PlasAnn: a curated plasmid-specific database and annotation pipeline for standardized gene and function analysis is a dataset published in Nucleic Acids Research (2025). On theSindex it has a DataRank of 0, placing it in the top 100% of the data-sharing corpus. Its calibrated FAIR score is 71/100.
Ranks in the top 100% 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.
“All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
The paper provides a DOI (10.5281/zenodo.17886383) for the dataset, which is a persistent identifier scheme.
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'
“All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
Zenodo is a named data repository.
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
“All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
The dataset identifier (DOI) appears only in the body text of the Data availability section, not as a formal 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 source code for database preparation and annotation pipeline development is open source and available on the lab’s GitHub: https://github.com/ajlopatkin/PlasAnn . The final PlasAnn database and all the other databases used for the pipeline are hosted and readily available on the PlasAnn website: https://plasann.rochester.edu . All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
The statement points to a repository record (Zenodo with a DOI) and a website, both of which are persistent links. [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
“Table 1. Summary of sequences included in the PlasAnn database”
Table 1 provides an itemised inventory of the dataset, listing counts of annotated CDSs, protein clusters, plasmids, etc.
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'
“All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
The Zenodo archive is publicly accessible without any stated precondition or registration requirement.
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
“All source code for database preparation and annotation pipeline development is open source and available on the lab’s GitHub: https://github.com/ajlopatkin/PlasAnn . The final PlasAnn database and all the other databases used for the pipeline are hosted and readily available on the PlasAnn website: https://plasann.rochester.edu . All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
The paper states the data are 'hosted and readily available' and 'open source', but does not apply a standard access-rights label such as 'open access' or 'freely available' to the data in a controlled 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 PlasAnn database is not derived from human subjects and no sensitive data are involved; the paper does not name any 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, persistence commitment, or timeline for data availability. [majority verdict 'no' (4/5 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'
The paper does not specify the file format of the released database (e.g., FASTA, TSV, JSON). [majority verdict 'no' (4/5 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
“GO (Gene Ontology) annotations [45] using Pannzer2 [46], KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology functional descriptions [47] using the KEGG API, and COG (Clusters of Orthologous Groups) classification schemes”— not found in the paper; verdict downgraded
The paper explicitly names community standards (GO, KEGG, COG) that are applied to the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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'
No persistent identifier (DOI, accession, RRID) for an external resource is given in the text; references to databases are by name only. [majority verdict 'no' (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 name any licence or terms document for the database itself; the article's CC BY-NC licence applies to the paper, 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 final curated dataset (Database v4.1.5) comprised 12 256 unique plasmids and 227 714 annotated CDSs.”
The paper explicitly states the version (v4.1.5) of the database. [majority verdict 'yes' (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'
“All code and databases are also archived on Zenodo under DOI 10.5281/zenodo.17886383.”
The paper provides a machine-resolvable locator (Zenodo DOI) and a GitHub URL for the 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)
“National Institutes of Health award #1R35GM150871-01”
The paper states specific grant numbers 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
“DIAMOND [32]”— not found in the paper; verdict downgraded
The Materials and methods section names specific software tools (DIAMOND, BLAST+, Prodigal, etc.) used to produce the database. [downgraded to 'partial' — no verifiable quote from the paper]
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
“Table 1. Summary of sequences included in the PlasAnn database”
The variable-level definitions are provided inside the article via Table 1, not in a separate documentation object shipped 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 →
National Institutes of Health
Grant: 1R35GM150871-01
Determinants underlying horizontal gene transfer-mediated pathogen success
National Science Foundation
Grant: 2440082
CAREER: Programmable microbial community composition and function using plasmid conjugation
NIGMS NIH HHS
Grant: R35 GM150871
Edward Mallinckrodt Jr. Foundation
Pew Charitable Trusts Foundation
Edward Mallinckrodt Jr. Foundation
Pew Charitable Trusts Foundation
FWCI
0.94
Citation Percentile
0.8%
Citation Trend
Fields of Study
MeSH Terms
Keywords