{"doi":"10.3390/app13031614","title":"GDReBase: A Knowledge Base for Relations between Human Gut Microbes and Diseases Based on Deep Learning","abstract":"<jats:p>Gut microbes play a prominent role in many aspects of human health, as seen through the increasing number of related studies. The accumulation of intestinal-flora-related studies enables us to better understand the various relationships between human gut microbes and other factors that affect the human body. However, the existing database does not meet the requirements of scientists to browse or retrieve the latest and most comprehensive published data. Thus, a knowledge base containing data related to gut microbes with updates occurring in real time would be highly valuable. We present a knowledge base of consistently curated relationships between human gut microbes and disease. By continuously and automatically collecting papers published in mainstream journals and using deep learning and NLP methods for entity relationship identification, GDReBase has now integrated 3674 diseases, 687 microbes, 7068 relationships, and 13,553 pieces of evidence from 518,286 papers, a figure that will continue to grow. GDReBase is a convenient and comprehensive resource for gut microbiology research and can be accessed free of charge.</jats:p>","journal":"Applied Sciences","year":2023,"id":369,"datarank":0.12297772558321611,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.019005648499224304,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.019005648499224304,"corpus_percentile":42.47355573637103,"corpus_rank":708,"citation_count":1,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7988,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-27","fair_score":29.1667,"fair_percentile":10.29023746701847,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":59323,"name":"Simon G. Gregory","orcid":"0000-0002-7805-1743","position":1,"is_corresponding":false},{"id":3424,"name":"Xiaolong Dai","orcid":"0000-0003-1570-9349","position":2,"is_corresponding":false},{"id":3425,"name":"Chunhao Liu","orcid":null,"position":3,"is_corresponding":false},{"id":3426,"name":"Dongxiao Wang","orcid":"0000-0001-8200-0730","position":4,"is_corresponding":false},{"id":3427,"name":"Chenghao Zheng","orcid":null,"position":5,"is_corresponding":false},{"id":3428,"name":"Kaihua Liu","orcid":"0000-0002-3727-0034","position":6,"is_corresponding":false},{"id":3429,"name":"Sitong Liu","orcid":"0000-0002-5884-7488","position":7,"is_corresponding":false},{"id":3430,"name":"Yufei Zeng","orcid":null,"position":8,"is_corresponding":false},{"id":3431,"name":"Ziyang Song","orcid":"0000-0002-9660-7514","position":9,"is_corresponding":false},{"id":3432,"name":"Shanzhu Cui","orcid":"0000-0002-2907-4236","position":10,"is_corresponding":false},{"id":3433,"name":"Yongdong Xu","orcid":"0000-0003-2349-5643","position":11,"is_corresponding":false},{"id":3422,"name":"Haolei Xu","orcid":"0000-0001-5397-8422","position":0,"is_corresponding":true}],"reference_count":30,"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":"gold","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":37.0,"fair_a":58.0,"fair_i":5.0,"fair_r":16.6667,"fair_zscore":-1.4513,"fair_rationale":{"fair_score":29.17,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":37.0,"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":0.25,"signal":null,"rationale":"No machine-readable metadata is mentioned or described; the text only describes the database content in prose without references to standards for metadata."}]},"A":{"name":"Accessible","score":58.0,"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":0.5,"signal":null,"rationale":"The database is stated to be accessible free of charge, but no clear protocol or access method (e.g., API, query interface) is provided."}]},"I":{"name":"Interoperable","score":5.0,"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":0.25,"signal":null,"rationale":"No standard formats, vocabularies, or identifiers (e.g., DOIs, ontology terms) are mentioned for the data or relationships."}]},"R":{"name":"Reusable","score":16.67,"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":0.167,"signal":null,"rationale":"No data-availability statement, license, or detailed description of reproducibility is provided; only a vague claim of continuous updating."}]}},"suggestions":["Add machine-readable metadata (e.g., RDF/JSON-LD) with controlled vocabularies for microbes and diseases.","Provide a clear access protocol, such as an API with documented endpoints or a downloadable dataset.","Use standard identifiers (e.g., NCBI Taxonomy for microbes, UMLS/DO for diseases) in the database.","Include a data-availability statement with a license (e.g., Creative Commons) and versioning for reproducibility."],"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":"2026-06-18T06:41:27.043073Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}