{"doi":"10.1093/nar/gkl808","title":"PigGIS: Pig Genomic Informatics System","abstract":"Pig Genomic Information System (PigGIS) is a web-based depository of pig (Sus scrofa) genomic learning mainly engineered for biomedical research to locate pig genes from their human homologs and position single nucleotide polymorphisms (SNPs) in different pig populations. It utilizes a variety of sequence data, including whole genome shotgun (WGS) reads and expressed sequence tags (ESTs), and achieves a successful mapping solution to the low-coverage genome problem. With the data presently available, we have identified a total of 15 700 pig consensus sequences covering 18.5 Mb of the homologous human exons. We have also recovered 18 700 SNPs and 20 800 unique 60mer oligonucleotide probes for future pig genome analyses. PigGIS can be freely accessed via the web at http://www.piggis.org/ and http://pig.genomics.org.cn/.","journal":"Nucleic Acids Research","year":2007,"id":1300,"datarank":0.6654243399343258,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.32003657598521895,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.32003657598521895,"corpus_percentile":69.99303782780227,"corpus_rank":3880,"citation_count":9,"citer_count":8,"citers_with_citation_signal":7,"citers_with_endowment":7,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9143,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2007-01-03","fair_score":47.7083,"fair_percentile":40.618101545253865,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":76771,"name":"P. 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Lewis","orcid":"0000-0002-6195-4786","position":11,"is_corresponding":false},{"id":16363,"name":"Yu‐Chen Hu","orcid":"0000-0002-9997-4467","position":12,"is_corresponding":false},{"id":16364,"name":"Fei Song","orcid":"0000-0002-8825-6494","position":13,"is_corresponding":false},{"id":16365,"name":"Xiangang Huang","orcid":"0000-0001-8948-7879","position":14,"is_corresponding":false},{"id":16366,"name":"Lars Bolund","orcid":null,"position":15,"is_corresponding":false},{"id":828,"name":"Jian Wang","orcid":"0000-0002-9589-4056","position":16,"is_corresponding":false},{"id":16354,"name":"J. Ruan","orcid":null,"position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"17090590","pmcid":"PMC1669765","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"gold","license":"cc-by-nc","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":25.0,"fair_r":33.3333,"fair_zscore":-0.2199,"fair_rationale":{"fair_score":47.71,"has_llm":true,"dimensions":{"F":{"name":"Findable","score":65.0,"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":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":0.5,"signal":null,"rationale":"The paper provides some metadata (e.g., data types, counts, coverage) but lacks structured, machine-readable metadata like standardized schemas or persistent identifiers."}]},"A":{"name":"Accessible","score":67.5,"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":0.75,"signal":null,"rationale":"The paper states PigGIS is freely accessible via the web and provides URLs, but does not specify a formal access protocol or authentication/authorization details."}]},"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 paper uses standard formats (e.g., FASTA, GenBank) and mentions some identifiers (e.g., human gene names), but lacks explicit use of standard vocabularies or persistent identifiers for data."}]},"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 includes a data-availability statement and a Creative Commons license, but does not provide a formal data/code repository or detailed reproducibility instructions."}]}},"suggestions":["Provide machine-readable metadata in a structured format (e.g., JSON-LD or RDF) with persistent identifiers.","Specify a clear access protocol (e.g., REST API or SPARQL endpoint) with authentication details if needed.","Use standard ontologies and persistent identifiers (e.g., DOIs for datasets, ORCID for authors) to enhance interoperability.","Include a formal data-availability statement with a link to a public repository and a license for reuse.","Add detailed reproducibility steps, such as versioned code and data in a repository like GitHub or Zenodo."],"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":"2026-06-18T00:50:39.984416Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}