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Neuroscience Multi-Omic Archive (NeMO)

Description

The Neuroscience Multi-Omic (NeMO) Archive is a data repository specifically focused on the storage and dissemination of omic data generated by the BRAIN Initiative and related brain research projects.

Roles

Definitions [Optional]

Define entity specific terminology to ensure that your charter is comprehensible to new community members.

  • OSDF - Open Science Data Framework architecture

Objectives

The NeMO Archive encompasses the following data types:

  • Genomic regions associated with brain abnormalities and disease
  • Transcription factor binding sites and other regulatory elements
  • Transcription activity
  • Levels of cytosine modification
  • Histone modification profiles and chromatin accessibility

By containing knowledge from varied sources in one resource, we allow traversal between datatypes based on common metadata.

Our specific stated aims are:

  • Aim 1. Establish the Neuroscience Multi-Omic (NeMO) Data Store, encompassing data ingestion, and identification and development of controlled vocabularies & ontologies, working closely with the BD2K working groups and others to encourage the use of established standards commonly used for omics data; provision of stable and unique identifiers; and data storage and integration, utilizing OSDF.
  • Aim 2. Perform Data Processing, from quality control processing through analysis pipelines, and promote accessibility of public and controlled datasets as well as standard operating procedures and documentation through the NeMO website and NeMO data portal.
  • Aim 3. Provide Resources for Users to Engage in Analysis and Visualization, by performing continuous use case review and development, enabling analysis and data visualization for individual users, and enabling appropriate data nad analysis access to the BRAIN Initiative Analysis centers

In-scope

Describe the boundaries of this entity's efforts as defined by the specific user or technical needs [without implementation details].

  • Serve as a primary data archive for BICCN omics, supporting access to and enrichment of integrated datasets within the BCDC Cell Registry, facilitating linkage between datasets, modalities and updates, integrating secondary analysis by extracting pipelines into the computing environment and publishing results back to the BCDC Cell Registry and data archives.
  • Provide a web portal for basic NeMO information
  • Support BICCN researchers in deposition of raw and processed data to NeMO archives
  • Perform basic checksum-based QC and reorganization of submitted data before public release
  • Allow for restricted access to private/protected datasets
  • Provide public browsable and queryable access to BICCN consortium metadata and data types described above
  • Allow for easy exchange of raw and processed data between NeMO and Broad Institute's Terra Platform
  • Allow for easy exchange of data between NeMO and NeMO Analytics, a tool for analysis and visualization of omic data
  • Work with BCDC and consortium members to develop, establish, or adapt community generated metadata standards
  • Support API to access indexed sequence files from select dataset to enable the visualization and analysis of genomic data in third party system such as the BCDC Cell Registry
  • Engage in community outreach to understand community needs, develop tools to meet these needs, and ensure the utilization of tools and data by the community

Out-of-scope

  • Non-genomic, non-sequence datatypes.

Disambiguation [Optional]

All metadata development will be fully in coordination, and highly complementary, with all other BICCN data archives and centers.

Communication

Mailing Lists

Github repositories

  • Documentation Documentation on submitting, viewing, browsing or searching for data, downloading data, or exporting data to Broad Institute's Terra Platform
  • Analytics Repository for the NeMO Analytics project
  • Terra Utility for data and metadata transfers between NeMO and Terra, formerly called Firecloud

Funding