{"doi":"10.1093/nar/gkaf1209","title":"JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models","abstract":"JASPAR (https://jaspar.elixir.no/) is an open-access database that has provided high-quality, manually curated, and non-redundant DNA binding profiles for transcription factors (TFs) as position frequency matrices (PFMs) for over 20 years. We expanded the CORE (306 new profiles, 12% increase) and UNVALIDATED (433, 60% increase) collections with new PFMs and updated 13 existing profiles. We updated the TF binding site predictions and genome tracks for eight species. TF binding profile clusters and familial TF binding sites were updated accordingly. We integrate the inMOTIFin software to easily simulate regulatory sequences using JASPAR PFMs. To enrich TFs' annotations, we provide scientific literature-based human TF target information. Notably, this release features a deep learning (DL) collection, providing a paradigm shift in modeling and characterizing TF-DNA interactions with 1259 BPNet models trained on Homo sapiens ENCODE chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets from 240 TFs and interpreted to reveal predictive motif patterns for the models. The motifs associated with the same TF were clustered to provide a summary of the binding properties, resulting in 240 primary and 113 alternative motif patterns in the DL collection. The JASPAR 2026 collections lay a foundation for future endeavors in genomic research, serving the scientific community in uncovering the mechanisms of gene regulation.","journal":"Nucleic Acids Research","year":2025,"id":508987,"datarank":0.6924059024494715,"base_score":4.04305126783455,"endowment":4.04305126783455,"self_citation_contribution":0.6064576901751826,"citation_network_contribution":0.08594821227428893,"self_endowment_contribution":0.6064576901751826,"citer_contribution":0.08594821227428893,"corpus_percentile":71.09151388566566,"corpus_rank":3738,"citation_count":56,"citer_count":55,"citers_with_citation_signal":5,"citers_with_endowment":5,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.951,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":20.8333,"fair_percentile":36.38031183124427,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1361560,"name":"Ieva Rauluševičiūtė","orcid":"0000-0001-9253-8825","position":1,"is_corresponding":false},{"id":1361561,"name":"Dina Ruud Aronsen","orcid":"0009-0001-1293-7293","position":2,"is_corresponding":false},{"id":1361562,"name":"Romain Blanc‐Mathieu","orcid":"0000-0002-9485-6330","position":3,"is_corresponding":false},{"id":1361563,"name":"Ine Bonthuis","orcid":"0009-0000-2048-4821","position":4,"is_corresponding":false},{"id":1361564,"name":"Herman De Beukelaer","orcid":"0000-0002-3968-7386","position":5,"is_corresponding":false},{"id":1361565,"name":"Katalin Ferenc","orcid":"0000-0002-3006-4297","position":6,"is_corresponding":false},{"id":1361566,"name":"Alice Jegou","orcid":"0009-0002-1713-8412","position":7,"is_corresponding":false},{"id":439959,"name":"Vipin Kumar","orcid":"0000-0003-2533-9089","position":8,"is_corresponding":false},{"id":1361567,"name":"Roza Berhanu Lemma","orcid":"0000-0003-1069-8011","position":9,"is_corresponding":false},{"id":1361568,"name":"Jérémy Lucas","orcid":"0000-0002-2252-4732","position":10,"is_corresponding":false},{"id":1361569,"name":"Mathis Pochon","orcid":"0009-0004-4088-3319","position":11,"is_corresponding":false},{"id":1361570,"name":"Chang Min Yun","orcid":"0000-0003-3793-8265","position":12,"is_corresponding":false},{"id":557264,"name":"Vivekanandan Ramalingam","orcid":"0000-0002-3631-8913","position":13,"is_corresponding":false},{"id":1173422,"name":"Salil Deshpande","orcid":"0009-0009-5776-8428","position":14,"is_corresponding":false},{"id":983412,"name":"Aman Patel","orcid":"0000-0003-2113-3251","position":15,"is_corresponding":false},{"id":11727,"name":"Georgi K. Marinov","orcid":"0000-0003-1822-7273","position":16,"is_corresponding":false},{"id":404866,"name":"Austin T. Wang","orcid":"0000-0001-6096-9444","position":17,"is_corresponding":false},{"id":1170625,"name":"Alejandro Aguirre","orcid":"0000-0002-3390-8301","position":18,"is_corresponding":false},{"id":1361571,"name":"Jaime A. Castro-Mondragón","orcid":"0000-0003-4069-357X","position":19,"is_corresponding":false},{"id":1361572,"name":"Damir Baranas̆ić","orcid":"0000-0001-5948-0932","position":20,"is_corresponding":false},{"id":1361573,"name":"Jeanne Chèneby","orcid":"0000-0003-4553-3110","position":21,"is_corresponding":false},{"id":49326,"name":"Sveinung Gundersen","orcid":"0000-0001-9888-7954","position":22,"is_corresponding":false},{"id":113951,"name":"Morten Johansen","orcid":null,"position":23,"is_corresponding":false},{"id":816892,"name":"Aziz Khan","orcid":"0000-0002-6459-6224","position":24,"is_corresponding":false},{"id":226260,"name":"Marieke L. Kuijjer","orcid":"0000-0001-6280-3130","position":25,"is_corresponding":false},{"id":12355,"name":"Eivind Hovig","orcid":"0000-0002-9103-1077","position":26,"is_corresponding":false},{"id":11666,"name":"Boris Lenhard","orcid":"0000-0002-1114-1509","position":27,"is_corresponding":false},{"id":19907,"name":"Albin Sandelin","orcid":"0000-0002-7109-7378","position":28,"is_corresponding":false},{"id":850002,"name":"Klaas Vandepoele","orcid":"0000-0003-4790-2725","position":29,"is_corresponding":false},{"id":77770,"name":"Wyeth W. Wasserman","orcid":"0000-0001-6098-6412","position":30,"is_corresponding":false},{"id":1361574,"name":"François Parcy","orcid":"0000-0003-2191-500X","position":31,"is_corresponding":false},{"id":360,"name":"Anshul Kundaje","orcid":"0000-0003-3084-2287","position":32,"is_corresponding":false},{"id":77698,"name":"Anthony Mathelier","orcid":"0000-0001-5127-5459","position":33,"is_corresponding":false},{"id":792248,"name":"Damla