{"doi":"10.1038/s41597-024-03031-7","title":"The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes","abstract":"More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.","journal":"Scientific Data","year":2024,"id":483851,"datarank":3.7193369287913587,"base_score":5.8944028342648505,"endowment":5.8944028342648505,"self_citation_contribution":0.8841604251397277,"citation_network_contribution":2.8351765036516308,"self_endowment_contribution":0.8841604251397277,"citer_contribution":2.8351765036516308,"corpus_percentile":93.9738531755241,"corpus_rank":780,"citation_count":362,"citer_count":100,"citers_with_citation_signal":100,"citers_with_endowment":100,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":79.1667,"fair_percentile":97.67655151329869,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":621217,"name":"Adam Micco","orcid":"0000-0001-6016-964X","position":1,"is_corresponding":false},{"id":255453,"name":"Matthew Mah","orcid":"0000-0001-8987-6436","position":2,"is_corresponding":false},{"id":551930,"name":"Harald Ringbauer","orcid":"0000-0002-4884-9682","position":3,"is_corresponding":false},{"id":69375,"name":"Iosif Lazaridis","orcid":"0000-0002-4094-9347","position":4,"is_corresponding":false},{"id":255447,"name":"Íñigo Olalde","orcid":"0000-0002-2660-6807","position":5,"is_corresponding":false},{"id":255477,"name":"Nick Patterson","orcid":"0000-0003-0302-684X","position":6,"is_corresponding":false},{"id":724,"name":"David Reich","orcid":"0000-0002-7037-5292","position":7,"is_corresponding":false},{"id":708,"name":"Swapan Mallick","orcid":"0000-0002-4531-4439","position":0,"is_corresponding":true}],"reference_count":261,"raw_metadata":null,"created_at":"2026-07-19T02:07:33.718973Z","pmid":"38341426","pmcid":"PMC10858950","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":88.8889,"fair_a":62.5,"fair_i":20.0,"fair_r":58.3333,"fair_zscore":1.77,"fair_rationale":{"fair_score":79.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":88.89,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"29. Mallick, S. & Reich, D. The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes. Harvard Dataverse, https://doi.org/10.7910/DVN/FFIDCW (2023).","grounded":true,"rationale":"The dataset's DOI is given in the reference list entry. 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[majority verdict 'no' (4/5 passes agreed)]","anchors":["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'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":20.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"EIGENSTRAT format ( .ind,.snp, and.geno)","grounded":true,"rationale":"The released data are in EIGENSTRAT format, which is not among the listed open/community-standard formats (e.g., CSV, FASTA, BAM) and is considered a proprietary format. 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[majority verdict 'no' (4/5 passes agreed)]","anchors":["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'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide a persistent identifier (DOI, accession, RRID) for any external resource that the data depend on; it only mentions names like 'European Nucleotide Archive' without identifiers. [majority verdict 'no' (4/5 passes agreed)]","anchors":["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'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":58.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not state a license for the data; the CC BY 4.0 license applies to the article, not the data.","anchors":["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'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"We create a bam file aligned to the hg19 genome reference sequence.","grounded":true,"rationale":"The paper describes the data production process in generic terms without naming specific instruments, software versions, or kits. 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Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Data Record","why":"The paper has a dedicated 'Data Record' section that itemises the dataset's files and variables in a bulleted list, constituting an itemised inventory. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"a_access_conditions_stated","dimension":"A","label":"Access level labelled","action":"State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. 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In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name a community-standard vocabulary or ontology; it mentions only format and methods. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_provenance_methods","dimension":"R","label":"Provenance of the data","action":"Name the instruments, kits, and software — with versions — that produced the data, not just the verbs. 'Reads were aligned' is not provenance; 'aligned with STAR v2.7.9a to GRCh38' is, because someone else can rerun it.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"We create a bam file aligned to the hg19 genome reference sequence.","why":"The paper describes the data production process in generic terms without naming specific instruments, software versions, or kits. [majority verdict 'partial' (2/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data. 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A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not provide a persistent identifier (DOI, accession, RRID) for any external resource that the data depend on; it only mentions names like 'European Nucleotide Archive' without identifiers. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not state any retention period or persistence commitment for the data. [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open genomics / sequencing formats such as FASTQ, BAM or VCF.","Add a 'Data Records' section: itemise every file in the deposit and every variable or sample it holds, with counts and units. Describe the dataset as an object in its own right, not as a by-product of the findings — this is what makes it discoverable to someone who is not looking for your paper.","State the access level in words, using the standard vocabulary: 'These data are open access' / 'These data are controlled access'. A reader — and a harvester — should not have to infer the access level from the presence of a download link.","Adopt and NAME your domain's data standard — the minimum-information checklist, metadata schema, or ontology your community uses (MIAME/MINSEQE, ISA-Tab, BIDS, an OBO ontology, HL7 FHIR/OMOP) — and say which one you followed. A reporting checklist standardises your paper; it does nothing for your data. In genomics / sequencing, describe the data with MIAME, MINSEQE or MIxS."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T10:50:38.367757Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}