This is the page for help documents and resources for BICCN data submitters. Use the following links to navigate to important documents and tools that are needed for submitting data and metadata to the BICCN.
Our goals for Data Curation at the BCDC are:
- Building the BICCN Data Catalog as a key point of access and valuable resource for users
- Coordinating with the data archives to maintain an updated inventory of all BICCN specimens for grant reporting purposes
The BICCN Data Catalog is organized into Projects that have one or many associated Data Collections. Data Collections consist of a collection of Specimens that have data assets at the archives.
- General grant and dataset level metadata, E.g. Text descriptions of datasets, Protocols, Licensing, Contributors, Institutions, Funding
- This is recorded when registering new projects/data collections, so that BCDC can plan for what data we will have coming in
- Project and Data Collection metadata is displayed on the Project landing pages in the BCDC Data Catalog [SCREENSHOT to Data Catalog page]
- This is individual sample and file level metadata, E.g. Species, Genotype, Age, Specimen Type, File Type
- These metadata are displayed on Specimen pages in the BCDC Catalog, and are also used for searching/filtering the data
- Specimen metadata is used to maintain a census of all data collected by BICCN, for alignment with the archives and reporting research output to NIH
- A manifest of file metadata indexed by specimen is created by the archives and shared with BCDC, with file metadata including file type, unique ID, URI
- BICCN Portal: https://biccn.org
- BICCN Data Catalog: https://knowledge.brain-map.org/
- BIL: https://www.brainimagelibrary.org/
- DANDI: https://www.dandiarchive.org/
- NeMO: https://nemoarchive.org/
- BossDB: https://bossdb.org/
Projects and their associated data collections are registered at BCDC at the start of the grant/project. New data collections must be registered with BCDC before submitting data to the relevant archives. For this, you will need to fill out a project/data collection template and submit this to the BCDC Data Curation team. Contact the Data Curation team to guide you through the process of registering your project and associated data collections.
Changes to Project metadata such as adding new Contributors, editing project or data collection descriptions, or editing contact information, can be made online through the BCDC Project Data Curation tool - for a personalized login and link to the tool, contact the BCDC Data Curation team.
- Project/Data Collection Template and Instructions: Project Template
- Registering a protocol at protocols.io: Protocol publishing
- Getting an ORCID: ORCID
- NeMO Registration Page: NeMO Data Submission
- BIL Registration Page: BIL Data Submission
- DANDI Registration Page: DANDI Data Submission
- BossDB Registration Page: BossDB Data Submission
Specimen metadata is collected on a quarterly basis to align with reporting requirements for the NIH. Specimen metadata is reported to BCDC at the time when data is deposited at the archives. Specimen metadata includes the name of the data collection that the specimens are added to, so projects and data collections must be registered before a specimen inventory can be created and data submitted to archives. Please contact the BCDC Data Curation team when submitting data for the first time for help in completing the inventory template.
Specimen metadata inventories are submitted through our online portal, which is currently under active development. Please contact BCDC to set up an account for the ingest portal. Once metadata has been submitted, uploads can be reviewed and data receipts generated for NIH reporting purposes in the ingest portal itself.
- Specimen Metadata Template and Instructions: Specimens Template
- BCDC Specimen Ingest Portal: https://bcdc.ingest.brain.allentech.org/
File manifests for newly added specimens are created by the archives when data is submitted, and shared by the archives with the BCDC Data Curation team. The archives collect metadata about files when data is ingested, and BCDC receives that information from the archives, along with critical metadata about data publication such as archive-assigned file UIDs and URIs. For more information on file metadata collection, contact the archives.
As part of our commitment to following community standards in curating BICCN data, BCDC uses controlled vocabularies and ontologies for metadata. The list of controlled terms for selected fields are included on both the Project and Specimen metadata templates, and lists of controlled terms including definitions are maintained on a separate site here:
- BCDC Data Curation Team: data.curation@alleninstitute.org
- Email for any assistance and/or questions about submission requirements and deadlines
- BCDC Metadata Github: https://github.com/BICCN/BCDC-Metadata
- Templates for submitting project and specimen metadata, archived inventories of all BCDC Specimens