{"doi":"10.1093/database/baad097","title":"An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP)","abstract":"IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn's and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.","journal":"Database","year":2024,"id":1169,"datarank":0.23841471818650695,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.030470564018523327,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.030470564018523327,"corpus_percentile":45.32139951179821,"corpus_rank":673,"citation_count":4,"citer_count":4,"citers_with_citation_signal":2,"citers_with_endowment":2,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9427,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":36.25,"fair_percentile":17.963940193491645,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":15551,"name":"Cai Qingsong","orcid":null,"position":1,"is_corresponding":false},{"id":15552,"name":"Ma Kejia","orcid":null,"position":2,"is_corresponding":false},{"id":15554,"name":"Wu Xing","orcid":"0000-0002-5371-6198","position":4,"is_corresponding":false},{"id":15556,"name":"Cai Lixia","orcid":null,"position":6,"is_corresponding":false},{"id":15557,"name":"Deng Minzi","orcid":null,"position":7,"is_corresponding":false},{"id":15558,"name":"Yang Yuanyuan","orcid":null,"position":8,"is_corresponding":false},{"id":15560,"name":"Kai Nie","orcid":"0000-0003-1536-6550","position":10,"is_corresponding":false},{"id":15561,"name":"Qingsong Cai","orcid":"0000-0003-2439-4051","position":11,"is_corresponding":false},{"id":15562,"name":"Weiwei Luo","orcid":"0000-0002-0000-420X","position":12,"is_corresponding":false},{"id":15563,"name":"Xuejie Chen","orcid":"0000-0001-8459-2557","position":13,"is_corresponding":false},{"id":15564,"name":"Lixia Cai","orcid":null,"position":14,"is_corresponding":false},{"id":15565,"name":"Yuanyuan Yang","orcid":"0009-0003-9056-0772","position":15,"is_corresponding":false},{"id":15566,"name":"Xiaoyan Wang","orcid":"0000-0002-7281-1078","position":16,"is_corresponding":false},{"id":15550,"name":"Nie Kai","orcid":null,"position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"38227799","pmcid":"PMC10791110","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":52.5,"fair_a":55.0,"fair_i":12.5,"fair_r":25.0,"fair_zscore":-0.8106,"fair_rationale":{"fair_score":36.25,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":52.5,"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":0.25,"signal":null,"rationale":"The paper describes a web portal with manually curated data but provides no machine-readable metadata (e.g., structured JSON-LD, schema.org annotations) for the data or the portal itself."}]},"A":{"name":"Accessible","score":55.0,"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 paper states the portal is accessible at www.ibdirp.com and lists external data sources, but does not specify a formal access protocol (e.g., API, authentication, or download terms) for the portal's own data."}]},"I":{"name":"Interoperable","score":12.5,"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":0.25,"signal":null,"rationale":"The paper mentions using standard databases (e.g., GEO, PubMed) but does not specify use of standard formats, controlled vocabularies, or persistent identifiers for the integrated data within the portal."}]},"R":{"name":"Reusable","score":25.0,"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":0.333,"signal":null,"rationale":"The paper includes a data availability statement pointing to external sources and a CC BY license for the article, but lacks a clear license for the portal's data and does not provide a reproducibility protocol for the integration process."}]}},"suggestions":["Add machine-readable metadata (e.g., JSON-LD with schema.org/Dataset) to the portal and paper to improve findability.","Provide a clear data access protocol, such as a REST API or SPARQL endpoint, with documentation on authentication and usage limits.","Use standard formats (e.g., CSV, RDF) and controlled vocabularies (e.g., NCBI Taxonomy, HPO) for all integrated data, and assign DOIs or other persistent identifiers to datasets.","Include a formal license (e.g., CC0 or ODC-BY) for the portal's data and a detailed reproducibility section describing how the integration was performed."],"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":"2026-06-18T00:52:58.964777Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}