biccn/biccn-infrastructure

Documentation about BICCN Infrastructure and Data Policies

biccn-infrastructure's Issues

Patch-seq Data Linkage

This issue is for discussion around Data Linkage for Patch-seq. The goal is to determine the requirements for Data Linkage across archives.
Please feel free to comment and add to the discussion.

Patch-Seq consists of data that will be housed at 3 archives:

Archive	Data Type	File Type (Minimum)	Note
DANDI	Patch Ephys	NWB
BIL	Morphology	SWC	Images optional
NEMO	Transcriptomics	Fastq

Here is a first use case to support:

1. Use Case: User wants to find data associated with only those cells that have all 3 data types.
   Necessary information:

• Cell specimen id for linking data across all three archives
• Availability of each data type for that cell - some cells will have all 3, some will have 2, some cells may only have ephys.

Move charters into charter folder

Need help with moving charters into charter folder

Data Level Policy

It would be great to have a concise and centralized policy for data levels.

Hashing for files

Consortium should decide on a standard for hashing methods.

DOI Support for Manuscripts

There are multiple strategies for DOI support for manuscripts. We need to decide on appropriate strategies to group data for DOIs at each archive.

TYPE of Data	SETS of data	RELATIONSHIP to Paper	LOCATION of Data
Raw data (e.g., fastq, NWB, Stitched images)	Subset of “project” explicitly reported to date	All applicable data, whether explicitly reported in paper or not	Within one archive
Processed Data (e.g., BAM/counts, registered images)	Subset of “project” that is all MOp data to date for that project	Data reported to whole paper	Across multiple archives
Annotations	Whole “project” to date (including non-MOp)	Data per figure	At other sites (e.g., Neuromorpho, Mouse Brain Architecture, etc)
	Combinations of subsets of projects	Data per analysis
	Combinations of projects to date

 

Data Ingest Guidelines

It would be great to have a policy in the repo a consistent description of data levels, the expected level of ingestion (per assay group).

Embargo Policy

It is important we codify an embargo policy in GitHub here so it is public and centralized.