BioLiP2: an updated structure database for biologically relevant ligand–protein interactions is a dataset published in Nucleic Acids Research (2023). On theSindex it has a DataRank of 3.0, placing it in the top 7.4% of the data-sharing corpus. It has been cited 140 times, with 100 citing works in its 1-hop citation network. Its calibrated FAIR score is 67/100.
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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The database itself is given a web address (https://zhanggroup.org/BioLiP/), not a persistent identifier; the DOI is for the source code, not the dataset. [majority verdict 'partial' (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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The database is hosted on a lab website (zhanggroup.org), not a named data repository. [majority verdict 'partial' (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
“The BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The dataset's identifier (the URL) appears only in the body text, not as a reference-list entry. [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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The data-availability statement points to a lab website and a code repository, not to a repository record with an accession for the database itself. [majority verdict 'partial' (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
“BioLiP2 contains 385 160 protein chains involved in 781 684 protein–ligand interactions, including 35 167 (4%), 36 784 (5%), 127 525 (33%), 174 257 (45%) and 40 7951 (52%) interactions with peptides, DNAs, RNAs, metal ions, and other small molecules (which are referred to as 'regular' ligands by BioLiP2), respectively.”
The dataset's content is described in running prose, not in an itemised inventory (section, table, or enumerated 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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The text gives a route to the data with no stated precondition; the database is stated to be available without any requirement to await, register, or apply. [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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The paper describes the access action of where the data can be obtained but does not label the access level with an explicit term from the controlled vocabulary. [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 or human-subject, so 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 paper does not state how long the data will remain available, nor does it make a persistence commitment. [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 is named for the released data. [majority verdict 'no' (3/5 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 ligand binding information is further enriched with other function annotations, including Enzyme Commission numbers, Gene Ontology terms, catalytic sites, and binding affinities collected from other databases and a manual literature survey.”
The paper names community standards (GO terms, EC numbers) that are 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'
“BioLiP2 contains 3385 protein–ligand interactions from 812 protein chains extracted from mmCIF file of the phycobilisome structure (PDB 5y6p, https://zhanggroup.org/BioLiP/qsearch.cgi?&page=last&order=pdbid&pdbid=5y6p )”— not found in the paper; verdict downgraded
The paper provides identifiers (e.g., PDB ID 5y6p) for external resources used or referenced. [downgraded to 'no' — no verifiable quote from the paper] [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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
The BSD license is an open standard license named for the data. [majority verdict 'yes' (4/5 passes agreed)]
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 given to identify a specific snapshot of the database. [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 BioLiP2 database and source code are available at https://zhanggroup.org/BioLiP/ and https://github.com/kad-ecoli/mmCIF2BioLiP (permanent doi: https://doi.org/10.6084/m9.figshare.23641701 ) under the BSD license.”
A machine-resolvable locator (GitHub URL and figshare DOI) is given 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 of General Medical Sciences [GM136422 and S10OD026825 to Y.Z.]; National Institute of Allergy and Infectious Diseases [AI134678 to L.F. and Y.Z.]; National Science Foundation [IIS1901191 and DBI2030790 to Y.Z. and MTM2025426 to L.F. and Y.Z.].”
Award numbers are attached to named funders. [majority verdict 'yes' (4/5 passes agreed)]
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
“In the first step, the mmCIF files of all protein-containing structures are downloaded from the PDB database and split into chains by a modified version of the BeEM tool (43).”— not found in the paper; verdict downgraded
The paper names specific tools (BeEM, Foldseek, US-align, etc.) used to produce the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (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
“The 'BROWSE' interface displays the PDB ID and chain ID, resolution, ligand, EC number, GO terms, UniProt accessions, PubMed citations and binding affinities, either for all protein–ligand interactions or for the subset of interactions with regular ligands, metal ions, RNAs, DNAs, and peptides (Figure 3A).”— not found in the paper; verdict downgraded
Variable-level definitions are described inside the article, but no documentation object is said to accompany the data. [downgraded to 'no' — no verifiable quote from the paper] [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
0.742
From this paper's citation signal
Citation Network Contribution
2.2
From 92 citing papers with measurable signal
Ranked by each citer's contribution to N(p) — log1p(Cq) divided by its reference count — out of 100 citers.
National Institute of General Medical Sciences
Grant: GM136422
National Institute of General Medical Sciences
Grant: S10OD026825
National Institute of Allergy and Infectious Diseases
Grant: AI134678
National Science Foundation
Grant: IIS1901191
National Science Foundation
Grant: DBI2030790
National Science Foundation
Grant: MTM2025426
National Institutes of Health
Grant: 1S10OD026825-01A1
High-Performance Computing Cluster for Biomedical Research
National Science Foundation
Grant: 2138307
Track 3: COre National Ecosystem for CyberinfrasTructure (CONECT)
National Science Foundation
Grant: 1901191
III: Medium: Collaborative Research: Multi-level computational approaches to protein function prediction
National Science Foundation
Grant: 2138286
Track 2: Customized Multi-tier Assistance, Training, and Computational Help (MATCH) for End User ACCESS to CI
National Institutes of Health
Grant: 5R35GM136422-02
Advanced approaches to protein structure prediction
National Science Foundation
Grant: 2138296
ACO: An Open CI Ecosystem to Advance Scientific Discovery (OpenCI)
National Science Foundation
Grant: 2137603
Track 4: Advanced CI Coordination Ecosystem: Monitoring and Measurement Services
National Science Foundation
Grant: 2025426
MTM 2: Combining structural informatics and crosslinking mass spectrometry to predict the key protein-protein interactions shaping symbiotic microbial communities
National Science Foundation
Grant: 2030790
IIBR: Informatics: RAPID: Genome-wide Structure and Function Modeling of the SARS-CoV-2 Virus
National Institutes of Health
Grant: 5R01AI134678-03
Structure-based functional annotation of microbial genomes
National Science Foundation
Grant: 2138259
Track 1: ACCESS Resource Allocations Marketplace and Platform Services (RAMPS)
NIAID NIH HHS
Grant: R01 AI134678
FWCI
20.26
Citation Percentile
1.0%
Influential Citations
6
Citation Trend
Fields of Study
MeSH Terms
Keywords