From SHARP Project Wiki
- age-adjusted rate
- An age-adjusted incidence or mortality rate is a weighted average of the age-specific incidence or mortality rates, where the weights are the proportions of persons in the corresponding age groups of a standard million population. The potential confounding effect of age is reduced when comparing age-adjusted rates computed using the same standard million population.
- (HOSS Pipeline) Executes recipes. Takes in an electronic transaction, applies a recipe (set of transformations) to it, and returns the transformed electronic transaction. Agents move electronic transactions from waypoint to waypoint.
- Annual Percent Change is used to measure trend or the change in rate over time. It is the "average" annual rate of change over the time series selected.
- Application Programming Interface
- Annual Report to the Nation
- An annual update of cancer death rates, incidence rates (new cases), and trends in the United States. The Centers for Disease Control and Prevention, the American Cancer Society, the National Cancer Institute, and the North American Association of Central Cancer Registries collaborate to create this report.
- cancer burden
- A measure of the incidence of cancer within the population and an estimate of the financial, emotional, or social impact it creates. The burden of disease is not borne equally by all population groups in the United States.
- Common Analysis Structure/System
- Continuity of Care Document
- Clinical Document Architecture
- Consolidated Clinical Document Architecture
- Clinical Element Model
- Clinical Information Modeling Initiative
- Center for Integration of Medicine & Innovative Technology
- complete prevalence
- Complete Prevalence represents the proportion of people alive on a certain day who previously had a diagnosis of the disease, regardless of how long ago the diagnosis was, or if the patient is still under treatment or is considered cured.
- confidence interval
- A range of values that has a specified probability of containing the rate or trend. The 95% (p-value = .05) and 99% (p-value = .01) confidence intervals are the most commonly used.
- (HOSS Pipeline) A recipient (and user) of electronic transactions that have reached a particular waypoint.
- crude rate
- A crude rate is the number of new cases (or deaths) occurring in a specified population per year, usually expressed as the number of cases per 100,000 population at risk.
- The Collection Processing Engine is a tool shipped with UIMA. SHARP uses cTAKES for Natural Language Processing. cTAKES is based on UIMA.
- The Cancer Statistics Review is an annual report containing the most recent incidence, mortality, and survival statistics, published by the Cancer Statistics Branch of the NCI. It presents a broad profile of the cancer burden.
- Clinical Text Analysis and Knowledge Extraction System - An open-source NLP tool developed by Mayo. It is available for download here: https://cabig-kc.nci.nih.gov/Vocab/KC/index.php/OHNLP_Documentation_and_Downloads
- Common Type System - SHARPn NLP Common Type System is an effort for defining common NLP types used in SHARPn.
- Common Terminology Services 2
- Data Pipeline
- (HOSS Pipeline) Complex arrangement of technical components including injectors, waypoints, persistent waypoints, recipes, agents, and consumers. The data pipeline is designed to manage and transform a broad variety of standardized, non-standardized, malformed electronic transactions into a format usable by multiple data consumers.
- delay adjusted rate
- A cancer rate adjusted for reporting delay, the time elapsed before a diagnosed cancer case is reported to the NCI.
- Domain Specific Language
- Electronic Health Record
- Electronic Medical Records and Genomics Network
- Electronic Medical Record
- (HOSS Pipeline) A mechanism used to deliver payloads to a consumer. Reads envelopes from a waypoint and delivers them to a consumer according to a "subscription" contract that the consumer has with the pipeline.
- (HOSS Pipeline) A wrapper containing both the payload and metadata describing the payload.
- Exception Waypoint
- (HOSS Pipeline) A waypoint containing electronic transactions that threw exceptions when being processed by an agent.
- extent of disease
- Refers to the stage of the disease and details the degree to which the cancer has advanced. Extent of disease records the number of lymph nodes involved, metastases and size of primary tumor
- Fast Stats
- Fast Stats is designed to allow quick and easy access to key statistics for all major cancer sites by age, sex, race, and geographic area. The statistics include incidence, mortality, prevalence, and the probability of developing or dying from cancer.
- five-year survival rate
- The percentage of people in a study or treatment group who are alive five years after they were diagnosed with or treated for a disease, such as cancer. The disease may or may not have come back.
- georeferenced statistics
- Statistics reported by geographic location of the events (e.g., residence of the cancer case)
- Health Insurance Portability and Accountability Act of 1996
- The U.S. Department of Health and Human Services (HHS)
- Health Level Seven International
- Healthcare Services Specification Project
- Informatics for Integrating Biology and the Bedside
- Infrastructure As A Service. Access to a collection of virtualized computer resources such as CPUs, networks, storage, and so on.
- ICCC classification
- At the time the World Health Organizations (WHO) International Agency for Research on Cancer (IARC) published their first monograph on Childhood Cancer in 1988, Dr. R. Marsden published an annex giving a classification scheme for childhood cancer that consisted of 12 groups based chiefly on histologic type. The classification by Marsden has been modified and is now called the International Classification of Childhood Cancers.
