Dataset Information

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

ABSTRACT: Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. We present the ontology we developed to address this issue.Radiation Oncology anatomical and target volumes were categorized in anatomical and treatment planning classes. International delineation guidelines specific to radiation oncology were used for lymph nodes areas and target volumes. Hierarchical classes were created to generate The Radiation Oncology Structures (ROS) Ontology. The ROS was then applied to the data from our institution.Four hundred and seventeen classes were created with a maximum of 14 children classes (average = 5). The ontology was then converted into a Web Ontology Language (.owl) format and made available online on Bioportal and GitHub under an Apache 2.0 License. We extracted all structures delineated in our department since the opening in 2001. 20,758 structures were exported from our "record-and-verify" system, demonstrating a significant heterogeneity within a single center. All structures were matched to the ROS ontology before integration into our clinical data warehouse (CDW).In this study we describe a new ontology, specific to radiation oncology, that reports all anatomical and treatment planning structures that can be delineated. This ontology will be used to integrate dosimetric data in the Assistance Publique-Hôpitaux de Paris CDW that stores data from 6.5 million patients (as of February 2017).

SUBMITTER: Bibault JE

PROVIDER: S-EPMC5774757 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

Bibault Jean-Emmanuel JE Zapletal Eric E Rance Bastien B Giraud Philippe P Burgun Anita A

PloS one 20180119 1

<h4>Purpose</h4>Leveraging Electronic Health Records (EHR) and Oncology Information Systems (OIS) has great potential to generate hypotheses for cancer treatment, since they directly provide medical data on a large scale. In order to gather a significant amount of patients with a high level of clinical details, multicenter studies are necessary. A challenge in creating high quality Big Data studies involving several treatment centers is the lack of semantic interoperability between data sources. ...[more]

PMID: 29351341

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Project description:PurposeTo prepare for big data analyses on radiation therapy data, we developed Stature, a tool-supported approach for standardization of structure names in existing radiation therapy plans. We applied the widely endorsed nomenclature standard TG-263 as the mapping target and quantified the structure name inconsistency in 2 real-world data sets.Methods and materialsThe clinically relevant structures in the radiation therapy plans were identified by reference to randomized controlled trials. The Stature approach was used by clinicians to identify the synonyms for each relevant structure, which was then mapped to the corresponding TG-263 name. We applied Stature to standardize the structure names for 654 patients with prostate cancer (PCa) and 224 patients with head and neck squamous cell carcinoma (HNSCC) who received curative radiation therapy at our institution between 2007 and 2017. The accuracy of the Stature process was manually validated in a random sample from each cohort. For the HNSCC cohort we measured the resource requirements for Stature, and for the PCa cohort we demonstrated its impact on an example clinical analytics scenario.ResultsAll but 1 synonym group ("Hydrogel") was mapped to the corresponding TG-263 name, resulting in a TG-263 relabel rate of 99% (8837 of 8925 structures). For the PCa cohort, Stature matched a total of 5969 structures. Of these, 5682 structures were exact matches (ie, following local naming convention), 284 were matched via a synonym, and 3 required manual matching. This original radiation therapy structure names therefore had a naming inconsistency rate of 4.81%. For the HNSCC cohort, Stature mapped a total of 2956 structures (2638 exact, 304 synonym, 14 manual; 10.76% inconsistency rate) and required 7.5 clinician hours. The clinician hours required were one-fifth of those that would be required for manual relabeling. The accuracy of Stature was 99.97% (PCa) and 99.61% (HNSCC).ConclusionsThe Stature approach was highly accurate and had significant resource efficiencies compared with manual curation.

Project description:ObjectiveThe clinical features of epilepsy determine how it is defined, which in turn guides management. Therefore, consideration of the fundamental clinical entities that comprise an epilepsy is essential in the study of causes, trajectories, and treatment responses. The Human Phenotype Ontology (HPO) is used widely in clinical and research genetics for concise communication and modeling of clinical features, allowing extracted data to be harmonized using logical inference. We sought to redesign the HPO seizure subontology to improve its consistency with current epileptological concepts, supporting the use of large clinical data sets in high-throughput clinical and research genomics.MethodsWe created a new HPO seizure subontology based on the 2017 International League Against Epilepsy (ILAE) Operational Classification of Seizure Types, and integrated concepts of status epilepticus, febrile, reflex, and neonatal seizures at different levels of detail. We compared the HPO seizure subontology prior to, and following, our revision, according to the information that could be inferred about the seizures of 791 individuals from three independent cohorts: 2 previously published and 150 newly recruited individuals. Each cohort's data were provided in a different format and harmonized using the two versions of the HPO.ResultsThe new seizure subontology increased the number of descriptive concepts for seizures 5-fold. The number of seizure descriptors that could be annotated to the cohort increased by 40% and the total amount of information about individuals' seizures increased by 38%. The most important qualitative difference was the relationship of focal to bilateral tonic-clonic seizure to generalized-onset and focal-onset seizures.SignificanceWe have generated a detailed contemporary conceptual map for harmonization of clinical seizure data, implemented in the official 2020-12-07 HPO release and freely available at hpo.jax.org. This will help to overcome the phenotypic bottleneck in genomics, facilitate reuse of valuable data, and ultimately improve diagnostics and precision treatment of the epilepsies.

Dataset Information

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

Publications

Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology.

Similar Datasets

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