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In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools.","journal":"Nucleic Acids Research","year":2008,"id":6541,"datarank":17.404921999870034,"base_score":7.392647520721623,"endowment":7.392647520721623,"self_citation_contribution":1.1088971281082436,"citation_network_contribution":16.29602487176179,"self_endowment_contribution":1.1088971281082436,"citer_contribution":16.29602487176179,"corpus_percentile":90.96826688364524,"corpus_rank":112,"citation_count":1650,"citer_count":199,"citers_with_citation_signal":199,"citers_with_endowment":199,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9514,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2008-10-02","fair_score":43.8333,"fair_percentile":42.74406332453826,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":60532,"name":"Kira Anthony","orcid":null,"position":1,"is_corresponding":false},{"id":60533,"name":"Shiva Krupa","orcid":null,"position":2,"is_corresponding":false},{"id":60534,"name":"Jeffrey Buchoff","orcid":null,"position":3,"is_corresponding":false},{"id":60535,"name":"Matthew Day","orcid":"0000-0003-4095-520X","position":4,"is_corresponding":false},{"id":60536,"name":"Timo Hannay","orcid":"0000-0002-5941-3390","position":5,"is_corresponding":false},{"id":32907,"name":"Kenneth H. Buetow","orcid":"0000-0003-4439-0939","position":6,"is_corresponding":false},{"id":37094,"name":"Carl F. Schaefer","orcid":null,"position":0,"is_corresponding":true}],"reference_count":15,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"18832364","pmcid":"PMC2686461","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":74.0,"fair_a":63.0,"fair_i":15.0,"fair_r":23.3333,"fair_zscore":-0.1247,"fair_rationale":{"fair_score":43.83,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":74.0,"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 mentions a URL and basic search features but does not describe machine-readable metadata like structured schemas or standard metadata formats."}]},"A":{"name":"Accessible","score":63.0,"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 paper states the database is freely available and provides a URL, but does not specify a formal access protocol or authentication requirements."}]},"I":{"name":"Interoperable","score":15.0,"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":0.75,"signal":null,"rationale":"The paper mentions XML and BioPAX Level 2 formats, which are standard, but does not specify use of standard identifiers or controlled vocabularies."}]},"R":{"name":"Reusable","score":23.33,"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 states the database is freely available and updated monthly, but lacks a formal data-availability statement, license, or reproducibility details."}]}},"suggestions":["Add a machine-readable metadata schema (e.g., JSON-LD) to describe the database content.","Specify a formal access protocol (e.g., REST API or SPARQL endpoint) with clear authentication steps.","Use standard identifiers (e.g., UniProt IDs) and controlled vocabularies (e.g., GO terms) in the data.","Include a clear data-availability statement with a license (e.g., CC0 or CC-BY) and versioning details.","Provide a downloadable example dataset or code to reproduce the analysis shown in the paper."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v2","fulltext_source":"abstract_only"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v2","fair_fulltext_source":"abstract_only","fair_has_llm":true,"fair_computed_at":"2026-06-18T00:30:56.611273Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}