- Integrating Data for Analysis, Anonymization and SHaring
- Information Extraction
- The number of newly diagnosed cases during a specific time period
- (HOSS Pipeline) A component that receives payloads from sources, wraps them in an envelope, and places them into the initial waypoint. A receiver can provide source validation -- e.g., messages from an unknown IP address can be rejected -- and simple pattern matching validation -- e.g., regular expressions. Rejected messages may optionally be logged. An injector declares which types of payloads it can handle.
- Initial Waypoint
- (HOSS Pipeline) An initial waypoint contains envelopes delivered from one or more injectors and cannot receive envelopes from other waypoints/agents. Envelopes within an initial waypoint, by definition, contain unaltered payloads. A message cannot be in more than one initial waypoint -- i.e., the sum of all messages across all initial waypoints represent all received messages for the pipeline.
- Generically, a real and working copy of an abstract notion.
For SHARP, a Ubuntu Enterprise Cloud virtual machine instance is a copy of an image that can be started by a user. Once started an instance is a working system setup having the hardware properties associated with it at launch.
For SHARP, a CEM instance is the actual XML file or object based on the CEM object templates.
- A Ubuntu Enterprise Cloud virtual machine image is a set of software, including the operating system, that is available to be started by users. When launched a copy of the image is made and it is associated with a set of hardware settings such as number of processors, memory, etc. Many copies of an image can be started as instances.
- A Java EE certified platform for developing and deploying enterprise Java applications, Web applications, and Portals. JBoss Application Server provides the full range of Java EE 5 features as well as extended enterprise services including clustering, caching, and persistence.
- JBOSS will host the ODE (BPEL engine) enabling the execution of WS-BPEL processes.
- Joinpoint software
- Statistical software for the analysis of trends using a regression model that describes trends by a sequence of straight line segments, connected at "joinpoints" where significant changes in trend have been calculated.
- life tables
- A table for a given population listing, for each sex and each age from 0 to 120, how many members die at that age and how many survive one more year.
- lifetime risk
- The probability of developing or dying from cancer in the course of ones lifespan. Read more >
- limited-duration prevalence
- Represents the proportion of people alive on a certain day who had a diagnosis of the disease within the past x years.
- MD SHARP
- NIH SHARP Program Affiliate
- Multi-source Integrated Platform for Answering Clinical Questions
- Mirth Connect
- Designed as an interface engine, Mirth Connect provides the necessary tools for developing, testing, deploying, and monitoring interfaces.
- Serving as the hub for both UIMA-AS and BPEL (ODE) services, Mirth Connect will be used to:
- Run single transactions through UIMA or BPEL processing, based upon the connection or parameters passed.
- Run batch transactions through UMIA or BPEL via iterations thru previously stored data sets found in the SHARP – MySQL repository.
- Transactions once completed, will have their results persisted in the MySQL repository for later analysis or processing.
- Machine Learning
- The number of deaths during a specific time period. Read more >
- Meaningful Use
- The MySQL database has become one of the world's most popular open source databases, because of its high performance, high reliability and ease of use.
- The SHARP project will use MySQL as a persistent store for the batch input files, intermediate results and final processing results from the various pipelines (UIMA-AS / BPEL). As such a number of databases will be created as needed to store data in various formats, e.g. Clinical Element Models (CEM), run statistics, intermediate datasets.
- NHIN CONNECT
- CONNECT enables secure electronic health data exchange among healthcare providers, insurers, government agencies and consumer services.
- It will enable data sets to be submitted across the internet to the SHARP Area 4 cloud patch to show case NLP, Data Normalization and Phenotyping algorithms.
- National Library of Medicine
- Natural Language Processing
- National Quality Forum
- Nationwide Health Information Network
- BPEL Engine - Apache ODE (Orchestration Director Engine) executes business processes written following the WS-BPEL standard. It talks to web services, sending and receiving messages, handling data manipulation and error recovery as described by your process definition.
- Within the SHARP project, the ODE will be installed in JBOSS and will be invoked via Web Service calls from the Mirth Connect hub. It is intended to run WS-BPEL scripts created by the SHARP Phenotyping team. Results generated from the execution of the BPEL processing will be persisted in the MySQL repository for later analysis or processing.
- Open Health Natural Language Processing
- Object Management Group
- The Office of the National Coordinator for Health Information Technology (ONC) is at the forefront of the administration’s health IT efforts and is a resource to the entire health system to support the adoption of health information technology and the promotion of nationwide health information exchange to improve health care. ONC is organizationally located within the Office of the Secretary for the U.S. Department of Health and Human Services (HHS).
- Machine learning toolset
- Web Ontology Language
- (HOSS Pipeline) In healthcare these can exist in broad variety of forms. They include HL7 v2 messages, HL7 v3 documents (e.g., CCD, etc.), and NCPDP messages, among others. They may also include ASCII delimited files (e.g., Delimited Text) and other "non-standard" formats.
