How to use SSBD:repository
Viewing project list
Registered project are listed from Resources. Narrowed-down search is also possible.
Searching
SSBD:repository provides a search system for metadata.
The projects in SSBD:repository reproduces the folder structure provided by the authors. Projects are categorized primarily by the papers and contain multiple folders.
Available keys for searching:
- Organism
- Project ID (project name)
- Title, Description
- Person (Contact or data contributors)
- Method Summary (experimental description or bibliography)
- Paper Information (title, author, abstract, and MeSH ontology for the paper)
The search function explores whether the exact word is included in the metadata.
Viewing images
SSBD:repository users the OMERO.web system for previewing microscopy images and checking metadata on some projects. For details on how to use OMERO.web, please refer to the OMERO.web document.
- OMERO.gellery is displayed like a gallery; This is suitable for viewing data at a glance.
- OMERO.index
provide more detailed structure of projects; This is
suitable for viewing details of the images
- Light pane: List of projects and datasets
- Middle pane: Collection of microscopy images in the dataset
- Right pane: Detail information of projects, datasets, images includes metadata
Downloading
SSBD:repository provides bioimaging data and related data. The data can be downloaded as individual files or in zip format.
How to use SSBD:database
Viewing project list
Registered project are listed from Resources. Narrowed-down search is also possible.
Searching
SSBD:database provides a search system for metadata.
The data in SSBD:database is structured. Projects are categorized primarily by papers; and a project contains multiple datasets. Datasets are categorized by organisms, experimental conditions, microscope settings, or data formats; and a dataset contains multiple images. Search for project is available from “Project search”. Search for dataset is available from “Dataset search”.
Available keys for searching:
- Organism, Strain, Cell Line
- Gene symbol, Protein name, Protein Tag, and Reporter
- Project ID (project name), Dataset ID (dataset name)
- Title, Description, Data Type
- Gene Ontology（Biological Process, Molecular Function, Cellular Component）
- Method Summary (experimental description or bibliography)
- Paper Information (title, author, abstract, and MeSH ontology for the paper)
- Medical Subject Headlines (MeSH ontology)
- Person (Contact or data contributors)
The search function explores whether the exact word is included in the metadata.
Viewing
SSBD:database users the OMERO.web system for previewing microscopy images and checking metadata on projects and datasets. For details on how to use OMERO.web, please refer to the OMERO.web document.
- OMERO.gellery is displayed like a gallery; This is suitable for viewing data at a glance.
- OMERO.index
provide more detailed structure of projects; This is
suitable for viewing details of the images
- Light pane: List of projects and datasets
- Middle pane: Collection of microscopy images in the dataset
- Right pane: Detail information of projects, datasets, images includes metadata
Visualizing
SSBD:database provides visualization for quantitative biological dynamics data. For details on how to use webbd5viewer, please refer to the manual.
Downloading
SSBD:database provides microscope images in original format. The data can be downloaded in zip format.
SSBD:database also provides quantitative biological data in BDML/BD5 format. The data can be downloaded in zip format. The downloaded data can be visualized with QTBD5viewer etc.
