{"doi":"10.1186/gb-2003-4-8-r51","title":"A comparative proteomics resource: proteins of Arabidopsis thaliana","abstract":"Using an integrative genome annotation pipeline (iGAP) for proteome-wide protein structure and functional domain assignment, we analyzed all the proteins of Arabidopsis thaliana. Three-dimensional structures at the level of the domain are assigned by fold recognition and threading based on a novel fold library that extends common domain classifications. iGAP is being applied to proteins from all available proteomes as part of a comparative proteomics resource. 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Bourne","orcid":"0000-0002-7618-7292","position":3,"is_corresponding":false},{"id":5827,"name":"Ilya N. Shindyalov","orcid":null,"position":4,"is_corresponding":false},{"id":20104,"name":"Greg Quinn","orcid":null,"position":5,"is_corresponding":false},{"id":20105,"name":"Nickolai Alexandrov","orcid":"0000-0003-3381-0918","position":6,"is_corresponding":false},{"id":20101,"name":"Wilfred W. Li","orcid":"0009-0007-1702-7196","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"12914659","pmcid":"PMC193643","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":52.5,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":-0.0568,"fair_rationale":{"fair_score":44.58,"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 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URL, but does not describe an explicit, detailed protocol for programmatic or automated access (e.g., API, SPARQL endpoint)."}]},"I":{"name":"Interoperable","score":25.0,"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":0.5,"signal":null,"rationale":"The resource uses standard identifiers (e.g., SCOP, PDB, PFAM, GO) and terms, but there is no mention of standard formats for data download (e.g., JSON, RDF) or use of controlled vocabularies beyond those inherent to the source databases."}]},"R":{"name":"Reusable","score":33.33,"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 contains a statement that the software is available for academic use under a copyright agreement, but does not provide a formal data license, a data-availability statement 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