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FAANG metadata experiment specification standard

General Information

The FAANG metadata experiment specification document describes the principles and structure for the FAANG metadata guidance. The main goal of the FAANG standards is to ensure all FAANG experiments are well described and that the description is well structured. We support the MIAME and MINSEQE guidelines, and aim to convert them to a concrete specification. The FAANG project will establish an infrastructure capable of efficiently analyzing genome-wide functional data for animal species.

Homepage https://github.com/FAANG/faang-metadata/blob/master/docs/faang_experiment_metadata.md

Countries that developed this resource European Union , United Kingdom , United States

Created in 2016

Taxonomic range

Knowledge Domains

Subjects

User-defined Tags

Experimental condition

General purpose

How to cite this record FAIRsharing.org: FAANG metadata experiment specification standard; FAANG metadata experiment specification standard; DOI: https://doi.org/10.25504/FAIRsharing.fztr98; Last edited: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jan 24 2022 11:11 a.m.

This record is maintained by peter ORCID

Record added: Aug. 19, 2016, 11:53 a.m.
Record updated: Feb. 6, 2021, 11:06 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.fztr98' by 'The FAIRsharing Team' at 11:06, 06 Feb 2021 (approved):

	'user_defined_tags' has been modified:
		Before:
			Data standards
			General purpose
		After:
			Data standards
			Experimental condition
			General purpose
		Added:
			Experimental condition
		Removed:

	'dataProcesses' has been modified:
		Before:
		After:
			Specification, data release, https://github.com/FAANG/dcc-metadata/blob/master/docs/faang_experiment_metadata.md
		Added:
			Specification, data release, https://github.com/FAANG/dcc-metadata/blob/master/docs/faang_experiment_metadata.md
		Removed:

	'onto_domains' has been modified:
		Before:
			Experiment report
		After:
			Biospecimen
			Experimental measurement
			experimentally_determined
			genome-wide association study
			protocol
			sample preparation for assay
			study design
			None
		Added:
			Biospecimen
			Experimental measurement
			experimentally_determined
			genome-wide association study
			protocol
			sample preparation for assay
			study design
			None
		Removed:
			Experiment report

Edits to 'https://fairsharing.org/FAIRsharing.fztr98' by 'The FAIRsharing Team' at 13:39, 13 Feb 2020 (approved):

	'organizations' has been modified:
		Before:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
			Functional Annotation of Animal Genomes (FAANG) Administrators|http://www.faang.org/|Maintains
		After:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
			Functional Annotation of Animal Genomes (FAANG) Administrators|http://www.faang.org/|Maintains
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.fztr98' by 'The FAIRsharing Team' at 09:48, 13 Feb 2020 (approved):

	'related_standards' has been modified:
		Before:
			Cell Ontology
			UBER anatomy ONtology
			BRENDA tissue / enzyme source
			Experimental Factor Ontology
			Phenotypic QualiTy Ontology
			NCBI Taxonomy
			FAANG metadata sample specification standard
		After:
			Cell Ontology
			UBER anatomy ONtology
			BRENDA tissue / enzyme source
			Experimental Factor Ontology
			Phenotypic QualiTy Ontology
			NCBI Taxonomy
			Minimal Information about a high throughput SEQuencing Experiment
			Minimum Information About a Microarray Experiment
			FAANG metadata sample specification standard
		Added:
			Minimal Information about a high throughput SEQuencing Experiment
			Minimum Information About a Microarray Experiment
		Removed:

	'onto_domains' has been modified:
		Before:
		After:
			Experiment report
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			Experiment report
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Edits to 'https://fairsharing.org/FAIRsharing.fztr98' by 'The FAIRsharing Team' at 18:34, 10 Feb 2020 (approved):

	'user_defined_tags' has been modified:
		Before:
		After:
			Data standards
			General purpose
		Added:
			Data standards
			General purpose
		Removed:

	'organizations' has been modified:
		Before:
			Functional Annotation of Animal Genomes (FAANG) Administrators|http://www.faang.org/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined
		After:
			Functional Annotation of Animal Genomes (FAANG) Administrators|http://www.faang.org/|Maintains
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Added:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Funds
		Removed:
			European Commission under FP7 Grant Agreement|http://ec.europa.eu/research/fp7/index_en.cfm?pg=documents|Undefined

	'miriam_id' has been modified:
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	'onto_disciplines' has been modified:
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			Life Science
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			Life Science
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Support

General

support email	General Contact
support email	DCC General Contact

Additional Information

Contact

Peter Harrison ORCID

Tools

FAANG metadata validation tool

http://www.ebi.ac.uk/vg/faang

Schemas

No XSD schemas defined

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Fort Lauderdale Principles

Applies to: Database software

FAANG Apache License

Data Release

Specification

https://github.com/FAANG/dcc-metadata/blob/master/docs/faang_experimen ...

Publications

No publications available

Related Standards

Reporting Guidelines

Terminology Artifacts

Models and Formats

FAANG metadata analysis specification

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases (5)

BioSamples at the European Bioinformatics Institute
The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides links to assays and specific samples, and accepts direct submissions of sample information.

ArrayExpress
ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Experiments are submitted directly to ArrayExpress or are imported from the NCBI GEO database.

Gene Expression Omnibus
The Gene Expression Omnibus (GEO) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the studies and gene expression patterns stored in GEO.

Sequence Read Archive
The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submission. The SRA study contains high-level information including goals of the study and literature references, and may be linked to the INSDC BioProject database.

NCBI BioSample
The NCBI BioSample database stores submitter-supplied descriptive information, or metadata, about the biological materials from which data stored in NCBI’s primary data archives are derived. NCBI’s archives host data from diverse types of samples from any species, so the BioSample database is similarly diverse; typical examples of a BioSample include a cell line, a primary tissue biopsy, an individual organism or an environmental isolate. The BioSample database promotes the use of structured and consistent attribute names and values that describe what the samples are as well as information about their provenance, where appropriate.

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by peter ORCID

Funds

European Commission under FP7 Grant Agreement (Government body)

Maintains

Functional Annotation of Animal Genomes (FAANG) Administrators (Consortium) Lead
European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute)

FAANG metadata experiment specification standard

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