{"doi":"10.1038/s41467-017-01316-7","title":"The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA","abstract":"Frogs play important ecological roles, and several species are important model organisms for scientific research. The globally distributed Ranidae (true frogs) are the largest frog family, and have substantial evolutionary distance from the model laboratory Xenopus frog species. Unfortunately, there are currently no genomic resources for the former, important group of amphibians. More widely applicable amphibian genomic data is urgently needed as more than two-thirds of known species are currently threatened or are undergoing population declines. We report a 5.8 Gbp (NG50 = 69 kbp) genome assembly of a representative North American bullfrog (Rana [Lithobates] catesbeiana). The genome contains over 22,000 predicted protein-coding genes and 6,223 candidate long noncoding RNAs (lncRNAs). RNA-Seq experiments show thyroid hormone causes widespread transcriptional change among protein-coding and putative lncRNA genes. This initial bullfrog draft genome will serve as a key resource with broad utility including amphibian research, developmental biology, and environmental research.","journal":"Nature Communications","year":2017,"id":1629,"datarank":3.236018173772418,"base_score":4.762173934797756,"endowment":4.762173934797756,"self_citation_contribution":0.7143260902196635,"citation_network_contribution":2.5216920835527543,"self_endowment_contribution":0.7143260902196635,"citer_contribution":2.5216920835527543,"corpus_percentile":68.34825061025224,"corpus_rank":390,"citation_count":119,"citer_count":96,"citers_with_citation_signal":75,"citers_with_endowment":75,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7544,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2017-11-10","fair_score":50.8333,"fair_percentile":78.6499560246262,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":18717,"name":"René L. 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Austin Hammond","orcid":"0000-0003-3082-760X","position":0,"is_corresponding":true}],"reference_count":68,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"29127278","pmcid":"PMC5681567","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":37.5,"fair_r":33.3333,"fair_zscore":0.5085,"fair_rationale":{"fair_score":50.83,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"criteria":[{"key":"f_has_doi","label":"Has a persistent DOI","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"DOI present","rationale":null},{"key":"f_repository_presence","label":"Indexed in repositories / literature DBs","kind":"deterministic","weight":1.0,"fraction":1.0,"signal":"datacite=0, pmcid=True, pmid=True","rationale":null},{"key":"f_persistent_ids","label":"Resolvable scholarly identifiers (OpenAlex)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no OpenAlex id","rationale":null},{"key":"f_metadata_richness","label":"Rich, machine-readable metadata","kind":"llm","weight":1.0,"fraction":0.5,"signal":null,"rationale":"The paper provides accession numbers and a DOI, but does not describe machine-readable metadata or structured metadata beyond identifiers."}]},"A":{"name":"Accessible","score":67.5,"criteria":[{"key":"a_open_access","label":"Open Access / files deposited","kind":"deterministic","weight":1.5,"fraction":1.0,"signal":"Open Access","rationale":null},{"key":"a_retrievable","label":"Free full text retrievable","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"0 OA location(s)","rationale":null},{"key":"a_access_protocol","label":"Clear data/code access protocol","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Data access is clearly described via NCBI and an FTP site, but no code or software access protocol is provided."}]},"I":{"name":"Interoperable","score":37.5,"criteria":[{"key":"i_linked_data","label":"Linked datasets / DataCite relations","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"linked_datasets=0, datacite=0","rationale":null},{"key":"i_standard_ids","label":"References data via standard accessions","kind":"deterministic","weight":1.0,"fraction":0.0,"signal":"accessions=0, trials=0","rationale":null},{"key":"i_standards","label":"Standard formats, vocabularies & identifiers","kind":"llm","weight":1.0,"fraction":0.75,"signal":null,"rationale":"Standard identifiers (GenBank, BioProject) and vocabularies (GO, SwissProt, Pfam) are used, but file formats for annotations are not explicitly stated."}]},"R":{"name":"Reusable","score":33.33,"criteria":[{"key":"r_license","label":"Clear, open reuse license","kind":"deterministic","weight":1.5,"fraction":0.0,"signal":"no license","rationale":null},{"key":"r_downloads","label":"Demonstrated reuse (downloads)","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"downloads=0","rationale":null},{"key":"r_version","label":"Versioned / maintained","kind":"deterministic","weight":0.5,"fraction":0.0,"signal":"no version chain","rationale":null},{"key":"r_dataset","label":"Classified as a data resource","kind":"deterministic","weight":0.5,"fraction":1.0,"signal":"is_dataset","rationale":null},{"key":"r_reusability","label":"Data-availability statement, license & reproducibility","kind":"llm","weight":2.0,"fraction":0.5,"signal":null,"rationale":"A data availability statement and open-access license are present, but no data license, code repository, or explicit reproducibility measures are provided."}]}},"suggestions":["Provide machine-readable metadata (e.g., JSON-LD) for the genome assembly and annotations.","Deposit analysis scripts and software pipelines in a public repository (e.g., GitHub) with a clear license.","Specify a data license (e.g., CC0 or CC BY) for the deposited data in the data availability statement.","Use standard file formats (e.g., GFF3 for gene annotations, VCF for variants) and include a README file.","Add a reproducibility statement listing exact software versions and parameters used."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"epmc_xml"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"epmc_xml","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:38:43.788201Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}