Long-read genome assemblies for the study of chromosome expansion: Drosophila kikkawai, Drosophila takahashii, Drosophila bipectinata, and Drosophila ananassae is a dataset published in G3 Genes Genomes Genetics (2023). On theSindex it has a DataRank of 0.318, placing it in the top 53.3% of the data-sharing corpus. It has been cited 5 times, with 4 citing works in its 1-hop citation network. Its calibrated FAIR score is 58/100.
Ranks in the top 53% 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.
“Gene annotations for each assembly in GFF3 format are available via figshare under the DOI: 10.6084/m9.figshare.23737671.”
The paper provides a DOI for the gene annotations, which is a persistent identifier scheme. [majority verdict 'yes' (4/5 passes agreed)]
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 Hi-C-scaffolded genome assemblies ... have been deposited at GenBank”— not found in the paper; verdict downgraded
GenBank is a named repository (a re3data-registered archive). [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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
“The Hi-C-scaffolded genome assemblies for D. bipectinata , D. takahashii , D. kikkawai , and D. ananassae have been deposited at GenBank under the accession numbers JARPSB000000000 , JARPSC000000000 , JARPSD000000000 , and JASIRA000000000 , respectively.”
The dataset identifiers appear only in the body text (Data availability section), not in the reference list. [majority verdict 'partial' (3/5 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 PacBio sequencing data are available through the NCBI BioProject database under the accession number PRJNA948012, and the Hi-C data are available through accession numbers PRJNA961071 and PRJNA967347. The Hi-C-scaffolded genome assemblies for D. bipectinata, D. takahashii, D. kikkawai, and D. ananassae have been deposited at GenBank under the accession numbers JARPSB000000000, JARPSC000000000, JARPSD000000000, and JASIRA000000000, respectively. ... Gene annotations for each assembly in GFF3 format are available via figshare under the DOI: 10.6084/m9.figshare.23737671.”— not found in the paper; verdict downgraded
The statement points to repository records with accessions and DOIs (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
“The total assembly sizes for each species are 192.2 ( D. ananassae , excluding a putative Y chromosome scaffold), 194.5 ( D. bipectinata ), 188.5 ( D. kikkawai ), and 198.1 Mb ( D. takahashii ), all close to, but slightly less than, the 205-Mb size estimate from flow cytometry.”— not found in the paper; verdict downgraded
The dataset's content (assembly sizes) is described in running prose, not in an itemised section, table, or list. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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 Hi-C-scaffolded genome assemblies for D. bipectinata , D. takahashii , D. kikkawai , and D. ananassae have been deposited at GenBank under the accession numbers JARPSB000000000 , JARPSC000000000 , JARPSD000000000 , and JASIRA000000000 , respectively.”
The data are deposited in public repositories (GenBank, figshare) with no stated precondition, thus freely accessible. [majority verdict 'yes' (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 Hi-C-scaffolded genome assemblies for D. bipectinata , D. takahashii , D. kikkawai , and D. ananassae have been deposited at GenBank under the accession numbers JARPSB000000000 , JARPSC000000000 , JARPSD000000000 , and JASIRA000000000 , respectively.”
The paper describes the action of depositing in GenBank but does not apply an explicit access-level label such as 'open access' or 'publicly available'. [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 non-sensitive Drosophila genome assemblies, and no gatekeeper of any kind 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
No statement about how long the data will be retained or when they become available. [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'
“GFF3”— not found in the paper; verdict downgraded
Gene annotations are provided in GFF3 format, which is an open, community-standard format. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (2/5 passes agreed)]
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
“The diptera_odb10 (release date 2020-08-05) lineage dataset was used with BUSCO ( Manni et al . 2021 ) in 'genome' mode to assess the quality of the assembled genomes.”— not found in the paper; verdict downgraded
The paper uses the diptera_odb10 lineage dataset, a community standard for genome quality assessment. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 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 Illumina genomic reads used for polishing were obtained from the NCBI Sequence Read Archive (SRA) under the accession numbers SRR345537 ( D. kikkawai ), SRR13070706 ( D. takahashii ), and SRR6425989 ( D. bipectinata ).”
The paper provides external identifiers (SRA accessions, RefSeq accessions, etc.) for resources used in the study. [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'
No license is stated for the deposited data; the CC-BY license applies to the article, not 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 versions of the D. bipectinata , D. takahashii , D. kikkawai , and D. ananassae genome assemblies described in this paper are JARPSB010000000 , JARPSC010000000 , JARPSD010000000 , and JASIRA010000000 , respectively.”
Version-specific accession numbers (e.g., JARPSB010000000) are provided, pinning the snapshot. [majority verdict 'yes' (4/5 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'
No code availability statement or locator for custom code is provided; only third-party tools are mentioned.
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 material is based upon work supported by the National Science Foundation (NSF) under grant no. 2114661 to CJA at New Jersey City University and the National Institutes of Health (NIH) under grant number R01GM130698 to CE and Fellowship F32GM140669 to NT.”
Multiple grant numbers are provided alongside funder names.
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 PacBio subreads were analyzed by the icecreamfinder.sh script in BBMap to remove adapter sequences and filter potential chimeric reads. Trimmed PacBio subreads that passed the filter and have a read length of at least 5,000 nt were used as input to the Canu assembler ( Koren et al . 2017 ) with the genomeSize parameter set to 205 m.”
The paper names specific tools and versions (Canu, Flye, etc.) 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 README, data dictionary, or codebook is mentioned; variable definitions are not provided in 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
0.269
From this paper's citation signal
Citation Network Contribution
0.0489
From 4 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 4 citers.
National Institutes of Health
Grant: F32GM140669
NIGMS NIH HHS
Grant: R01 GM130698
National Institutes of Health
Grant: R25GM130517
NSF
Grant: 1915544
Sustaining and Growing a Dispersed Community of Practice that Engages Undergraduates in Course-Based Genomics Research
National Science Foundation
Grant: 2114661
RUI:Drosophila F Element Expansion: A Window on the C-value Paradox.
National Institutes of Health
Grant: 5R01GM130698-02
Genetic Specification and Evolution of 3D Genome Organization
National Institutes of Health
Grant: 5R25GM130517-05
Expanding the Genomics Education Partnership: Regional Mentoring and Training Networks to Diversify Bioinformatics Education and Research
National Institutes of Health
Grant: 1F32GM013039-01
MOLECULAR ANALYSIS OF THE YEAST HEAT SHOCK TRANSCRIPTION
National Institutes of Health
Grant: 1F32GM140669-01A1
3D Genome Organization and Gene Expression in Drosophila
National Institute of General Medical Sciences
FWCI
1.13
Citation Percentile
0.8%
Citation Trend
Fields of Study
MeSH Terms
Keywords
Sustainable Development Goals