ArticleJournal of biomedical semantics2011
Developing a kidney and urinary pathway knowledge base.
Article in Journal of biomedical semantics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Rewiring Drug Research and Development through Human Data-Driven Discovery (HDPharmaceutics · 2023Review
- Big Data in Nephrology.Nature reviews. Nephrology · 2021Review
- Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization.International journal of molecular sciences · 2020Review
- Urinary Peptidomic Biomarkers in Kidney Diseases.International journal of molecular sciences · 2019Review
- Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.PloS one · 2018Article
- The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.Journal of biomedical semantics · 2016Article
- Current state of the art for enhancing urine biomarker discovery.Expert review of proteomics · 2016Review
- PeptiCKDdb-peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease.Database : the journal of biological databases and curation · 2016Article
- Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.Journal of biomedical semantics · 2016Article
- Finding gene regulatory network candidates using the gene expression knowledge base.BMC bioinformatics · 2014Article
- State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.Journal of proteome research · 2014Article
- The genetics of diabetic nephropathy.Genes · 2013Article
- The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases.BMC bioinformatics · 2013Article
- Analysing Syntactic Regularities and Irregularities in SNOMED-CT.Journal of biomedical semantics · 2012Article
- Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.Journal of biomedical semantics · 2012Article
- Populous: a tool for building OWL ontologies from templates.BMC bioinformatics · 2012Article
- Semantically enabling pharmacogenomic data for the realization of personalized medicine.Pharmacogenomics · 2012Review
- Developing a kidney and urinary pathway knowledge base.Journal of biomedical semantics · 2011Article
- Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting.Journal of biomedical semantics · 2011Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChronic renal disease is a global health problem. The identification of suitable biomarkers could facilitate early detection and diagnosis and allow better understanding of the underlying pathology. One of the challenges in meeting this goal is the necessary integration of experimental results from multiple biological levels for further analysis by data mining. Data integration in the life science is still a struggle, and many groups are looking to the benefits promised by the Semantic Web for data integration.
resultsWe present a Semantic Web approach to developing a knowledge base that integrates data from high-throughput experiments on kidney and urine. A specialised KUP ontology is used to tie the various layers together, whilst background knowledge from external databases is incorporated by conversion into RDF. Using SPARQL as a query mechanism, we are able to query for proteins expressed in urine and place these back into the context of genes expressed in regions of the kidney.
conclusionsThe KUPKB gives KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. The Semantic Web technologies we use, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. The KUPKB is still relatively small, but questions remain about scalability, maintenance and availability of the knowledge itself. AVAILABILITY: The KUPKB may be accessed via http://www.e-lico.eu/kupkb.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.