{"doi":"10.1093/database/bau083","title":"Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain","abstract":"The study of developmental processes in the mouse and other vertebrates includes the understanding of patterning along the anterior-posterior, dorsal-ventral and medial- lateral axis. Specifically, neural development is also of great clinical relevance because several human neuropsychiatric disorders such as schizophrenia, autism disorders or drug addiction and also brain malformations are thought to have neurodevelopmental origins, i.e. pathogenesis initiates during childhood and adolescence. Impacts during early neurodevelopment might also predispose to late-onset neurodegenerative disorders, such as Parkinson's disease. The neural tube develops from its precursor tissue, the neural plate, in a patterning process that is determined by compartmentalization into morphogenetic units, the action of local signaling centers and a well-defined and locally restricted expression of genes and their interactions. While public databases provide gene expression data with spatio-temporal resolution, they usually neglect the genetic interactions that govern neural development. Here, we introduce Mouse IDGenes, a reference database for genetic interactions in the developing mouse brain. The database is highly curated and offers detailed information about gene expressions and the genetic interactions at the developing mid-/hindbrain boundary. To showcase the predictive power of interaction data, we infer new Wnt/β-catenin target genes by machine learning and validate one of them experimentally. The database is updated regularly. Moreover, it can easily be extended by the research community. Mouse IDGenes will contribute as an important resource to the research on mouse brain development, not exclusively by offering data retrieval, but also by allowing data input.<h4>Database url</h4>http://mouseidgenes.helmholtz-muenchen.de.","journal":"Database","year":2014,"id":12112,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"citer_contribution":0.0,"corpus_percentile":29.844511487584125,"corpus_rank":8690,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8443,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2014-08-20","fair_score":41.4583,"fair_percentile":25.827814569536425,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":10783,"name":"J. Zhang","orcid":"0000-0002-4380-1655","position":2,"is_corresponding":false},{"id":96325,"name":"J. Schechter","orcid":null,"position":3,"is_corresponding":false},{"id":96327,"name":"B. Lentes","orcid":null,"position":5,"is_corresponding":false},{"id":6512,"name":"Martin Preusse","orcid":"0000-0003-4789-0592","position":10,"is_corresponding":false},{"id":27403,"name":"Jian Zhang","orcid":"0000-0002-8824-8574","position":11,"is_corresponding":false},{"id":96330,"name":"Joel Schechter","orcid":"0000-0001-8392-9672","position":12,"is_corresponding":false},{"id":11318,"name":"David A Mayer","orcid":"0000-0002-6056-9771","position":13,"is_corresponding":false},{"id":96331,"name":"Beatrice Lentes","orcid":null,"position":14,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":15,"is_corresponding":false},{"id":49058,"name":"Nilima Prakash","orcid":"0000-0002-0568-6262","position":16,"is_corresponding":false},{"id":7259,"name":"Wolfgang Wurst","orcid":"0000-0003-4422-7410","position":17,"is_corresponding":false},{"id":7241,"name":"Dietrich Trümbach","orcid":"0000-0001-9027-3704","position":18,"is_corresponding":false},{"id":96323,"name":"M. Matthes","orcid":null,"position":0,"is_corresponding":true}],"reference_count":70,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":"25145340","pmcid":"PMC4139671","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":25.0,"fair_r":33.3333,"fair_zscore":-0.6065,"fair_rationale":{"fair_score":41.46,"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 provides a human-readable description of the database structure, but no explicit mention of machine-readable metadata (e.g., XML/JSON-LD schema) or formal metadata standards (e.g., Dublin Core, schema.org) is made."}]},"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 database URL is given (http://mouseidgenes.helmholtz-muenchen.de) and data can be downloaded as tab-delimited flat files, but no formal access protocol (e.g., REST API, SPARQL endpoint) nor persistent identifiers for individual records are described."}]},"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 EMAP/EMAPA ontology identifiers, MGI gene symbols and links to NCBI, UCSC and Ensembl, but does not define standardized vocabularies for interaction types or provide formal machine-readable representation in standard formats like RDF or OWL."}]},"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 states the database is freely available under a CC BY 4.0 license and provides downloads, but does not describe a formal data-availability statement for the paper itself, nor does it deposit data in a long-term repository or provide explicit reproducibility instructions for the machine learning analysis."}]}},"suggestions":["Add a data-availability statement to the paper that specifies the exact repository (e.g., Zenodo) and persistent identifier for the database snapshots used.","Expose the database with a RESTful API to allow programmatic access and machine-readable retrieval of individual interaction records.","Publish the database content as RDF using standard ontologies (e.g., OBO Foundry) to enhance interoperability with other resources.","Document the complete pipeline (including software versions and parameters) for the SVM prediction in a reproducible manner, e.g., as a Jupyter notebook or workflow in a repository.","Include formal machine-readable metadata (e.g., JSON-LD with schema.org) on the database homepage to improve findability by search engines."],"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":"2026-06-18T03:56:06.571105Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}