- percent change
- The percent change (PC) in a statistic over a given time interval is Percent change = (Final value - Initial value) / Initial value * 100. A positive PC corresponds to an increasing trend, a negative PC to a decreasing trend.
- Pharmacogenomics Research Network
- The number of cases alive on a certain date. Read more >
- primary tumor
- The original tumor.
- progression-free survival
- The length of time during and after treatment in which a patient is living with a disease that does not get worse. Progression-free survival may be used in a clinical study or trial to help find out how well a new treatment works.
- Quality Data Model
- Resource Description Framework
- (HOSS Pipeline) An ordered collection of transformations to be performed on an electronic transaction. A recipe defines how to transform an electronic transaction from one waypoint to another waypoint. Transformations that are bundled into a recipe have the ability to be contingent to other transformations.
- relative survival rate
- A specific measurement of survival where the rate is calculated by adjusting the rate to remove all causes of death except cancer. It is the ratio of a cancer patients chance of surviving a given time interval to that of an average person of the same age and sex.
- reporting delay
- The time elapsed before a diagnosed cancer case is reported to the NCI. Currently, the NCI allows a standard delay of 22 months between the end of the diagnosis year and the time the cancers are first reported to the NCI in November, almost two years later.
- Representational State Transfer
- Surveillance, Epidemiology, and End Results (SEER) Program of the NCI is a collection of population-based cancer registries in the United States which collect and submit cancer incidence and follow up data to the National Cancer Institute. The National Cancer Act of 1971 mandated the collection, analysis, and dissemination of data useful in the prevention, diagnosis, and treatment of cancer leading to the establishment of the SEER Program.
- SEER registries
- SEER Program collects cancer incidence and survival data from the SEER registries, geographic areas selected for inclusion in the SEER Program based on their ability to operate and maintain a high quality population-based cancer reporting system and for their epidemiologically significant population subgroups.
- Strategic Health IT Advanced Research Projects (SHARP) Program. The SHARP program supports the discovery of “breakthrough” research findings that will accelerate the nationwide use of health IT and will support dramatic improvements in health care.
- SHARP Area 2 Projects on patient centered cognitive support research
- SHARP Area 4 Projects on Secondary Use of EHR Data Program
- SHARP Area 1 Projects on Security
- Standards & Interoperability Framework, ONC Funded
- SHARP Area 3 Substitutable Medical Apps, reusable technologies
- spatial correlation
- A measure of the tendency for places that are near to each other to have more similar (positive correlation) or dissimilar (negative correlation) values of their statistics.
- Subject of Analysis (UIMA Term)
- The extent of a cancer within the body. If the cancer has spread, the stage describes how far it has spread from the original site to other parts of the body.
- standard error
- The standard error of a rate is a measure of the sampling variability of the rate.
- standard million population
- A standard million population for a geographic area is a table giving the number of persons in each age group 0, 1-4, ... , 85+ out of a theoretical cohort of 1,000,000 persons that is distributed by age in the same proportions as the population.
- standard population
- A standard population for a geographic area, such as the U.S. or the world, is a table giving the proportions of the population falling into the age groups 0, 1-4, 5-9,…, 80-84, and 85+.
- statistically significant
- Describes a mathematical measure of difference between groups. The difference is said to be statistically significant if it is greater than what might be expected to happen by chance alone.
- surveillance data (cancer)
- Measures of cancer incidence, morbidity, survival, and mortality for persons with cancer. It also includes the assessment of genetic predisposition, environmental and behavioral risk factors, screening practices, and the quality of care from prevention through palliation.
- The proportion of patients alive at some point after the diagnosis of their cancer. Read more >
- Semantic Web Rule Language
- Temporal Histories for Your Medical Events
- trends over time
- The change in rate over time expressed as an annual percent change.
- (HOSS Pipeline) Discrete instructions for altering an electronic transaction built into a class that implements the Transformer interface. A transformation may depend on other transformations -- i.e., a transformation may require that one or more other transformations have occurred before it will run.
- Unstructured Information Management Architecture
- UIMA is an open, industrial-strength, scaleable and extensible platform for creating, integrating and deploying unstructured information management solutions from powerful text or multi-modal analysis and search components.
- Within the SHARP project, the UIMA-AS infrastructure will be used to host natural language processing (NLP), data normalization algorithms and potentially some phenotype processing.
- Unified Medical Language System
- Virtual Private Networking is a secure method to access a particular resource or resources typically enforced by user ID and password access via a network connection. http://en.wikipedia.org/wiki/Vpn
- (HOSS Pipeline) A defined state of an electronic transaction that conforms to a set of particular criteria, such as semantic and/or syntactic rules. Most waypoints result from running an agent against another waypoint. Electronic transactions at a particular waypoint may or may not be persisted (a "persisted waypoint"), depending on the specific use-case.
- Extensible Markup Language