{"doi":"10.1093/nar/gkab897","title":"CeDR Atlas: a knowledgebase of cellular drug response","abstract":"Drug response to many diseases varies dramatically due to the complex genomics and functional features and contexts. Cellular diversity of human tissues, especially tumors, is one of the major contributing factors to the different drug response in different samples. With the accumulation of single-cell RNA sequencing (scRNA-seq) data, it is now possible to study the drug response to different treatments at the single cell resolution. Here, we present CeDR Atlas (available at https://ngdc.cncb.ac.cn/cedr), a knowledgebase reporting computational inference of cellular drug response for hundreds of cell types from various tissues. We took advantage of the high-throughput profiling of drug-induced gene expression available through the Connectivity Map resource (CMap) as well as hundreds of scRNA-seq data covering cells from a wide variety of organs/tissues, diseases, and conditions. Currently, CeDR maintains the results for more than 582 single cell data objects for human, mouse and cell lines, including about 140 phenotypes and 1250 tissue-cell combination types. All the results can be explored and searched by keywords for drugs, cell types, tissues, diseases, and signature genes. Overall, CeDR fine maps drug response at cellular resolution and sheds lights on the design of combinatorial treatments, drug resistance and even drug side effects.","journal":"Nucleic Acids Research","year":2021,"id":98,"datarank":1.2121043674134429,"base_score":3.58351893845611,"endowment":3.58351893845611,"self_citation_contribution":0.5375278407684165,"citation_network_contribution":0.6745765266450264,"self_endowment_contribution":0.5375278407684165,"citer_contribution":0.6745765266450264,"corpus_percentile":59.560618388934095,"corpus_rank":498,"citation_count":42,"citer_count":33,"citers_with_citation_signal":25,"citers_with_endowment":25,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9267,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-10-11","fair_score":47.7083,"fair_percentile":44.415127528583994,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":749,"name":"Hongen Kang","orcid":"0000-0002-9581-1329","position":1,"is_corresponding":false},{"id":750,"name":"Tianyi Xu","orcid":"0000-0003-4197-8163","position":2,"is_corresponding":false},{"id":751,"name":"Lili Hao","orcid":"0000-0003-3432-7151","position":3,"is_corresponding":false},{"id":752,"name":"Yiming Bao","orcid":null,"position":4,"is_corresponding":false},{"id":753,"name":"Peilin Jia","orcid":"0000-0003-4523-4153","position":5,"is_corresponding":false},{"id":754,"name":"Yin‐Ying Wang","orcid":null,"position":6,"is_corresponding":false},{"id":755,"name":"Yīmíng Bào","orcid":"0000-0002-9922-9723","position":7,"is_corresponding":false},{"id":748,"name":"Yin-Ying Wang","orcid":null,"position":0,"is_corresponding":true}],"reference_count":49,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"34634794","pmcid":"PMC8728137","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by-nc","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":0.2259,"fair_rationale":{"fair_score":47.71,"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 a web interface and documentation but does not describe machine-readable metadata (e.g., structured JSON-LD, schema.org) for the knowledgebase."}]},"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":"The data is accessible via a public website (https://ngdc.cncb.ac.cn/cedr) and a download page, but no API or programmatic access protocol is mentioned."}]},"I":{"name":"Interoperable","score":25.0,"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":0.5,"signal":null,"rationale":"The paper uses standard formats (e.g., AnnData, MySQL) and some identifiers (e.g., GEO accessions), but does not specify use of community standard vocabularies or persistent identifiers for drugs or cell types."}]},"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":"The paper includes a data-availability statement and a CC BY-NC license, but lacks explicit reproducibility details (e.g., code repository, versioned data releases) and a formal license for the database itself."}]}},"suggestions":["Add machine-readable metadata (e.g., JSON-LD with schema.org/Dataset) to the website for automated discovery.","Provide a REST API or SPARQL endpoint for programmatic access to the data.","Use standard ontologies (e.g., Cell Ontology, ChEBI) and persistent identifiers (e.g., DOIs) for drugs and cell types.","Include a clear data-availability statement with a link to a versioned code repository (e.g., GitHub) and a formal license for the database.","Document the exact software versions and parameters used for reproducibility of the analysis pipeline."],"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":"2026-06-18T00:43:26.794527Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}