Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 0.756, placing it in the top 26.6% of the data-sharing corpus. It has been cited 28 times, with 23 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 27% 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.
“For access to content described in this manuscript see: http://doi.org/10.7303/syn26164834 . Raw data can be downloaded from http://doi.org/10.7303/syn26148119 .”
The paper provides DOIs (10.7303/syn26164834 and 10.7303/syn26148119) for the dataset, which are persistent identifiers.
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 source data described in this manuscript are available via the PsychENCODE Knowledge Portal”
The PsychENCODE Knowledge Portal is a named data repository. [majority verdict 'yes' (4/5 passes agreed)]
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
“For access to content described in this manuscript see: http://doi.org/10.7303/syn26164834 . Raw data can be downloaded from http://doi.org/10.7303/syn26148119 .”
The dataset identifiers appear only in the body text of the data-availability statement, not in the reference list.
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 source data described in this manuscript are available via the PsychENCODE Knowledge Portal (https://psychencode.synapse.org/). The PsychENCODE Knowledge Portal is a platform for accessing data, analyses and tools generated through grants funded by the National Institute of Mental Health (NIMH) PsychENCODE program. Data is available for general research use according to the following requirements for data access and data attribution: (https://psychencode.synapse.org/DataAccess). For access to content described in this manuscript see: http://doi.org/10.7303/syn26164834 . Raw data can be downloaded from http://doi.org/10.7303/syn26148119 .”— not found in the paper; verdict downgraded
The data-availability statement points to a repository record with DOIs, fitting Colavizza category 3. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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
“After pooling reads from biological replicates, we obtained 1.2 billion unique cis contacts from fetal cortical plate tissue, and 1.6 and 1.8 billion from adult neurons and glia, respectively, producing ultra-deep 3D genome maps in primary human brain tissue across development ( Supplementary Table S5 ).”
The dataset's content is described in running prose (size in contacts) but not in an itemized inventory. [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'
“Data is available for general research use according to the following requirements for data access and data attribution”
The access route carries a precondition: users must follow the requirements for data access and attribution, which is a specified followable process. [majority verdict 'partial' (4/5 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 source data described in this manuscript are available via the PsychENCODE Knowledge Portal ( https://psychencode.synapse.org/ ). The PsychENCODE Knowledge Portal is a platform for accessing data, analyses and tools generated through grants funded by the National Institute of Mental Health (NIMH) PsychENCODE program. Data is available for general research use according to the following requirements for data access and data attribution: ( https://psychencode.synapse.org/DataAccess ).”
The paper states that the data are available for general research use with requirements, but does not use an explicit label from the standard access-rights vocabulary. [majority verdict 'partial' (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
“The source data described in this manuscript are available via the PsychENCODE Knowledge Portal (https://psychencode.synapse.org/).”— not found in the paper; verdict downgraded
The paper names the PsychENCODE Knowledge Portal, a controlled-access repository, as the gatekeeper for the sensitive human-subject data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]
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
No sentence in the paper states the timing or persistence of the data's 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'
No file format 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
“Gene expression was quantified using RSEM (v1.3.1) tools (22) with GENCODE V30 as a reference”— not found in the paper; verdict downgraded
The paper uses GENCODE V30, a community standard for gene annotation, for the data analysis. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 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'
“aligned to human genome hg38 (GRCh38)”
The paper references the GRCh38 human genome assembly, which is an identifier for an external resource. [majority verdict 'yes' (3/5 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'
No license is named for the data; the article's CC-BY-NC license applies only to the article text.
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'
No version token or date is provided for the dataset.
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'
“Code used throughout this study is available at Zenodo ( https://zenodo.org/record/8190413 ).”
The paper gives a machine-resolvable URL to a Zenodo archive for the code. [majority verdict 'yes' (4/5 passes agreed)]
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)
“National Institute on Aging, National Institutes of Health [U01-MH116442 to P.R., R01-MH109897 to P.R., K.J.B., R01-MH109677 to P.R., R01-MH110921 to P.R. R01MH106056 to K.J.B., U01DA047880 to K.J.B., R01DA048279 to K.J.B., 6R56MH101454 to K.J.B., R01MH121074 to K.J.B.]”
The paper lists specific grant numbers (e.g., U01-MH116442) attached to 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
“Uniquely barcoded Hi-C libraries were pooled and deep sequenced on the Illumina NovaSeq S4 platform obtaining 100 bp paired end reads”
The paper names the specific sequencing platform (Illumina NovaSeq S4) used to produce the data.
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) is mentioned as accompanying the data, and no variable-definition table is provided inside the article. [majority verdict 'no' (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
0.505
From this paper's citation signal
Citation Network Contribution
0.251
From 13 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 23 citers.
National Institute on Aging
Grant: U01-MH116442
National Institute on Aging
Grant: R01-MH109897
National Institute on Aging
Grant: R01-MH109677
National Institute on Aging
Grant: R01-MH110921
National Institute on Aging
Grant: R01MH106056
National Institute on Aging
Grant: U01DA047880
National Institute on Aging
Grant: R01DA048279
National Institute on Aging
Grant: 6R56MH101454
National Institute on Aging
Grant: R01MH121074
National Alliance for Research on Schizophrenia & Depression
Grant: 27209]
NARSAD Young Investigator Grant
Grant: 29683
Alzheimer's Association Research Fellowship
Grant: AARF-21-722582
NIDA NIH HHS
Grant: R01 DA047880
NIMH NIH HHS
Grant: R56 MH101454
NIMH NIH HHS
Grant: U01 MH116442
NIH HHS
Grant: S10 OD030463
NIDA NIH HHS
Grant: R01 DA034279
NIMH NIH HHS
Grant: R01 MH110921
NIH HHS
Grant: S10 OD026880
NIMH NIH HHS
Grant: R01 MH109677
NIMH NIH HHS
Grant: R01 MH109897
National Institutes of Health
Grant: 5U01MH116442-03
The 3D genome in transcriptional regulation across the postnatal life span, with implications for schizophrenia and bipolar disorder
National Institutes of Health
Grant: 1R01MH109897-01
Integrated Multiscale Networks in Schizophrenia
National Institutes of Health
Grant: 5R01DA047880-04
TRANSCRIPTOME AND EPIGENOME MAPPING IN DOPAMINE NEURONS FROM THE OPIOID EXPOSED HUMAN BRAIN
National Institutes of Health
Grant: 5R56MH101454-07
Modeling the contribution of common variants to schizophrenia risk
National Institutes of Health
Grant: 5R01MH121074-02
Cell-type-specific NRXN1alpha alternative splicing changes in psychiatric disease
National Institutes of Health
Grant: 5R01MH109677-02
Risk genetic variants and cis regulation of gene expression in Bipolar Disorder
National Institutes of Health
Grant: 5R01MH106056-08
Higher Order Chromatin and Genetic Risk for Schizophrenia
National Institutes of Health
Grant: 3U01DA048279-03S1
Functional genomic resource and integrative model of dopaminergic circuitry associated with psychiatric disease
National Institutes of Health
Grant: 5R01MH110921-04
Molecular Profiling of Schizophrenia
Brain and Behavior Research Foundation
National Institutes of Health
FWCI
2.77
Citation Percentile
0.9%
Citation Trend
Fields of Study
MeSH Terms
Keywords