Ovek","orcid":"0000-0001-5300-8098","position":0,"is_corresponding":true}],"reference_count":38,"raw_metadata":null,"created_at":"2026-07-19T02:47:00.188082Z","pmid":"41325984","pmcid":"PMC12807658","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":33.3333,"fair_a":50.0,"fair_i":0.0,"fair_r":41.6667,"fair_zscore":-0.5389,"fair_rationale":{"fair_score":20.83,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":33.33,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"https://jaspar.elixir.no/","grounded":false,"rationale":"The paper gives a web address for the data, not a PID-scheme string. [downgraded to 'no' — no verifiable quote from the paper]","anchors":["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'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","grounded":false,"rationale":"The paper names JASPAR as the database, which is a project website and not a repository in the curated list (e.g., GEO, Zenodo). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","anchors":["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"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","grounded":false,"rationale":"The statement points to the repository URL. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"f_discovery_metadata","label":"Description of the dataset as an object","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"Table 1. Summary of the JASPAR 2026 CORE collection update compared to the previous release","grounded":true,"rationale":"Table 1 provides an itemised inventory of the dataset. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["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'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","grounded":false,"rationale":"The dataset identifier appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","anchors":["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'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","grounded":false,"rationale":"The text states the data are openly accessible with no precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["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'"],"scored":true,"signal":null},{"key":"a_access_conditions_stated","label":"Access level labelled","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"JASPAR is an open-access database","grounded":true,"rationale":"The paper explicitly labels the data as 'open-access', which is a standard access-level label.","anchors":["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"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are not sensitive human-subject data, and no gatekeeper is named.","anchors":["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"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No sentence addresses the persistence or retention timeline of the data.","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":0.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No file format token is named for the released data. [majority verdict 'no' (3/5 passes agreed)]","anchors":["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"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not name any community-standard vocabulary or checklist from FAIRsharing or other registries. [majority verdict 'no' (3/5 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":"https://doi.org/10.5281/zenodo.4485856","grounded":false,"rationale":"The paper provides a DOI for the pyJASPAR package, which is a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The CC BY license is for the article, not the data; no license for the data is stated.","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 trained a specific BPNet [25] model for each ChIP-seq dataset","grounded":false,"rationale":"The paper names the specific software (BPNet) used to produce the deep learning models. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"Table 1. Summary of the JASPAR 2026 CORE collection update","grounded":true,"rationale":"Documentation of the data's contents is provided inside the article (tables and text), not as a separate file shipped with the data. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["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"],"scored":false,"signal":null},{"key":"r_versioning","label":"Snapshot identified","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"the current JASPAR 2026 release provides a total of 2633 and 1231 non-redundant TF DNA-binding profiles","grounded":true,"rationale":"JASPAR 2026 is a version token for the data. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["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'"],"scored":true,"signal":null},{"key":"x_code_availability","label":"Analysis code available","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"https://github.com/asntech/pyjaspar ; https://doi.org/10.5281/zenodo.4485856","grounded":false,"rationale":"The paper provides a machine-resolvable locator (URL and DOI) for the study's code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","anchors":["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)"],"scored":true,"signal":null},{"key":"x_funding_attribution","label":"Funder and award number","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"Research Council of Norway [187615]","grounded":true,"rationale":"The paper includes an award number attached to a named funder. