{"doi":"10.1093/nar/gkn317","title":"BioLit: integrating biological literature with databases","abstract":"BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed Central. Specifically, these metadata include database identifiers and ontology terms found within the full text of the article. BioLit delivers these metadata in the form of XML-based article files and as a custom web-based article viewer that provides context-specific functionality to the metadata. This resource aims to integrate the traditional scientific publication directly into existing biological databases, thus obviating the need for a user to search in multiple locations for information relating to a specific item of interest, for example published experimental results associated with a particular biological database entry. As an example of a possible use of BioLit, we also present an instance of the Protein Data Bank fully integrated with BioLit data. We expect that the community of life scientists in general will be the primary end-users of the web-based viewer, while biocurators will make use of the metadata-containing XML files and the BioLit database of article data. BioLit is available at http://biolit.ucsd.edu.","journal":"Nucleic Acids Research","year":2008,"id":9775,"datarank":4.07633062658205,"base_score":3.6635616461296463,"endowment":3.6635616461296463,"self_citation_contribution":0.5495342469194471,"citation_network_contribution":3.5267963796626027,"self_endowment_contribution":0.5495342469194471,"citer_contribution":3.5267963796626027,"corpus_percentile":94.53082695134215,"corpus_rank":708,"citation_count":38,"citer_count":35,"citers_with_citation_signal":30,"citers_with_endowment":30,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9287,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2008-05-19","fair_score":56.0417,"fair_percentile":63.57615894039735,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":81128,"name":"S. Kushch","orcid":null,"position":1,"is_corresponding":false},{"id":81129,"name":"P. R. Williams","orcid":null,"position":2,"is_corresponding":false},{"id":13092,"name":"J. Lynn Fink","orcid":"0000-0003-2912-6048","position":4,"is_corresponding":false},{"id":81130,"name":"Sergii Kushch","orcid":"0000-0002-5908-7169","position":5,"is_corresponding":false},{"id":69614,"name":"Paul Williams","orcid":"0000-0001-6259-0390","position":6,"is_corresponding":false},{"id":125,"name":"Philip  E. Bourne","orcid":"0000-0002-7618-7292","position":7,"is_corresponding":false},{"id":13073,"name":"Lars Feuerbach","orcid":"0000-0003-1503-437X","position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"18515836","pmcid":"PMC2447735","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":77.5,"fair_a":67.5,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.2955,"fair_rationale":{"fair_score":56.04,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":77.5,"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":0.75,"signal":null,"rationale":"The paper describes rich metadata (PDB IDs, GO terms) embedded in XML files but lacks formal machine-readable metadata (e.g., schema.org or DataCite) for the resource itself."}]},"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 paper specifies URLs, FTP retrieval, and a URI-based access protocol for XML files, but does not describe an explicit authentication or licensing barrier; access is open but protocol is partially detailed."}]},"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":"The paper uses NLM DTD XML, OBO ontologies, and standard identifiers (PDB ID, GO ID, PMID, DOI), but does not adopt widely accepted vocabularies like DCAT or PROV for provenance."}]},"R":{"name":"Reusable","score":41.67,"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":0.667,"signal":null,"rationale":"The paper includes an open-access license (CC BY-NC 2.0 UK) and provides XML files for reuse, but lacks an explicit data-availability statement for code or a reproducibility recipe with dependencies and versioning."}]}},"suggestions":["Add structured machine-readable metadata (e.g., JSON-LD with schema.org) to the BioLit website for better Findability.","Document the exact file formats, API endpoints, and authentication requirements for all machine-access methods.","Adopt a standard provenance vocabulary (e.g., PROV-O) to track metadata generation and updates.","Include a formal data-availability statement that specifies licensing, download URLs, and terms for all derived data.","Provide a minimal example workflow or container to reproduce the metadata extraction process independently."],"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":"2026-06-18T00:44:02.185256Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}