SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor is a dataset published in Bioinformatics (2022). On theSindex it has a DataRank of 3.1, placing it in the top 7.1% of the data-sharing corpus. It has been cited 140 times, with 89 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 7% for downstream scientific impact
DataRank reads this dataset's downstream impact straight off the citation graph — no black box, no proprietary weighting. How is this computed?
FAIR checklist signals are shown for context only and do not affect DataRank scoring.
Full FAIR picture · advisory
The headline score is computed from the scored criteria — the fact-shaped checks (a repository, an accession, a licence) that two independent models agree on. The advisory criteria below are real FAIR guidance but rest on judgment calls that models read differently, so they inform without moving the number.
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment .”
The data are given a web URL (https) rather than a persistent identifier scheme (DOI, handle, or repository accession).
RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit · RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier' · FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment .”
Bioconductor is a named repository (curated archive for R/Bioconductor packages).
RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed ( · NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived · NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment .”
The dataset identifier (URL) appears only in body text, not in the reference list. [majority verdict 'partial' (4/5 passes agreed)]
FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first- · RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes · FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'
Advisory · not in the published score
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment . The STexampleData , TENxVisiumData and ggspavis packages are available from Bioconductor at https://bioconductor.org/packages/STexampleData , https://bioconductor.org/packages/TENxVisiumData and https://bioconductor.org/packages/ggspavis , respectively. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards. Datasets from Supplementary Tables S1 and S2 and Supplementary Figure S1 are available as SpatialExperiment objects from the STexampleData and TENxVisiumData packages, and the full original datasets are available from the sources listed in Supplementary Tables S1 and S2 ( 10x Genomics, 2021b ; Lohoff et al. , 2021 ; Maynard et al. , 2021 ; Pardo et al. , 2022 ).”
The data-availability statement points to a public repository (Bioconductor) with links, fulfilling Colavizza category 3. [majority verdict 'yes' (4/5 passes agreed)]
Colavizza, Hrynaszkiewicz, Staden, Whitaker & McGillivray (2020), 'The citation advantage of li · Springer Nature research data policy — Data Availability Statements: standard statement templat · RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes
“The SpatialExperiment package provides access to the core data infrastructure (referred to as a class), as well as functions to create, modify and access instances of the class (objects).”
The dataset's content is described in running prose rather than an itemised inventory (section, table, or list). [majority verdict 'partial' (4/5 passes agreed)]
RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential) · FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability' · FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment .”
The data are available from Bioconductor with no stated precondition. [majority verdict 'yes' (3/5 passes agreed)]
RDA-A1.1-01D — 'Data is accessible through a free access protocol' · FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data' · NSTC Desirable Characteristics of Data Repositories (2022) — 'Free and Easy Access'
Advisory · not in the published score
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment .”
The paper describes the action of accessing the data (via Bioconductor URL) but does not explicitly label the access level. [majority verdict 'partial' (4/5 passes agreed)]
FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data' · RDA-A1-01M — metadata contains information to enable the user to get access to the data · COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl
The data are not sensitive (software and example datasets), and no gatekeeper is named.
NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee · RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and · NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse
“The SpatialExperiment, STexampleData, TENxVisiumData and ggspavis packages are available from Bioconductor”— not found in the paper; verdict downgraded
The text states that the data are available now (availability timing) but makes no commitment about how long they will persist. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 passes agreed)]
NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines · NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy' · RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'
No file format token is named for the released data.
FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co · RDA-R1.3-02D — data is expressed in a machine-understandable community standard · RDA-I1-01D — data uses a knowledge representation expressed in a standardised format
Advisory · not in the published score
No data/metadata community standard (e.g., MIAME, MIxS, ontology) is named for the dataset.
RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential) · RDA-R1.3-01D — 'Data complies with a community standard' · RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'
No identifier for a non-own resource (e.g., accession, DOI, RRID) is given in the text beyond reference citations.
RDA-I3-01M — '(meta)data include references to other (meta)data' · RDA-I3-03M — 'metadata includes qualified references to other metadata' · FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'
No license is named for the data; the article's CC-BY license does not apply to the data.
RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu · RDA-R1.1-02M — 'Metadata refers to a standard reuse licence' · RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'
“The package versions described in this manuscript are available in Bioconductor version 3.15 onwards.”
The text mentions a Bioconductor release version, but not a specific version token for the dataset itself. [majority verdict 'no' (3/5 passes agreed)]
DataCite Metadata Schema 4.6 — the 'Version' property · RDA-R1.2-01M — provenance information (which version was used is provenance) · NSTC Desirable Characteristics of Data Repositories (2022) — 'Provenance', 'Retention Policy'
“The SpatialExperiment package is available from Bioconductor at https://bioconductor.org/packages/SpatialExperiment .”
A machine-resolvable locator (Bioconductor URL) is given for the study's own code.
NIH DMS Policy Element 2 (NOT-OD-21-014) — 'Related Tools, Software and/or Code' · FAIR4RS Principles v1.0 (Chue Hong et al., 2022; RDA/FORCE11/ReSA) — FAIR Principles for Resear · FORCE11 Software Citation Principles (Smith, Katz & Niemeyer, 2016, PeerJ CS 2:e86)
“This work was supported by CZF2019-002443 [to L.M.W., D.Rig., S.C.H., D.Ris.] from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation. L.M.W., S.C.H. and L.C.-T. were supported by National Institutes of Health/NIMH U01MH122849 to S.C.H. and L.C.-T. D.Ris. was supported by ‘Programma per Giovani Ricercatori Rita Levi Montalcini’ granted by the Italian Ministry of Education, University, and Research and by the National Cancer Institute of the National Institutes of Health [2U24CA180996]. S.G. was supported by a Royal Society Newton International Fellowship [NIF\R1\181950].”
Multiple award/grant numbers are provided alongside named funders.
DataCite Metadata Schema 4.6 — 'FundingReference' property (funderName, funderIdentifier, award · Crossref Funder Registry — canonical funder identifiers for funding metadata · RDA-F2-01M — rich metadata provided to allow discovery (funding is part of the descriptive reco
Advisory · not in the published score
The paper does not name specific instruments, kits, or software used to produce the data (the data are the software itself).
RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa · FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati · W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance
No documentation object (README, codebook, data dictionary) is named as travelling with the data.
RDA-R1-01M — '(Meta)data are richly described with a plurality of accurate and relevant attribu · FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data' · NIH DMS Policy Element 3 (NOT-OD-21-014) — Standards (documentation and metadata to accompany t
Calibrated FAIR score — a parallel quality metric, independent of the DataRank citation score. See the full evaluation →
Base Score Contribution
0.742
From this paper's citation signal
Citation Network Contribution
2.4
From 61 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 89 citers.
Chan Zuckerberg Initiative DAF
Grant: CZF2019-002443
National Institutes of Health/NIMH
Grant: U01MH122849
University, and Research and by the National Cancer Institute of the National Institutes of Health
Grant: 2U24CA180996
Royal Society Newton International Fellowship
Grant: NIF\R1\181950
NHGRI NIH HHS
Grant: K99 HG012229
NCI NIH HHS
Grant: U24 CA180996
National Institutes of Health
Grant: 3U24CA180996-10S1
Cancer Genomics: Integrative and Scalable Solutions in R/Bioconductor
National Institutes of Health
Grant: 5U01MH122849-02
Spatial registration of gene expression in the human brain
Silicon Valley Community Foundation
Programma per Giovani Ricercatori Rita Levi Montalcini’ granted by the Italian Ministry of Education
Fields of Study
MeSH Terms
Keywords