2019
Recognizing software names in biomedical literature using machine learning
Wei Q, Zhang Y, Amith M, Lin R, Lapeyrolerie J, Tao C, Xu H. Recognizing software names in biomedical literature using machine learning. Health Informatics Journal 2019, 26: 21-33. PMID: 31566474, PMCID: PMC7334865, DOI: 10.1177/1460458219869490.Peer-Reviewed Original ResearchConceptsSoftware namesF-measureNatural language processing methodsBiomedical literatureWord representation featuresLanguage processing methodsEntity recognition systemSoftware catalogSoftware repositoriesFeature engineeringBiomedical softwareRecognition systemSoftware toolsBiomedical domainRepresentation featuresMEDLINE abstractsWord embeddingsKnowledge featuresManual curationSoftwareMachineProcessing methodsBest systemRepositorySystem
2017
Search Datasets in Literature: A Case Study of GWAS.
Dong X, Zhang Y, Xu H. Search Datasets in Literature: A Case Study of GWAS. AMIA Joint Summits On Translational Science Proceedings 2017, 2017: 40-49. PMID: 28815103, PMCID: PMC5543360.Peer-Reviewed Original ResearchRecognition systemMEDLINE abstractsDataset search enginePattern-based rulesText mining methodsData setsUnderlying data setSearch datasetsData discoverabilityUse casesSearch enginesDataset attributesMining methodsF-measureDomain dictionaryScalable approachHybrid approachDatasetFinderRetrieving literatureDiscoverabilityUltimate goalCase studySetScientific publications
2007
Gene symbol disambiguation using knowledge-based profiles
Xu H, Fan J, Hripcsak G, Mendonça E, Markatou M, Friedman C. Gene symbol disambiguation using knowledge-based profiles. Bioinformatics 2007, 23: 1015-1022. PMID: 17314123, DOI: 10.1093/bioinformatics/btm056.Peer-Reviewed Original ResearchConceptsKnowledge sourcesSimilarity scoresInformation retrieval methodsGene symbol disambiguationText mining systemKnowledge-based profilesTesting data setsBiomedical entitiesBiomedical domainMEDLINE abstractsHigh similarity scoresRetrieval methodAmbiguous genesEntrez GeneGene symbolsDisambiguation taskTesting set