Original repositories, software and standards, with guidance on what to look for before using them.
36 resources
Curated yeast genes, pathways, literature and analysis tools.
Before use: Begin with a gene symbol or identifier. Record the reference assembly and distinguish experimentally supported annotations from predictions.
Open providerNIST provides genome benchmarks and materials for evaluating sequencing accuracy.
Before use: Choose a benchmark appropriate to the variant type and difficult regions. Performance inside a benchmark’s scope does not prove accuracy everywhere.
Open providerNDSA Levels of Digital Preservation offers a staged framework; version 2.1 includes sustainability.
Before use: Use the matrix to identify work, responsibility and evidence of completion. A self-assigned level is not an independent audit.
Open providerLibrary of Congress 2025–2026 format recommendations address long-term access.
Before use: Choose by media type and requirements. A preferred format still needs metadata, backups and future review.
Open providerBagIt specifies collection packaging and manifests for transfer and integrity checks.
Before use: A valid bag helps verify transport and integrity. It does not encrypt the contents, prove authorship or guarantee continued custody.
Open providerLibrary of Congress documents file formats and preservation characteristics.
Before use: Compare documentation, adoption, dependencies and access constraints. Format selection should be revisited as the ecosystem changes.
Open providerFAIR principles address findable, accessible, interoperable and reusable research data.
Before use: Accessible does not necessarily mean public. A controlled-access resource can still provide clear metadata and a defined request process.
Open providerUSPTO provides federal trademark search tools and guidance.
Before use: Search variants and relevant goods or services, then record the search date. Absence of an exact match is not assurance of availability.
Open providerNCBI SRA provides sequencing-study records and raw data.
Before use: Start with an accession from a paper. Confirm organism, assay, access conditions and download size before analysis.
Open providerdbGaP links genotype and phenotype studies with controlled-access research data.
Before use: A visible study page does not imply unrestricted access to individual-level data. Follow the authorized access process.
Open providerEMBL-EBI introduces the European Nucleotide Archive's sequence holdings.
Before use: Use study, sample and run identifiers to trace relationships. A publication title alone may not identify the exact dataset.
Open providerGA4GH refget supports unambiguous reference-sequence identifiers and retrieval.
Before use: Record the identifier scheme and implementation version. A consistent reference identifier does not verify a sample’s identity.
Open providerENA documents programmatic sequence-record retrieval.
Before use: Begin with a known accession and read rate and format guidance. Store the query and retrieval date with the result.
Open providerGA4GH catalogs genomic data, security and interoperability standards.
Before use: Choose by the problem to solve, such as identity, access or workflow exchange. A catalog entry is not a deployed system.
Open providerGA4GH Starter Kit demonstrates genomic data-service implementations.
Before use: Treat examples as development aids. Production use needs configuration, security review and the relevant specification versions.
Open providerNCBI BLAST compares biological sequences with reference databases.
Before use: Similarity supports a comparison, not proof of identity or function. Database choice, alignment coverage and statistical significance matter.
Open providerGalaxy supports web-based, reproducible biomedical analyses.
Before use: Record the workflow, tool versions and inputs. Re-running a workflow does not repair an inappropriate analysis design.
Open providerBioStudies links data and supporting materials for biological studies.
Before use: Find the study accession and inspect its file list, licenses and associated publication. The collection may contain several data types.
Open providerNCBI Datasets packages genomes, annotations and metadata.
Before use: Specify the assembly accession and version. A species name alone can select a different reference from the one used in a paper.
Open providerEnsembl supplies genome annotation and comparative-genomics resources.
Before use: Check the species, assembly and release. An annotation is an interpretation layered on sequence and may change between releases.
Open providerUCSC supports genome visualization, track queries and coordinate conversion.
Before use: Tracks must use compatible coordinates. A visually plausible overlap is not by itself evidence of a causal relationship.
Open providerMetaboLights holds metabolomics studies, raw measurements and metadata.
Before use: Inspect sample preparation context, instrument information and processing. Metabolite identifiers and abundance estimates need careful interpretation.
Open providerPRIDE archives mass-spectrometry evidence for proteins and peptides.
Before use: Start with the dataset accession and distinguish raw measurements from processed identifications. Processing choices affect interpretation.
Open providerPRIDE documents project, file and metadata queries.
Before use: Save accession numbers and query parameters. Check documentation before depending on a route in a production workflow.
Open providerQIIME 2 provides reproducible microbiome and multi-omics analysis.
Before use: Choose methods appropriate to the assay and experimental design. A pipeline cannot compensate for missing controls or biased sampling.
Open providerBioconductor supplies open-source biological data-analysis tools.
Before use: Check package and release versions, vignettes and assumptions. Different packages can answer different questions from the same data.
Open providerEurope PMC documents publication and preprint search.
Before use: Save the exact query and date, then deduplicate and screen results. A returned abstract is not a completed quality appraisal.
Open providerCrossref exposes bibliographic metadata, identifiers and publication updates.
Before use: Match the title and authors before accepting a DOI. Deposit completeness varies; a missing field should remain unknown rather than be invented.
Open providerOpenAlex supports discovery across works, authors, institutions and topics.
Before use: Treat graph links as discovery aids. Verify decisive claims and identities against original records, and check current access conditions.
Open providerStandards help researchers characterize and report stem-cell-derived model systems.
Before use: A useful model description names what the tissue reproduces and what it does not. Use documented criteria before presenting a model as brain-like.
Open providerExplore linked structural and functional measurements from mouse cortex.
Before use: Begin with the tutorial and a small query. Record the release rather than downloading a huge dataset without a research question.
Open providerSearch and explore neurons, annotations and connections in fly connectome datasets.
Before use: Start with a neuron or annotated type, then compare inputs and outputs. The map is an observation platform, not an uploaded mind.
Open providerBrowse measurements of human and mouse neurons, including morphology and electrical responses.
Before use: Compare like species, tissue sources and assays. Cell-level differences can inform models without defining an entire brain.
Open providerDiscover shared neurophysiology datasets, their versions and associated metadata.
Before use: Choose a dataset by modality and experimental question. Read its license and documentation, and cite the specific version used.
Open providerA shared format organizes neurophysiology measurements and their context.
Before use: A common format supports reuse, but compatible files may still describe incompatible experiments. Keep the experimental context.
Open providerHeritability describes genetic contributions to variation within a population under particular conditions.
Before use: Do not use a heritability percentage to claim that a genome archive preserves that percentage of a person.
Open provider