Functional Genomics Experiment Markup Language
Names
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Functional Genomics Experiment Markup Language
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
FuGE-ML
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Names
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Functional Genomics Experiment Markup Language
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
FuGE-ML
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Names
More detailed information about this field from each metasource.
Functional Genomics Experiment Markup Language
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
FuGE-ML
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards.FuGE is a model of the shared components in different functional genomics domains. FuGE facilitates the development of data standards in functional genomics in two ways: 1. FuGE provides a model of common components in functional genomics investigations, such as materials, data, protocols, equipment and software. These models can be extended to develop modular data formats with consistent structure. 2. FuGE provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats. In this context, FuGE allows the capture of additional metadata that gives formats a context within the complete workflow. FuGE is available as a UML model and an XML Schema
Description
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Functional genomics experiments present many challenges in data archiving, sharing and querying. As the size and complexity of data generated from such experiments grows, so does the requirement for standard data formats. To address these needs, the Functional Genomics Experiment [Object Model / Markup-Language] (FuGE-OM, FuGE-ML) has been created to facilitate the development of data standards.FuGE is a model of the shared components in different functional genomics domains. FuGE facilitates the development of data standards in functional genomics in two ways: 1. FuGE provides a model of common components in functional genomics investigations, such as materials, data, protocols, equipment and software. These models can be extended to develop modular data formats with consistent structure. 2. FuGE provides a framework for capturing complete laboratory workflows, enabling the integration of pre-existing data formats. In this context, FuGE allows the capture of additional metadata that gives formats a context within the complete workflow. FuGE is available as a UML model and an XML Schema
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Webpage:
http://fuge.sourceforge.net/dev/index.phpWebpage
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http://fuge.sourceforge.net/dev/index.php
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications:
Publications
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The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
PMID: 17921998
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Publications
More detailed information about this field from each metasource.
The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
PMID: 17921998
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
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The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
PubMed citations: 39.
39 articles citing: The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data. PMID:32053657
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. PMID:30152011
Big data management challenges in health research-a literature review. PMID:28968677
Proteomics Standards Initiative: Fifteen Years of Progress and Future Work. PMID:28849660
How to make Mathematics Biology's next and better microscope. PMID:27920995
The Ontology for Biomedical Investigations. PMID:27128319
The Electron Microscopy eXchange (EMX) initiative. PMID:26873784
A digital repository with an extensible data model for biobanking and genomic analysis management. PMID:25077808
Semantic integration of gene expression analysis tools and data sources using software connectors. PMID:24341380
A repository based on a dynamically extensible data model supporting multidisciplinary research in neuroscience. PMID:23043673
File formats commonly used in mass spectrometry proteomics. PMID:22956731
DIPSBC--data integration platform for systems biology collaborations. PMID:22568834
BioQ: tracing experimental origins in public genomic databases using a novel data provenance model. PMID:22426342
The mzIdentML data standard for mass spectrometry-based proteomics results. PMID:22375074
Integration and analysis of genome-scale data from gliomas. PMID:21727940
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
Towards interoperable reporting standards for omics data: hopes and hurdles. PMID:21347181
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. PMID:20679334
The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. PMID:20677327
Application of genetic/genomic approaches to allergic disorders. PMID:20638111
Saliva Ontology: an ontology-based framework for a Salivaomics Knowledge Base. PMID:20525291
BioTorrents: a file sharing service for scientific data. PMID:20418944
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. PMID:20214801
SDOP-DB: a comparative standardized-protocol database for mouse phenotypic analyses. PMID:20194625
Head in the clouds: Re-imagining the experimental laboratory record for the web-based networked world. PMID:20098590
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. PMID:19941647
Megascience. 'Omics data sharing. PMID:19815759
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. PMID:19732427
FuGEFlow: data model and markup language for flow cytometry. PMID:19531228
Systems medicine: the future of medical genomics and healthcare. PMID:19348689
Modeling genomic data with type attributes, balancing stability and maintainability. PMID:19327130
Genotype-phenotype databases: challenges and solutions for the post-genomic era. PMID:19065136
MIFlowCyt: the minimum information about a Flow Cytometry Experiment. PMID:18752282
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. PMID:18688244
Making a new technology work: the standardization and regulation of microarrays. PMID:18449388
Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). PMID:18327244
Capture and analysis of quantitative proteomic data. PMID:17640002
An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ. PMID:17270041
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. PMID:17087822
Tags:
Tags
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assay
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
biological sample
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
device
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
reagent
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
report
metasource: Fairsharing.org
version: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
Tags
More detailed information about this field from each metasource.
assay
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
biological sample
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
device
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
reagent
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
report
metasource: Fairsharing.orgversion: FAIRsharing.org: FuGE-ML; Functional Genomics Experiment Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.namxfm; Last edited: Jan. 8, 2019, 1:31 p.m.; Last accessed: Jan 03 2022 7:13 p.m.
assay biological sample device reagent report
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