an identifier based on their measurements.

    Screenshot 11:

15. Measurements : Add the measurement type and technology type from their dropdown menus. Technology platform is a free-form text field. Measurement types and technology types are also controlled terms and can be added by BioConnect curators if needed.

16. Measurement Type : Select the category describing the nature of the data being measured by the assay.

17. Technology Type : Select a value that identifies the technology used to execute the assay.

18. Technology Platform : Enter the specific proprietary format of the assay technology type (e.g., Affymetrix, Illumina.)

19. Characteristic Categories : (optional) Select one or more categories that define the characteristics you will collect for assay samples. For example, if you will be recording the cell type for samples in the assay, select cell type as a characteristic category. All categories will be included in the samples grid below.

20. Samples : The sample table contains the factors you listed during the study creation as well as the characteristic categories for your assay. Multiple occurrences of the same assay type will be needed for multiple types of tissue/samples.

21. Data files : add information about your data files, including metadata, raw data, and derived data. Data files should include a URL to the storage system, such as google bucket or Box for access.

22. Process sequence : Select + for each process needed, each of the Protocols previously chosen will be available in a drop-down menu in the About section. Assay will not save if you do not choose a protocol after clicking + icon. You have to either delete protocol using the trash icon or add information in it. Add Performer and Date if known, can be left blank. Skip Parameters for now (for all processes). Next, select Inputs, a list of Input Types: Source, Sample, Data, and Material are available. After choosing Input type, select items from drop down list. These are the samples, sources, and data files that you have previously added to the assay. Then, select Outputs, Output type and Output items. Please see screenshot 13. Place processes in order performed, processes can be reordered by dragging and dropping as shown in screenshot 12.

    Screenshot 12:

    Screenshot 13:

    Comments: Select + to add any comments to the Assay.