Components of Genemde

The GAT

The GAT - Genemede Api and Tools - is a python project meant to be run locally. It will store data and allow for several operations, including search and export.

The GAT acts as the brain for all your local functionality. It holds the available metadata types and all the data, it provides an api to interact with it and it also has a set of command line tools to help you manage everything.

Folders

The first time the GAT runs, it will create a genemede folder under your local user folder. There you will find this folder structure:

genemede
  ├── data
  ├── logs
  ├── media
  ├── mtypes
  │   ├── imported
  │   └── user
  ├── scratch
  └── config.json

data is where all the local data is stored;

logs is where all the operating log files are stored;

media is where all the uploaded files are stored ((uploading is still under development));

mtypes holds non-curated metadata types. You can freely create your own metadata types under the user folder, and the imported folder is reserved for future use.

scratch holds temporary files, such as exported json files and debug dumps. It is safe to delete anything inside this folder.

Configuration

These are the contents of the current configuration file:

{
    "json_indent": 4,
    "user": {
        "name": "default user",
        "screen_name": "default user",
        "workspace": "genemede",
        "email": "example@example.com"
    },
    "folders": {
        "user_data": "<homefolder>/genemede/data",
        "user_media": "<homefolder>/genemede/media",
        "user_scratch": "<homefolder>/genemede/scratch",
        "system_mtypes": "<gat_repo_folder>/system/mtypes",
        "user_mtypes": "<homefolder>/genemede/mtypes/user",
        "imported_mtypes": "<homefolder>/genemede/mtypes/imported",
        "global_sources": "<gat_repo_folder>/system/sources",
        "logfiles": "<homefolder>/genemede/logs",
        "user_deleted_data": "<homefolder>/genemede/data/_deleted"
    }
}

Your screen_name will be displayed in the GUI, and the GUI will try to use your email to display a Gravatar image if you have one configured. The workspace field will be used in the future to differentiate different data workspaces, and the name field will be used for authentication in the HUB when available.

MTypes

Currently, the Genemede metadata types are included in the GAT itself (see The Metadata types).

You can create your own metadata types under the user_mtypes folder (default /genemede/mtypes/user).

The GUI

As the functionality of Genemede is relatively complex, it would be unwieldy to work exclusively through a command line interface or API. The GUI app provides a frontend for most of the system functionality, using the underlying GAT api, and storing no data at all.

The HUB

Currently in development, the Genemede HUB will be a central point to share and search data made available by any Genemede user that decides to make their data available to the public.

The Metadata types

Metadata types are the core of Genemede. Each metadata type defines a field structure and the rules on how a metadata type interacts and links with other types. The Genemede project will maintain a curated list of metadata types tailored for neuroscience but any user can create their own metadata types.

During the initial development phase, the curated metadata types are included in the GAT repository, but will eventually be moved out into their own repository.