2024
Automating literature screening and curation with applications to computational neuroscience
Ji Z, Guo S, Qiao Y, McDougal R. Automating literature screening and curation with applications to computational neuroscience. Journal Of The American Medical Informatics Association 2024, 31: 1463-1470. PMID: 38722233, PMCID: PMC11187430, DOI: 10.1093/jamia/ocae097.Peer-Reviewed Original ResearchComputational neuroscienceLanguage modeling techniquesNatural language processingDomain-specific resourcesComputational neuroscience approachNeuroscience workMetadata annotationsModel discoveryLanguage processingComputing elementsNeuron modelModelDBMetadataRelevant metadataStandardized metadataAuthor submission
2018
Automated Metadata Suggestion During Repository Submission
McDougal RA, Dalal I, Morse TM, Shepherd GM. Automated Metadata Suggestion During Repository Submission. Neuroinformatics 2018, 17: 361-371. PMID: 30382537, PMCID: PMC6494730, DOI: 10.1007/s12021-018-9403-z.Peer-Reviewed Original ResearchConceptsMetadata annotationMetadata tagsData providersAmount of dataDifferent text sourcesUser data entryData uploaderKnowledge discoveryText sourcesRelevant metadataMetadataHigh recallInformatics resourcesAnnotation schemeResearch communityData entryAnnotationBioinformatics resourcesDiscovery resourcesLow precisionMinimal costResourcesTagsModelDBUpload
2016
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience
McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hines ML. Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. Journal Of Computational Neuroscience 2016, 42: 1-10. PMID: 27629590, PMCID: PMC5279891, DOI: 10.1007/s10827-016-0623-7.Peer-Reviewed Original ResearchConceptsComputational neuroscience modelsHigh performance computationEssential modeling toolUser experienceData-based modelsPerformance computationModelDBGraphical toolUser-friendly databaseModeling toolsResearch topicNeuroscience modelsCollect dataNew challengesNeuron modelingConvenient venueMassive developmentComplex modelsNew technologiesLarge research groupsRunning modelFuture of neuroscienceUsersMultiple scalesModel of interest
2015
ModelView for ModelDB: Online Presentation of Model Structure
McDougal RA, Morse TM, Hines ML, Shepherd GM. ModelView for ModelDB: Online Presentation of Model Structure. Neuroinformatics 2015, 13: 459-470. PMID: 25896640, PMCID: PMC4618280, DOI: 10.1007/s12021-015-9269-2.Peer-Reviewed Original ResearchConceptsSource codeModel source codeComputational neuroscience modelsWeb applicationModel reuseUser interfaceVisualization algorithmsWeb presentationCode sharingGraphical viewModelDBContextual informationSearchable repositoryManual curationModel structureNeuroscience modelsOnline presentationCodeNecessary dataData analysisKey featuresUsersRepositoryStructures of hundredsSharing