{"doi":"10.1007/s00335-015-9573-z","title":"MouseMine: a new data warehouse for MGI","abstract":"MouseMine (www.mousemine.org) is a new data warehouse for accessing mouse data from Mouse Genome Informatics (MGI). Based on the InterMine software framework, MouseMine supports powerful query, reporting, and analysis capabilities, the ability to save and combine results from different queries, easy integration into larger workflows, and a comprehensive Web Services layer. Through MouseMine, users can access a significant portion of MGI data in new and useful ways. Importantly, MouseMine is also a member of a growing community of online data resources based on InterMine, including those established by other model organism databases. Adopting common interfaces and collaborating on data representation standards are critical to fostering cross-species data analysis. This paper presents a general introduction to MouseMine, presents examples of its use, and discusses the potential for further integration into the MGI interface.","journal":"Mammalian Genome","year":2015,"id":2459,"datarank":5.207269506023829,"base_score":5.003946305945459,"endowment":5.003946305945459,"self_citation_contribution":0.750591945891819,"citation_network_contribution":4.45667756013201,"self_endowment_contribution":0.750591945891819,"citer_contribution":4.45667756013201,"corpus_percentile":71.52156224572823,"corpus_rank":351,"citation_count":154,"citer_count":140,"citers_with_citation_signal":111,"citers_with_endowment":111,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.9271,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2015-06-20","fair_score":52.9167,"fair_percentile":79.11169744942832,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":29762,"name":"M. O’Keefe","orcid":null,"position":2,"is_corresponding":false},{"id":29764,"name":"Howie Motenko","orcid":null,"position":4,"is_corresponding":false},{"id":29765,"name":"Steven B. Neuhauser","orcid":"0000-0002-2993-9324","position":5,"is_corresponding":false},{"id":29766,"name":"Meghan O’Keefe","orcid":null,"position":6,"is_corresponding":false},{"id":29767,"name":"Joel E. Richardson","orcid":"0000-0003-3342-5753","position":7,"is_corresponding":false},{"id":29760,"name":"H. Motenko","orcid":null,"position":0,"is_corresponding":true}],"reference_count":7,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":"26092688","pmcid":"PMC4534495","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":"hybrid","license":"cc-by","views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":65.0,"fair_a":67.5,"fair_i":37.5,"fair_r":41.6667,"fair_zscore":0.697,"fair_rationale":{"fair_score":52.92,"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 describes MouseMine as a data warehouse with rich data types (e.g., genes, alleles, ontologies) but does not provide explicit machine-readable metadata or structured metadata descriptions beyond the text."}]},"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 clearly states that MouseMine is accessible via a web interface, web services API, and client libraries, with a public URL (www.mousemine.org) and mentions user login and anonymous access, but does not detail a formal access protocol or authentication mechanism for all users."}]},"I":{"name":"Interoperable","score":37.5,"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":0.75,"signal":null,"rationale":"The paper mentions use of InterMine framework, common interfaces, and data representation standards (e.g., OBO, InterMine data model), but does not explicitly specify standard formats, vocabularies, or identifiers used for all data types."}]},"R":{"name":"Reusable","score":41.67,"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":0.667,"signal":null,"rationale":"The paper includes a data-availability statement (Creative Commons Attribution 4.0 license), describes the build process and acceptance tests, but does not provide a direct link to the data or code repository for reproducibility."}]}},"suggestions":["Include explicit machine-readable metadata (e.g., schema.org annotations) on the MouseMine website to enhance findability.","Provide a formal data access protocol with authentication details and API documentation for all user levels.","Specify standard formats (e.g., JSON, XML) and controlled vocabularies (e.g., OBO, NCBI Taxonomy) used for data representation.","Add a direct link to the source code and data repository (e.g., GitHub) for reproducibility and reusability.","Include a data citation or persistent identifier (e.g., DOI) for the dataset to improve reusability."],"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":"2026-06-18T00:37:50.841203Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}