MetaSRA
MetaSRA is a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties.
Description
More detailed information about this field from each metasource.
MetaSRA is a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties.
metasource: Fairsharing.orgversion: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Webpage:
http://metasra.biostat.wisc.edu/Webpage
More detailed information about this field from each metasource.
http://metasra.biostat.wisc.edu/
metasource: Fairsharing.orgversion: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
PMID: 28535296
metasource: Fairsharing.org
version: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
PMID: 28535296
metasource: Fairsharing.org
version: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
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MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
PubMed citations: 31.
31 articles citing: MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata. PMID:35576001
Understanding the Nature of Metadata: Systematic Review. PMID:35014967
Bias-invariant RNA-sequencing metadata annotation. PMID:34553213
The role of metadata in reproducible computational research. PMID:34553169
STAT: a fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next-generation sequence submissions. PMID:34544477
Putatively cancer-specific exon-exon junctions are shared across patients and present in developmental and other non-cancer cells. PMID:34316681
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
Correlation AnalyzeR: functional predictions from gene co-expression correlations. PMID:33879054
Improving the completeness of public metadata accompanying omics studies. PMID:33858487
Large-scale labeling and assessment of sex bias in publicly available expression data. PMID:33784977
CellO: comprehensive and hierarchical cell type classification of human cells with the Cell Ontology. PMID:33364592
Expanding and Remixing the Metadata Landscape. PMID:33229213
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. PMID:33221926
Maximizing the reusability of gene expression data by predicting missing metadata. PMID:33156882
PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. PMID:32958497
Planet Microbe: a platform for marine microbiology to discover and analyze interconnected 'omics and environmental data. PMID:32735679
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). PMID:32463383
Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. PMID:32228719
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes. PMID:31728526
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID:31110304
Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data. PMID:30697483
Mining data and metadata from the gene expression omnibus. PMID:30594974
Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses. PMID:30519242
The fractured landscape of RNA-seq alignment: the default in our STARs. PMID:29718481
GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata. PMID:29688376
Improving the value of public RNA-seq expression data by phenotype prediction. PMID:29514223
Cloud computing for genomic data analysis and collaboration. PMID:29379135
Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. PMID:29364944
ALE: automated label extraction from GEO metadata. PMID:29297276
Tags:
Tags
More detailed information about this field from each metasource.
biological sample annotation
metasource: Fairsharing.org
version: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
nucleic acid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
rna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Tags
More detailed information about this field from each metasource.
biological sample annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
nucleic acid sequence
metasource: Fairsharing.orgversion: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
rna sequencing
metasource: Fairsharing.orgversion: FAIRsharing.org: MetaSRA; MetaSRA; DOI: https://doi.org/10.25504/FAIRsharing.ZS8uWa; Last edited: Feb. 9, 2021, 4 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
biological sample annotation nucleic acid sequence rna sequence
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