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EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

Nucleic Acids Research(2017)10.1093/nar/gkx967Source: DataRank Database

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies is a dataset published in Nucleic Acids Research (2017). On theSindex it has a DataRank of 6.9, placing it in the top 2.7% of the data-sharing corpus. It has been cited 238 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 84/100.

Top 3%percentile

6.9DataRank

Ranks in the top 3% for downstream scientific impact

Data paper Open Access238 citations · 100 citing works in its network

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Cite:

Linked data & code

bioproject gen

DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?

›Methodology & internals

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Pipeline:MetadataData-paper checkEnrichmentCitation networkScoring

Enrichment:Funding (8 grants)OA: goldTopics (52)Linked Datasets (25)DataCite Reuse (25)IDs (PubMed, PMC)Annotations (2)

FAIR Checklist

Context only (not used in score)

Findable (2/2)

Has DOI
Indexed in repositories

Accessible (1/2)

Open Access

Interoperable (2/2)

DataCite relations
Linked datasets

Reusable (1/3)

Dataset classification

FAIR checklist signals are shown for context only and do not affect DataRank scoring.

84FAIR score

Full FAIR picture · advisory

F Findable

100

A Accessible

I Interoperable

100

R Reusable

superseded rubric · not rankeddeterministic✓ full text read

How the score was derived

This score predates the current agent — it came from the earlier rubric, which blended repository metadata into the number and asked the model for a rating rather than an evidenced verdict. Re-evaluate the paper to score it against the current standards-anchored criteria, where every verdict is backed by a quote from the full text.

F Findable100

detHas a persistent DOI100

DOI present

detIndexed in repositories / literature DBs100

datacite=25, pmcid=True, pmid=True

detResolvable scholarly identifiers (OpenAlex)100

OpenAlex id present

A Accessible70

detOpen Access / files deposited50

files/OA location present but not flagged OA

detFree full text retrievable100

13 OA location(s)

I Interoperable100

detLinked datasets / DataCite relations100

linked_datasets=25, datacite=25

detReferences data via standard accessions100

accessions=2, trials=0

R Reusable67

detClear, open reuse license100

open license (cc-by)

detDemonstrated reuse (downloads)0

downloads=0

detVersioned / maintained0

no version chain

detClassified as a data resource100

is_dataset

Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →

DataRank Breakdown

Base Score 12%Citation Network 88%

Base Score Contribution

0.821

From this paper's citation signal

Citation Network Contribution

6.1

From 100 citing papers with measurable signal

Learn more about DataRank methodology →

Top 5 citers driving the network score

Ranked by each citer's contribution to N(p) — log1p(C_q) divided by its reference count — out of 100 citers.

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
Bioinformatics2018149 citations10 referencesContributes 0.501
Refget: standardized access to reference sequences
Bioinformatics202117 citations8 referencesContributes 0.361
UniProt: a worldwide hub of protein knowledge
Nucleic Acids Research20188,431 citations34 referencesContributes 0.266
Every fifth published metagenome is not available to science
PLoS Biology202030 citations17 referencesContributes 0.202
TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes
Nucleic Acids Research201946 citations20 referencesContributes 0.193

Authors (17)

Maxim Scheremetjew ORCID,Hubert Denise ORCID,Simon Potter ORCID,Aleksandra Tarkowska ORCID,Matloob Qureshi ORCID

Live enrichment

PubMed:29069476 PMC:PMC5753268

Biotechnology and Biological Sciences Research Council

Grant: BB/I02612X/1

Biotechnology and Biological Sciences Research Council

Grant: BB/M011453/1

Biotechnology and Biological Sciences Research Council

Grant: BB/M011755/1

EBI Metagenomics Portal - Towards a better understanding of community metabolism

Biotechnology and Biological Sciences Research Council

Grant: BB/N018354/1

Bilateral NSF/BIO-BBSRC:A Metagenomics Exchange - enriching analysis by synergistic harmonisation of MG-RAST and the EBI Metagenomics Portal

Wellcome Trust

Grant: unidentified

unidentified

European Commission

Grant: 676559

ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.

Biotechnology and Biological Sciences Research Council

goldLicense: cc-by

publisherhttps://academic.oup.com/nar/article-pdf/46/D1/D726/23162872/gkx967.pdf

publisherhttp://academic.oup.com/nar/article-pdf/46/D1/D726/23162872/gkx967.pdf

repositoryhttps://www.ncbi.nlm.nih.gov/pmc/articles/5753268

repositoryhttp://doi.org/10.1093/nar/gkx967

Europe_PMChttps://europepmc.org/articles/PMC5753268

Fields of Study

0301 basic medicine0303 health sciences03 medical and health sciencesAlgorithmsBase SequenceClassificationDatabases, GeneticDatasets as TopicMetagenomicsMicrobiotaRNA, ArchaealRNA, BacterialRNA, ViralRibotypingSoftwareTranscriptomeUser-Computer InterfaceWeb BrowserWorkflow

MeSH Terms

RNA, ArchaealRNA, BacterialRNA, ViralRibotypingBase SequenceAlgorithmsClassificationSoftwareUser-Computer InterfaceDatabases, GeneticMetagenomicsWorkflowTranscriptomeMicrobiotaWeb BrowserDatasets as Topic

Keywords

Base SequenceMicrobiotaDatasets as TopicRNA, ArchaealWeb BrowserClassificationRibotypingWorkflowRNA, BacterialUser-Computer InterfaceDatabases, GeneticDatabase IssueRNA, ViralMetagenomicsTranscriptomeAlgorithmsSoftware

Additional file 1 of geneRFinder: gene finding in distinct metagenomic data complexities

10.6084/m9.figshare.14121481.v1figshare

Additional file 1 of geneRFinder: gene finding in distinct metagenomic data complexities

10.6084/m9.figshare.14121481figshare

Additional file 1 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714184.v1figshare

Additional file 1 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714184figshare

Additional file 2 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714187.v1figshare

Additional file 2 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714187figshare

Additional file 3 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714190.v1figshare

Additional file 3 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714190figshare

Additional file 4 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714193.v1figshare

Additional file 4 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714193figshare

Additional file 5 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714196.v1figshare

Additional file 5 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714196figshare

Additional file 6 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714199.v1figshare

Additional file 6 of MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen

10.6084/m9.figshare.16714199figshare

Additional file 1 of MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes

10.6084/m9.figshare.21602005.v1figshare

Additional file 1 of MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes

10.6084/m9.figshare.21602005figshare

Additional file 1 of Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield

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Additional file 1 of Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield

10.6084/m9.figshare.26339939figshare

Additional file 5 of The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes

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Additional file 5 of The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes

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