Reference health
Sharing biological data: why, when, and how
108/108 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
12 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 108 checked references that resolve
resolves10.1038/sdata.2016.18
The FAIR Guiding Principles for scientific data management and stewardship
resolves10.1093/nar/gkz997
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species
resolves10.1371/journal.pbio.2001414
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data
resolves10.7717/peerj.148
On the reproducibility of science: unique identification of research resources in the biomedical literature
resolves10.1038/s41586-020-2493-4
Expanded encyclopaedias of DNA elements in the human and mouse genomes
resolves10.1371/journal.pone.0000308
Sharing Detailed Research Data Is Associated with Increased Citation Rate
resolves10.7717/peerj-cs.1
Achieving human and machine accessibility of cited data in scholarly publications
resolves10.56759/rgxl7405
International Ethical Guidelines for Health-related Research involving Humans
resolves10.1186/s13073-017-0476-3
Creating a data resource: what will it take to build a medical information commons?
resolves10.1038/s41576-020-0257-5
Responsible, practical genomic data sharing that accelerates research
resolves10.1038/ng1201-365
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data
resolves10.1100/tsw.2009.57
Minimum Information About a Microarray Experiment (MIAME) – Successes, Failures, Challenges
resolves10.1186/2041-1480-5-21
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon
resolves10.1371/journal.pone.0213090
An analysis and metric of reusable data licensing practices for biomedical resources
resolves10.1186/1471-2105-5-80
Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics
resolves10.1093/nar/gkp1137
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
resolves10.1101/gr.114819.110
Efficient storage of high throughput DNA sequencing data using reference-based compression
resolves10.1016/j.cell.2008.03.029
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
resolves10.1038/nature07002
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution
resolves10.1038/nmeth.2688
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
resolves10.1093/bioinformatics/btq033
BEDTools: a flexible suite of utilities for comparing genomic features
resolves10.12688/f1000research.2-264.v1
illuminaio: An open source IDAT parsing tool for Illumina microarrays
resolves10.1101/gr.213611.116
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
resolves10.1038/ng.3312
The European Genome-phenome Archive of human data consented for biomedical research
resolves10.1074/mcp.O113.036681
The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience
resolves10.1021/acs.jproteome.0c00376
Toward a Sample Metadata Standard in Public Proteomics Repositories
resolves10.1093/nar/gky1106
The PRIDE database and related tools and resources in 2019: improving support for quantification data
resolves10.1002/pmic.201100515
<scp>PASSEL</scp>: The <scp>P</scp>eptide<scp>A</scp>tlas <scp>SRM</scp>experiment library
resolves10.1074/mcp.RA117.000543
Panorama Public: A Public Repository for Quantitative Data Sets Processed in Skyline
resolves10.1111/jmi.12178
Pipeline for illumination correction of images for high‐throughput microscopy
resolves10.1038/ncomms14836
A BaSiC tool for background and shading correction of optical microscopy images
resolves10.1038/nmeth.2075
Icy: an open bioimage informatics platform for extended reproducible research
resolves10.1093/bioinformatics/btq046
EBImage—an R package for image processing with applications to cellular phenotypes
resolves10.1186/gb-2005-6-5-r47
The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging
resolves10.1186/s13326-019-0206-4
Ontology patterns for the representation of quality changes of cells in time
resolves10.1091/mbc.E17-05-0276
A beginner’s guide to rigor and reproducibility in fluorescence imaging experiments
resolves10.1093/bioinformatics/btu210
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents
resolves10.1093/bioinformatics/btw417
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena
resolves10.1016/S0006-3495(97)78689-2
Energy filtered electron tomography of ice-embedded actin and vesicles
resolves10.1016/S0006-3495(95)80314-0
Three-dimensional structure of lipid vesicles embedded in vitreous ice and investigated by automated electron tomography
resolves10.1063/1.5128672
The Integrated Resource for Reproducibility in Macromolecular Crystallography: Experiences of the first four years
resolves10.1007/s10858-005-2195-0
BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures
resolves10.1038/s42003-019-0437-z
SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM
resolves10.1038/s41467-020-18952-1
Topaz-Denoise: general deep denoising models for cryoEM and cryoET
resolves10.1126/science.1181369
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
resolves10.1073/pnas.89.5.1827
A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
resolves10.1093/bioinformatics/btq054
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
The 12 references without a DOI — listed, not checked
no DOI — not checkedHaendelM SuA McMurryJ ChuteCG MungallC GoodB WuC McWeeneyS HochheiserH RobinsonPet al.FAIR‐TLC: Metrics to Assess Value of Biomedical Digital Repositories: Response to RFI NOT‐OD‐16‐133.https://doi.org/10.5281/zenodo.203295
no DOI — not checkedUnreliable research: trouble at the lab
no DOI — not checkedNational Institutes of Health(2020)Final NIH Policy for Data Management and Sharing. NIH Guide to Grants and Contracts NOT‐OD‐21–013.https://grants.nih.gov/grants/guide/notice‐files/NOT‐OD‐21‐013.html
no DOI — not checkedNational Institutes of Health(2020)Supplemental information to the NIH Policy for Data Management and Sharing: selecting a repository for data resulting from NIH‐supported research. NIH Guide to Grants and Contracts NOT‐OD‐21–016.https://grants.nih.gov/grants/guide/notice‐files/NOT‐OD‐21‐016.html
no DOI — not checkedThe role of metadata in reproducible computational research
no DOI — not checkedResearch Rules & Policies
no DOI — not checkedGenomic Data Sharing
no DOI — not checkedISO/IEC 29500‐1:2016: Information Technology — Document Description and Processing Languages — Office Open XML File Formats — Part 1: Fundamentals and Markup Language Reference
no DOI — not checkedThe ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics
no DOI — not checkedA real‐time compression library for microscopy images
no DOI — not checkedImage‐based profiling for drug discovery: due for a machine‐learning upgrade?
no DOI — not checkedMinimum Information guidelines for fluorescence microscopy: increasing the value, quality, and fidelity of image data
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work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
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