A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features is a dataset published in Nature Medicine (2024). On theSindex it has a DataRank of 1.3, placing it in the top 15.3% of the data-sharing corpus. It has been cited 91 times, with 85 citing works in its 1-hop citation network. Its calibrated FAIR score is 67/100.
Ranks in the top 15% for downstream scientific impact
Linked data & code
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.
“phs002371”
The paper provides a dbGaP accession number (phs002371), which is a persistent identifier scheme for the dataset.
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'
“dbGaP”
The paper names dbGaP (database of Genotypes and Phenotypes) as a repository holding the data.
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
“accession number: phs002371”
The dataset identifier appears only in the body text of the Data availability section, not as a reference-list entry.
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
“All data can be retrieved from Synapse or the database of Genotypes and Phenotypes (dbGaP) (accession number: phs002371 ) through the HTAN Portal at https://humantumoratlas.org and the associated HTAN Publication Page https://humantumoratlas.org/publications/htapp_mbc_klughammer_2024 . For convenience, processed data are additionally available from the Single-Cell Portal ( https://singlecell.broadinstitute.org/single_cell/study/SCP2702 ) and interactively browsable through CELLxGENE ( https://cellxgene.cziscience.com/collections/a96133de-e951-4e2d-ace6-59db8b3bfb1d ).”
The data-availability statement points to repository records with accessions and persistent links, satisfying Colavizza category 3.
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
“We obtained high-quality Slide-seq and CODEX data from 15 of 15 and 13 of 13 biopsies, respectively, and MERFISH and ExSeq data from nine of 14 each (Fig. 1c , Extended Data Fig. 1b and Supplementary Tables 1 and 2 ).”— not found in the paper; verdict downgraded
The paper references Supplementary Tables 1 and 2, which are itemized inventories of the dataset, and Figure 1c provides an overview table. [downgraded to 'partial' — no verifiable quote from the paper] [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'
“processed data are additionally available from the Single-Cell Portal”
The paper provides an unconditional route to processed data via the Single-Cell Portal, with no stated precondition.
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 paper does not apply any explicit access-level label such as 'open access' or 'restricted access' to the data. [majority verdict 'no' (3/5 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
“dbGaP”
The paper states that data are deposited in dbGaP, a controlled-access repository that serves as an institutional gatekeeper.
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 paper does not mention any retention period, permanent archival, or timing for data availability.
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'
The paper does not name any file format for the released data, only mentions raw sequencing reads in the methods.
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
“PAM50 molecular subtype assignment”
The paper uses PAM50, a community-standard classification for breast cancer subtypes, applied to the data. [majority verdict 'yes' (4/5 passes agreed)]
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'
“The pre-built Cell Ranger reference GRCh38 version 3.0.0 (November 2016) in its spliced (scRNA-seq) and pre-mRNA (snRNA-seq) version was provided by 10x Genomics ( https://www.10xgenomics.com/support/software/cell-ranger/latest/release-notes/cr-reference-release-notes ).”
The paper provides a URL identifier for the reference genome (GRCh38) that the data depend on. [majority verdict 'yes' (4/5 passes agreed)]
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'
The paper does not state any license for the data; the Creative Commons license applies only to the article.
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 paper provides no version token or date for the dataset snapshot.
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'
“https://github.com/klarman-cell-observatory/HTAPP-Pipelines/tree/master/HTAPP_MBC”
The paper provides a GitHub repository URL for the code used in the analysis, which is a machine-resolvable locator.
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)
“HHSN261100039”
The paper includes specific grant numbers, such as HHSN261100039, in the Acknowledgements.
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
“Cell Ranger version 3.0.2 and Cell Bender version 0.1.0”
The paper names specific tools and software versions used to produce the data. [majority verdict 'yes' (4/5 passes agreed)]
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
“Supplementary Tables 1 and 2”
Variable and file definitions are provided in supplementary tables inside the article, but no documentation object is named as travelling with the deposited data. [majority verdict 'partial' (3/5 passes agreed)]
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
0.678
From this paper's citation signal
Citation Network Contribution
0.663
From 36 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 85 citers.
Conquer Cancer Foundation
Grant: 17095
European Molecular Biology Organization
Grant: ALTF 738-2017
Human Frontier Science Program
Grant: LT000452/2019-L
Else Kröner-Fresenius-Stiftung
Grant: 2019_A70
U.S. Department of Health & Human Services | National Institutes of Health
Grant: 1P50CA168504
U.S. Department of Health & Human Services | National Institutes of Health
Grant: HHSN261100039 / HHSN26120150000
NCI NIH HHS
Grant: HHSN261201500003I
NCI NIH HHS
Grant: T32 CA009172
NCI NIH HHS
Grant: P50 CA168504
NCI NIH HHS
Grant: HHSN261201500003C
National Institutes of Health
Grant: 5P50CA168504-03
Overcoming Resistance to Standard HER2-Directed Therapies for Breast Cancer
Howard Hughes Medical Institute
The Cancer Couch Foundation; Catholic Health Foundation; Friends of Dana-Farber Cancer Institute; Hope Scarves; Jamieson Family Fund for Early Career Breast Cancer Researchers; Saverin Family Fund
Terri Brodeur Breast Cancer Foundation
Lisa Yang; John Doerr
FWCI
15.25
Citation Percentile
1.0%
Influential Citations
7
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals