{"doi":"10.1093/nar/gkab804","title":"TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response","abstract":"Syngeneic mouse models are tumors derived from murine cancer cells engrafted on genetically identical mouse strains. They are widely used tools for studying tumor immunity and immunotherapy response in the context of a fully functional murine immune system. Large volumes of syngeneic mouse tumor expression profiles under different immunotherapy treatments have been generated, although a lack of systematic collection and analysis makes data reuse challenging. We present Tumor Immune Syngeneic MOuse (TISMO), a database with an extensive collection of syngeneic mouse model profiles with interactive visualization features. TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types, of which 195 underwent cytokine treatment. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types, of which 832 were from immune checkpoint blockade (ICB) studies. We manually annotated the sample metadata, such as cell line, mouse strain, transplantation site, treatment, and response status, and uniformly processed and quality-controlled the RNA-seq data. Besides data download, TISMO provides interactive web interfaces to investigate whether specific gene expression, pathway enrichment, or immune infiltration level is associated with differential immunotherapy response. TISMO is available at http://tismo.cistrome.org.","journal":"Nucleic Acids Research","year":2021,"id":148148,"datarank":3.1012430225749847,"base_score":4.912654885736052,"endowment":4.912654885736052,"self_citation_contribution":0.736898232860408,"citation_network_contribution":2.364344789714577,"self_endowment_contribution":0.736898232860408,"citer_contribution":2.364344789714577,"corpus_percentile":92.85990562388798,"corpus_rank":924,"citation_count":135,"citer_count":100,"citers_with_citation_signal":91,"citers_with_endowment":91,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9427,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":630369,"name":"Cheryl J. Wong","orcid":"0000-0003-2070-7495","position":1,"is_corresponding":false},{"id":282273,"name":"Lin Yang","orcid":"0000-0003-2372-7547","position":2,"is_corresponding":false},{"id":630370,"name":"Nofal Ouardaoui","orcid":"0000-0002-4517-2493","position":3,"is_corresponding":false},{"id":342304,"name":"Dian Li","orcid":"0000-0002-5374-7314","position":4,"is_corresponding":false},{"id":30772,"name":"Wubing Zhang","orcid":"0000-0003-2233-299X","position":5,"is_corresponding":false},{"id":243340,"name":"Shengqing Gu","orcid":"0000-0002-4200-0864","position":6,"is_corresponding":false},{"id":414222,"name":"Yi Zhang","orcid":"0000-0002-7453-6188","position":7,"is_corresponding":false},{"id":105301,"name":"Yang Liu","orcid":"0000-0002-5221-7725","position":8,"is_corresponding":false},{"id":484534,"name":"Xiaoqing Wang","orcid":"0000-0001-7476-8889","position":9,"is_corresponding":false},{"id":103597,"name":"Jingxin Fu","orcid":"0000-0002-4028-3661","position":10,"is_corresponding":false},{"id":234144,"name":"Liye Zhou","orcid":null,"position":11,"is_corresponding":false},{"id":474907,"name":"Boning Zhang","orcid":"0000-0001-8516-137X","position":12,"is_corresponding":false},{"id":533572,"name":"Sarah Kim","orcid":"0000-0003-2290-6025","position":13,"is_corresponding":false},{"id":36448,"name":"Kathleen B. Yates","orcid":"0000-0002-7383-5573","position":14,"is_corresponding":false},{"id":443,"name":"Myles Brown","orcid":"0000-0002-8213-1658","position":15,"is_corresponding":false},{"id":4539,"name":"Gordon J. Freeman","orcid":"0000-0002-7210-5616","position":16,"is_corresponding":false},{"id":506022,"name":"Ravindra Uppaluri","orcid":"0000-0001-5988-6828","position":17,"is_corresponding":false},{"id":16001,"name":"Robert T. Manguso","orcid":"0000-0003-1336-413X","position":18,"is_corresponding":false},{"id":671,"name":"X. Shirley Liu","orcid":"0000-0003-4736-7339","position":19,"is_corresponding":false},{"id":103598,"name":"Zexian Zeng","orcid":"0000-0002-3905-3244","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-18T23:42:41.063423Z","pmid":"34534350","pmcid":"PMC8728303","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":38.8889,"fair_a":81.25,"fair_i":0.0,"fair_r":33.3333,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":38.89,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"http://tismo.cistrome.org","grounded":true,"rationale":"The paper gives a web URL as the location of the data, which is not a persistent identifier scheme (DOI, Handle, ARK, URN, or repository accession).","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":0.5,"verdict":"partial","evidence":"TISMO is available at http://tismo.cistrome.org","grounded":true,"rationale":"The named holder is 'TISMO', a project-specific database website, not a standard repository listed in re3data or FAIRsharing.","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":"TISMO is available at http://tismo.cistrome.org to all users without restrictions. Annotated mouse syngeneic metadata are available on the website. All expression data and immune infiltration estimation can be downloaded from the data download page.","grounded":true,"rationale":"The statement points to a website URL, not a repository record with an accession or DOI, classifying it as a link to archived data in a non-repository host.","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":0.0,"verdict":"no","evidence":"TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types.","grounded":false,"rationale":"The dataset content is described in running prose, without an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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":0.5,"verdict":"partial","evidence":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","grounded":true,"rationale":"The dataset's identifier (URL) appears only in the body text (Data Availability section), not in the reference list, so it is a body-text occurrence.","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":81.25,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":1.0,"verdict":"yes","evidence":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","grounded":true,"rationale":"The text gives a route to the data with no stated precondition; the data are stated to be publicly available without any required action.","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":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","grounded":true,"rationale":"The paper explicitly states that the data are accessible without restrictions, which is a natural-language equivalent of 'open access'.","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":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","grounded":true,"rationale":"The data are from mouse models and are not human subject or sensitive; no gatekeeper is mentioned, and the data are openly available with no access control.","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":0.5,"verdict":"partial","evidence":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","grounded":true,"rationale":"The paper states that the data are available now but does not specify how long they will persist, so only availability timing is given. [majority verdict 'partial' (3/4 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":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 (open or proprietary) is named for the released data; the paper only mentions 'expression data' and 'immune infiltration estimation' without specifying formats.","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":"No community data or metadata standard is named. [majority verdict 'no' (3/4 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":"Read alignments were performed with STAR (v.2.4.2a) against the mm10 reference genome assembly (mm10, Genome Reference Consortium Mouse Build 38) from the NCI Genomic Data Commons (GDC).","grounded":false,"rationale":"The paper provides an identifier for the reference genome assembly (mm10/GRCm38), a resource the data depend on, which is a qualified reference. