2024
Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics
Mullin S, McDougal R, Cheung K, Kilicoglu H, Beck A, Zeiss C. Chemical entity normalization for successful translational development of Alzheimer’s disease and dementia therapeutics. Journal Of Biomedical Semantics 2024, 15: 13. PMID: 39080729, PMCID: PMC11290083, DOI: 10.1186/s13326-024-00314-1.Peer-Reviewed Original ResearchConceptsEntity normalizationChemical mentionsNatural language modelDictionary-based methodsDictionary-based approachCRAFT corpusDownstream tasksLanguage modelChemical Entities of Biological InterestPubMedBERT modelDisambiguationChEBIDownstream applicationsArticle abstractsRelationship typesMentionsPubMedBERTOntologyDementia literatureTaskDementia CohortMethodEntitiesAccuracyDementia
2013
Utilizing protein structure to identify non-random somatic mutations
Ryslik GA, Cheng Y, Cheung KH, Modis Y, Zhao H. Utilizing protein structure to identify non-random somatic mutations. BMC Bioinformatics 2013, 14: 190. PMID: 23758891, PMCID: PMC3691676, DOI: 10.1186/1471-2105-14-190.Peer-Reviewed Original ResearchConceptsProtein Data BankProtein structureSomatic mutationsTertiary structureDimensional protein structureProtein tertiary structureTertiary protein structureDriver mutationsMutation clustersTumor suppressorProteinMutational clusteringPharmacological successMutationsCancer proteinsNovel clusterMutational clustersOncogeneSingle strandsR packageData BankCurrent methodologiesGenomeEIF2AK2Suppressor
2012
A semantic web framework to integrate cancer omics data with biological knowledge
Holford ME, McCusker JP, Cheung KH, Krauthammer M. A semantic web framework to integrate cancer omics data with biological knowledge. BMC Bioinformatics 2012, 13: s10. PMID: 22373303, PMCID: PMC3471346, DOI: 10.1186/1471-2105-13-s1-s10.Peer-Reviewed Original ResearchConceptsBiological knowledgeOmics dataSemantic modelFundamental biological knowledgeGene ontology dataCancer omics dataEpigenomic dataRegulatory networksSemantic Web technologiesTranscription factorsSemantic Web frameworkUnified data sourceGene promoterDemethylating agentApoptosis pathwayAnti-cancer therapySemantic WebSPARQL endpointsWeb technologiesRDF triplesWeb frameworkOntology dataData warehouseUniform interfaceReasoning tools
2007
AlzPharm: integration of neurodegeneration data using RDF
Lam H, Marenco L, Clark T, Gao Y, Kinoshita J, Shepherd G, Miller P, Wu E, Wong GT, Liu N, Crasto C, Morse T, Stephens S, Cheung KH. AlzPharm: integration of neurodegeneration data using RDF. BMC Bioinformatics 2007, 8: s4. PMID: 17493287, PMCID: PMC1892101, DOI: 10.1186/1471-2105-8-s3-s4.Peer-Reviewed Original ResearchMeSH KeywordsBrainDatabase Management SystemsDatabases, FactualDocumentationHumansInformation DisseminationInformation Storage and RetrievalInternationalityInternetNatural Language ProcessingNerve Tissue ProteinsNeurodegenerative DiseasesNeurosciencesPilot ProjectsResearchResearch DesignSemanticsSystems IntegrationConceptsResource Description FrameworkSemantic Web approachWeb approachData modelData setsRDF data modelStandard data modelHeterogeneous data setsData integration approachData of interestMultiple research domainsRDF SchemaDescription FrameworkDomain ontologyAdvanced queriesOracle databaseDescription languageWeb interfaceBiomedical dataData integrationSeamless integrationNeuroscience dataOntological structureResearch domainNeuroscience researchers