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["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"],"scored":true,"signal":null}]}},"actions":[{"key":"f_dataset_pid","dimension":"F","label":"Persistent identifier for the data","action":"Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"https://jaspar.elixir.no/","why":"The paper gives a web address for the data, not a PID-scheme string. [downgraded to 'no' — no verifiable quote from the paper]","gain":16.67,"priority":"essential","scored":true},{"key":"f_repository_named","dimension":"F","label":"Named repository","action":"Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","why":"The paper names JASPAR as the database, which is a project website and not a repository in the curated list (e.g., GEO, Zenodo). [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/5 passes agreed)]","gain":16.67,"priority":"essential","scored":true},{"key":"r_reuse_license","dimension":"R","label":"Reuse licence","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The CC BY license is for the article, not the data; no license for the data is stated.","gain":16.67,"priority":"essential","scored":true},{"key":"a_data_openly_accessible","dimension":"A","label":"Access route free of preconditions","action":"Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","why":"The text states the data are openly accessible with no precondition. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":8.33,"priority":"essential","scored":true},{"key":"f_dataset_cited","dimension":"F","label":"Dataset formally cited","action":"Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) in the reference list.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","why":"The dataset identifier appears only in the body text, not as a reference-list entry. [downgraded to 'no' — no verifiable quote from the paper]","gain":8.33,"priority":"important","scored":true},{"key":"i_open_nonproprietary_format","dimension":"I","label":"Open file format","action":"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 chemistry / materials formats such as CIF or MOL.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format token is named for the released data. [majority verdict 'no' (3/5 passes agreed)]","gain":8.33,"priority":"important","scored":true},{"key":"x_code_availability","dimension":"R","label":"Analysis code available","action":"Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI).","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"https://github.com/asntech/pyjaspar ; https://doi.org/10.5281/zenodo.4485856","why":"The paper provides a machine-resolvable locator (URL and DOI) for the study's code. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":4.17,"priority":"important","scored":true},{"key":"f_data_availability_statement","dimension":"F","label":"Data-availability statement","action":"Replace the statement with the repository template: name the repository and give the accession or DOI (Colavizza category 3). This is the only DAS class associated with a measured citation advantage; 'available on reasonable request' and 'within the article' are not.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"JASPAR is an open-access database available at https://jaspar.elixir.no/","why":"The statement points to the repository URL. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","gain":0.0,"priority":"essential","scored":false},{"key":"i_community_standard_vocabulary","dimension":"I","label":"Community standard / vocabulary","action":"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 chemistry / materials, describe the data with InChI, CIF or SMILES.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The paper does not name any community-standard vocabulary or checklist from FAIRsharing or other registries. [majority verdict 'no' (3/5 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 trained a specific BPNet [25] model for each ChIP-seq dataset","why":"The paper names the specific software (BPNet) used to produce the deep learning models. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (4/5 passes agreed)]","gain":0.0,"priority":"important","scored":false},{"key":"r_documentation_codebook","dimension":"R","label":"Documentation / codebook","action":"Ship a README and a data dictionary IN the deposit — every file, every variable, its units, its allowed values, its missing-value codes. It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"Table 1. Summary of the JASPAR 2026 CORE collection update","why":"Documentation of the data's contents is provided inside the article (tables and text), not as a separate file shipped with the data. [majority verdict 'partial' (3/5 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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive human-subject data, and no gatekeeper is named.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). 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":"https://doi.org/10.5281/zenodo.4485856","why":"The paper provides a DOI for the pyJASPAR package, which is a resource other than the study's own dataset. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (3/5 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":"No sentence addresses the persistence or retention timeline of the data.","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","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.","Remove the precondition or justify it. Release the data at publication with no embargo, no registration wall, and no approval step — NIH's zero-embargo public- access rule (NOT-OD-25-101) has already made 'available at publication' the federal baseline for the article; the data should not lag behind it. For chemistry / materials data, deposit in Zenodo, PubChem or the Cambridge Structural Database (CSD).","Cite the dataset in the reference list like a publication — creator, year, title, repository, DOI/accession — and cite it in-text where it is used. Only a reference- list entry is machine-readable to Crossref/DataCite, and only a citation lets the data earn credit. Cite the chemistry / materials repository accession (e.g. from Zenodo, PubChem or the Cambridge Structural Database (CSD)) in the reference list."],"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":"2026-07-20T11:17:45.835231Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}