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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":33.33,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No licence for the data is stated; the Creative Commons Attribution License applies only to the article, not to the dataset.","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":"Read alignments were performed with STAR (v.2.4.2a) against the mm10 reference genome assembly (mm10, Genome Reference Consortium Mouse Build 38) from the NCI Genomic Data Commons (GDC).","grounded":false,"rationale":"The paper names specific tools and versions (STAR v2.4.2a, mm10 assembly) used to produce the data, providing provenance information. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No documentation object is named as travelling with the data. [majority verdict 'no' (2/4 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":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"Neither a version token nor a date is provided for the dataset; the data are referred to without a snapshot identifier.","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":1.0,"verdict":"yes","evidence":"The source code to search mouse-related studies, download sequencing data, perform batch effect correction and infer immune infiltration were deposited at the Github repository ( https://github.com/zexian/TISMO_data ).","grounded":true,"rationale":"A machine-resolvable locator (GitHub URL) is given for the study's own code, which is an authoritative versioned locator.","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":"National Institutes of Health [R01CA234018, U24CA224316, T15LM007092]","grounded":true,"rationale":"Award numbers are provided for a named funder, satisfying the requirement for specific grant identifiers.","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":"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":"No licence for the data is stated; the Creative Commons Attribution License applies only to the article, not to the dataset.","gain":16.67,"priority":"essential","scored":true},{"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.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"http://tismo.cistrome.org","why":"The paper gives a web URL as the location of the data, which is not a persistent identifier scheme (DOI, Handle, ARK, URN, or repository accession).","gain":8.33,"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.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TISMO is available at http://tismo.cistrome.org","why":"The named holder is 'TISMO', a project-specific database website, not a standard repository listed in re3data or FAIRsharing.","gain":8.33,"priority":"essential","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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No file format (open or proprietary) is named for the released data; the paper only mentions 'expression data' and 'immune infiltration estimation' without specifying formats.","gain":8.33,"priority":"important","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.","anchors":["yes","partial","no"],"verdict":"partial","current":0.5,"evidence":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","why":"The dataset's identifier (URL) appears only in the body text (Data Availability section), not in the reference list, so it is a body-text occurrence.","gain":4.17,"priority":"important","scored":true},{"key":"r_versioning","dimension":"R","label":"Snapshot identified","action":"Version the deposit and cite the exact version analysed (a version-specific DOI, or an accession with its version suffix). A reader reproducing your work against 'the current release' is reproducing it against a different dataset.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"Neither a version token nor a date is provided for the dataset; the data are referred to without a snapshot identifier.","gain":4.17,"priority":"useful","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":"TISMO is available at http://tismo.cistrome.org to all users without restrictions. Annotated mouse syngeneic metadata are available on the website. All expression data and immune infiltration estimation can be downloaded from the data download page.","why":"The statement points to a website URL, not a repository record with an accession or DOI, classifying it as a link to archived data in a non-repository host.","gain":0.0,"priority":"essential","scored":false},{"key":"f_discovery_metadata","dimension":"F","label":"Description of the dataset as an object","action":"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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"TISMO contains 605 in vitro RNA-seq samples from 49 syngeneic cancer cell lines across 23 cancer types. TISMO also includes 1518 in vivo RNA-seq samples from 68 syngeneic mouse tumor models across 19 cancer types.","why":"The dataset content is described in running prose, without an itemised inventory. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No community data or metadata standard is named. [majority verdict 'no' (3/4 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":"Read alignments were performed with STAR (v.2.4.2a) against the mm10 reference genome assembly (mm10, Genome Reference Consortium Mouse Build 38) from the NCI Genomic Data Commons (GDC).","why":"The paper names specific tools and versions (STAR v2.4.2a, mm10 assembly) used to produce the data, providing provenance information. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/4 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":"no","current":0.0,"evidence":null,"why":"No documentation object is named as travelling with the data. [majority verdict 'no' (2/4 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":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","why":"The data are from mouse models and are not human subject or sensitive; no gatekeeper is mentioned, and the data are openly available with no access control.","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":"Read alignments were performed with STAR (v.2.4.2a) against the mm10 reference genome assembly (mm10, Genome Reference Consortium Mouse Build 38) from the NCI Genomic Data Commons (GDC).","why":"The paper provides an identifier for the reference genome assembly (mm10/GRCm38), a resource the data depend on, which is a qualified reference. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (2/4 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":"partial","current":0.5,"evidence":"TISMO is available at http://tismo.cistrome.org to all users without restrictions.","why":"The paper states that the data are available now but does not specify how long they will persist, so only availability timing is given. [majority verdict 'partial' (3/4 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.","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.","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.","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.","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."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-07-20T11:02:00.197687Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}