Genomics

Standards Add

ABCD (Access to Biological Collection Data) Edit

The Access to Biological Collections Data (ABCD) Schema is an evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data). The ABCD Schema attempts to be comprehensive and highly structured, supporting data from a wide variety of databases. It is compatible with several existing data standards. Parallel structures exist so that either (or both) atomised data and free-text can be accommodated.

Sponsored by Biodiversity Information Standards TDWG - the Taxonomic Databases Working Group, the current specification was last modified in 2007.

Genome Metadata Edit

Genome metadata on PATRIC consists of 61 different metadata fields, called attributes, which are organized into the following seven broad categories: Organism Info, Isolate Info, Host Info, Sequence Info, Phenotype Info, Project Info, and Others.

ISA-Tab Edit

The Investigation/Study/Assay (ISA) tab-delimited (TAB) format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from 'omics-based' experiments employing a combination of technologies.

Created by core developers from the University of Oxford, ISA-TAB v1.0 was released in November 2008.

MIBBI (Minimum Information for Biological and Biomedical Investigations) Edit

A common portal to a group of nearly 40 checklists of Minimum Information for various biological disciplines. The MIBBI Foundry is developing a cross-analysis of these guidelines to create an intercompatible, extensible community of standards.

The concept was realized initially through the joint efforts of the Proteomics Standards Initiative, the Genomic Standards Consortium and the MGED RSBI Working Groups. The latest project to register with MIBBI is the MIABie guidelines for reporting biofilm research, as of January 2012.

Repository-Developed Metadata Schemas Edit

Some repositories have decided that current standards do not fit their metadata needs, and so have created their own requirements.

Extensions Add

ABCDDNA Edit

An extension of the ABCD standard for DNA data.

isaconfig-diXa Edit
MIBBI Portal Edit

A list of nearly 40 Minimum Information standards projects registered with the MIBBI initiative.

Tools Add

ISA Software Suite Edit

The open source ISA metadata tracking tools facilitate ISA-TAB-compliant collection, curation, local management and reuse of datasets in an increasingly diverse set of life science domains.

PATRIC Download Tool Edit

Tool for downloading data from PATRIC.

Use Cases Add

BioModels Database Edit

A repository hosting computational models of biological systems, using the MIBBI-registered MIRIAM and MIASE minimal metadata requirements.

dbEST (Expressed Sequence Tag Database) Edit

A repository-developed metadata schema for EST data in Genbank.

Harvard Medical School LINCS Database Edit

One of two research centers in the US creating libraries of signatures that describe how cells respond to perturbation, it uses the ISA-TAB standard to describe its data.

ISA Commons Edit

A network of systems and projects that use the ISA-Tab file format, and/or are powered by components of the ISA software suite.

MVID Patient Registry Edit
NEBC ISA Network BioInvestigationIndex Edit

The NERC Environmental Bioinformatics Centre ISA Network's index of ISA-Tab and MIBBI-compliant environmental 'omics data.

PRIDE (Proteomics Identifications Database) Edit

A centralized, MIBBI standards compliant, public data repository for proteomics data, post-translational modifications and supporting spectral evidence.

WormQTL-HD Edit