{"doi":"10.1093/bib/bbr003","title":"Building an HIV data mashup using Bio2RDF","abstract":"We present an update to the Bio2RDF Linked Data Network, which now comprises ∼30 billion statements across 30 data sets. Significant changes to the framework include the accommodation of global mirrors, offline data processing and new search and integration services. The utility of this new network of knowledge is illustrated through a Bio2RDF-based mashup with microarray gene expression results and interaction data obtained from the HIV-1, Human Protein Interaction Database (HHPID) with respect to the infection of human macrophages with the human immunodeficiency virus type 1 (HIV-1).","journal":"Briefings in Bioinformatics","year":2011,"id":1515,"datarank":1.2139565095711458,"base_score":3.1354942159291497,"endowment":3.1354942159291497,"self_citation_contribution":0.47032413238937254,"citation_network_contribution":0.7436323771817731,"self_endowment_contribution":0.47032413238937254,"citer_contribution":0.7436323771817731,"corpus_percentile":59.723352318958504,"corpus_rank":496,"citation_count":22,"citer_count":16,"citers_with_citation_signal":14,"citers_with_endowment":14,"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":"2011-03-24","fair_score":23.3333,"fair_percentile":2.550571679859279,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":52510,"name":"Francois Belleau","orcid":null,"position":2,"is_corresponding":false},{"id":17770,"name":"Marc-Alexandre Nolin","orcid":null,"position":4,"is_corresponding":false},{"id":74,"name":"Michel J. Dumontier","orcid":"0000-0003-4727-9435","position":5,"is_corresponding":false},{"id":17771,"name":"François Belleau","orcid":null,"position":6,"is_corresponding":false},{"id":17772,"name":"Jacques Corbeil","orcid":"0000-0002-9973-2740","position":7,"is_corresponding":false}],"reference_count":11,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"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":32.0,"fair_a":48.0,"fair_i":0.0,"fair_r":13.3333,"fair_zscore":-1.979,"fair_rationale":{"fair_score":23.33,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":32.0,"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":0.0,"signal":"datacite=0, pmcid=False, pmid=False","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":0.0,"signal":null,"rationale":"Paper lacks any description of rich, machine-readable metadata for the underlying data."}]},"A":{"name":"Accessible","score":48.0,"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":0.0,"signal":null,"rationale":"No clear protocol for accessing the data or code is provided."}]},"I":{"name":"Interoperable","score":0.0,"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":0.0,"signal":null,"rationale":"No explicit mention of standard formats, vocabularies, or identifiers used."}]},"R":{"name":"Reusable","score":13.33,"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":0.0,"signal":null,"rationale":"No data-availability statement, license, or reproducibility details are given."}]}},"suggestions":["Provide a publicly accessible URL or repository for the dataset with a stable identifier.","Include a data-availability statement specifying how to access the raw data and code.","Describe the machine-readable metadata (e.g., RDF schema, vocabularies) used in a dedicated section.","Add a license (e.g., Creative Commons) to clarify reuse permissions.","Document the exact formats and standards (e.g., SPARQL endpoint, standard ontologies) to enhance interoperability."],"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":"2026-06-18T00:47:19.479505Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}