{"doi":"10.1093/nar/gkl969","title":"Snap: an integrated SNP annotation platform","abstract":"Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical research. Using a user-friendly web interface, genes can be searched by name, description, position, SNP ID or clone name. Several public databases are integrated, including gene information from Ensembl, protein features from Uniprot/SWISS-PROT, Pfam and DAS-CBS. Gene relationships are fetched from BIND, MINT, KEGG and are integrated with ortholog data from TreeFam to extend the current interaction networks. Integrated tools for primer-design and mis-splicing analysis have been developed to facilitate experimental analysis of individual genes with focus on their variation. Snap is available at http://snap.humgen.au.dk/ and at http://snap.genomics.org.cn/.","journal":"Nucleic Acids Research","year":2006,"id":8190,"datarank":3.148028694543009,"base_score":4.007333185232471,"endowment":4.007333185232471,"self_citation_contribution":0.6010999777848708,"citation_network_contribution":2.546928716758138,"self_endowment_contribution":0.6010999777848708,"citer_contribution":2.546928716758138,"corpus_percentile":92.97594182718342,"corpus_rank":909,"citation_count":54,"citer_count":53,"citers_with_citation_signal":37,"citers_with_endowment":37,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9278,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2006-11-29","fair_score":36.25,"fair_percentile":14.79028697571744,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":20905,"name":"Christopher A. Bristow","orcid":"0009-0009-9266-6849","position":1,"is_corresponding":false},{"id":30887,"name":"Alexandra P. Lewis","orcid":"0000-0002-6195-4786","position":2,"is_corresponding":false},{"id":72431,"name":"Søren Vang","orcid":"0000-0002-1899-4205","position":3,"is_corresponding":false},{"id":72432,"name":"Yafeng Hu","orcid":null,"position":4,"is_corresponding":false},{"id":16366,"name":"Lars Bolund","orcid":null,"position":5,"is_corresponding":false},{"id":6308,"name":"Jun Wang","orcid":"0000-0003-2509-9599","position":6,"is_corresponding":false},{"id":28976,"name":"Shengting Li","orcid":"0000-0001-8156-9781","position":0,"is_corresponding":true}],"reference_count":22,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"17135198","pmcid":"PMC1751554","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":42.5,"fair_i":25.0,"fair_r":25.0,"fair_zscore":-0.9287,"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 does not mention machine-readable metadata such as structured schema.org markup or JSON-LD for the web resource."}]},"A":{"name":"Accessible","score":42.5,"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":0.25,"signal":null,"rationale":"The paper states the web interface is publicly accessible via two URLs but does not provide a clear protocol for automated programmatic 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 platform uses standard formats like FASTA for sequences and integrates well-known databases (Ensembl, UniProt, etc.) but does not explicitly state use of standard interoperability protocols like RESTful APIs with common formats."}]},"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 mentions a Creative Commons Non-Commercial License but does not provide a dedicated data-availability statement, deposit of data in a public repository, or details on reproducibility of the platform's code and data."}]}},"suggestions":["Include machine-readable metadata (e.g., JSON-LD) in the web resource to enhance findability by search engines and semantic tools.","Provide a documented RESTful API or SPARQL endpoint for programmatic access to the SNP annotations and other data.","Deposit the underlying database snapshots and code in a public repository (e.g., Zenodo, GitHub) with a clear license and versioning to enable reuse.","Add a detailed data-availability statement specifying how to obtain the exact dataset versions used and any conditions for reuse.","Use standardized vocabularies (e.g., EDAM) for describing the types of annotations and tools, and adopt RO-Crate packaging for reproducibility."],"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":"2026-06-18T00:42:59.155029Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}