Genetics

Standards Add

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

MIBBI Portal Edit

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

VarioML Edit

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.

MOLGENIS Edit

A software generator to rapidly build web databases and a suite of web databases for genotype, phenotype, QTL and analysis pipelines.

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.

CHD7 Database Edit
dbEST (Expressed Sequence Tag Database) Edit

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

International dystrophic eb Patient Registry Edit
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.

WormQTL-HD Edit
WormQTL Edit