COVID Scenario Pipeline
type: SoftwareApplication
description: A flexible scenario modeling pipeline that tailors models for decision makers seeking to compare projections of epidemic trajectories and healthcare impacts from multiple intervention scenarios in different locations. It projects epidemic trajectories and healthcare impacts under different suites of interventions in order to aid in scenario planning. The model is generic enough to be applied to different spatial scales given shapefiles, population data, and COVID-19 confirmed case data.
conforms to: Schema.org
conforms to: DCMI Metadata Terms
conforms to: PAV Ontology
conforms to: PROV Ontology
conforms to: MIDAS Metadata Vocabulary
conforms to: HL7 FHIR
conforms to: SNOMED Clinical Terms
conforms to: Logical Observation Identifiers Names and Codes
conforms to: Open Biological and Biomedical Ontology
conforms to: MIDAS Catalog JSON-LD Schema
included in data catalog: MIDAS Catalog
about: vaccine-preventable Disease
about: viral respiratory tract infection
about: modeling output
about: mortality data
about: COVID-19
about: control strategy census
about: behavior
about: Homo sapiens
about: Viruses
about: compartmental models
about: population
about: infectious disease
about: Severe acute respiratory syndrome coronavirus 2
about: pathogen
about: incident hospitalization count
about: hospital stay dataset
about: human daily movement data set
about: software
about: viral Infectious disease
about: modeling method
about: Population count
about: scenario analysis
about: disease
about: modeling
about: host organism
about: health system capacity
about: modeling purpose
subject: viral Infectious disease
subject: Population count
subject: disease
subject: Viruses
subject: host organism
subject: pathogen
subject: behavior
subject: Homo sapiens
subject: vaccine-preventable Disease
subject: modeling output
subject: software
subject: mortality data
subject: scenario analysis
subject: infectious disease
subject: Severe acute respiratory syndrome coronavirus 2
subject: incident hospitalization count
subject: hospital stay dataset
subject: health system capacity
subject: compartmental models
subject: control strategy census
subject: viral respiratory tract infection
subject: human daily movement data set
subject: population
subject: modeling purpose
subject: COVID-19
subject: modeling method
subject: modeling
access URL: https://github.com/HopkinsIDD/COVIDScenarioPipeline
landing page: https://github.com/HopkinsIDD/COVIDScenarioPipeline
endpoint URL: https://github.com/HopkinsIDD/COVIDScenarioPipeline
abstract: Landing page where users can browse and download dataset files in various formats.
endpoint description: Landing page where users can browse and download dataset files in various formats.
language: English
creator: Johns Hopkins University Infectious Disease Dynamics - COVID-19
keywords: control strategy census
keywords: human daily movement data set
keywords: COVID-19

Schema.org
type: Standard
description: Schema.org vocabulary for structured data on the web
subject: sciences
subject: web
type: generic

DCMI Metadata Terms
type: Standard
description: Dublin Core Metadata Initiative Terms - refined elements for precise resource description
subject: metadata
subject: resource description
subject: interoperability
subject: digital libraries
type: metadata schema

PAV Ontology
type: Standard
description: Provenance, Authoring and Versioning ontology for metadata about web resources
subject: provenance
subject: versioning
subject: authoring
subject: metadata
type: metadata schema

PROV Ontology
type: Standard
description: W3C Provenance Ontology for describing provenance information
subject: sciences
subject: epidemiology
type: generic

MIDAS Metadata Vocabulary
type: Standard
description: Custom MIDAS vocabulary for epidemiological data and modeling
subject: epidemiology
subject: public health
subject: infectious diseases
type: domain-specific

HL7 FHIR
type: Standard
description: Health Level 7 Fast Healthcare Interoperability Resources
subject: healthcare
subject: medical informatics
type: domain-specific

SNOMED Clinical Terms
type: Standard
description: Systematized Nomenclature of Medicine Clinical Terms
subject: healthcare
subject: clinical terminology
type: domain-specific

Logical Observation Identifiers Names and Codes
type: Standard
description: LOINC database for laboratory and clinical observations
subject: healthcare
subject: laboratory
subject: clinical
type: domain-specific

Open Biological and Biomedical Ontology
type: Standard
description: OBO Foundry ontologies for life sciences and biomedical research
subject: life sciences
subject: biomedical
subject: epidemiology
type: domain-specific

MIDAS Catalog JSON-LD Schema
type: Standard
description: JSON Schema (Draft 2020-12) defining the structure of MIDAS Catalog JSON-LD metadata records
subject: epidemiology
subject: metadata
subject: data validation
type: metadata schema

vaccine-preventable Disease
type: DefinedTerm
description: Vaccine preventable diseases are those infectious diseases that can be prevented by vaccination
alternate name: Vaccine-Preventable Disease

viral respiratory tract infection
type: DefinedTerm
description: A respiratory tract infection caused by a virus. Viruses represent the most common causes of upper and lower respiratory tract infections and include rhinoviruses, influenza viruses, parainfluenza viruses, and respiratory syncytial virus.
alternate name: Viral Respiratory Tract Infection

modeling output
type: DefinedTerm
description: The output of a model
alternate name: Modeling Output

mortality data
type: DefinedTerm
description: A data set that is about either some mortality rate or the death events themselves of some individuals of a given population of a particular biological taxon.
alternate name: Mortality

COVID-19
type: DefinedTerm
description: A Coronavirus infection that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.
alternate name: COVID-19

control strategy census
type: DefinedTerm
description: a census of infectious disease control strategies put into place to reduce infection acquisitions that are part of an infection in an ecosystem.
alternate name: Control Strategy

behavior
type: DefinedTerm
description: Actions of groups of people in response to outbreaks.
alternate name: Behavior

Homo sapiens
type: DefinedTerm
description: Members of the species Homo sapiens.
alternate name: Homo sapiens

Viruses
type: DefinedTerm
description: Minute infectious agents whose genomes are composed of DNA or RNA, but not both. They are characterized by a lack of independent metabolism and the inability to replicate outside living host cells.
alternate name: Viruses

compartmental models
type: DefinedTerm
description: Forecasts based on SIR (Susceptible, Infected, Recovered) models or any of the many variants of this basic famework.
alternate name: Compartmental Models

population
type: DefinedTerm
alternate name: Population

infectious disease
type: DefinedTerm
description: A disease whose physical basis is an infectious disorder
alternate name: Infectious Disease

Severe acute respiratory syndrome coronavirus 2
type: DefinedTerm
description: A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis.
alternate name: SARS-CoV2

pathogen
type: DefinedTerm
description: An organism of a particular biological taxon that is the bearer of an infectious dispositions towards an organism of a different particular biological taxon.
alternate name: Pathogen

incident hospitalization count
type: DefinedTerm
description: A count of hospital stays in a population that is the number of hospital stays that occurred during a proper part of a reference temporal interval.
alternate name: Incident Hospitalization

hospital stay dataset
type: DefinedTerm
description: a dataset that is about two or more hospital stays involving two or more patients.
alternate name: Hospitalization

human daily movement data set
type: DefinedTerm
description: a data set that is about the human daily movement behavior of the individual huamns in a given population.
alternate name: Human Movement

software
type: DefinedTerm
description: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
alternate name: Software

viral Infectious disease
type: DefinedTerm
description: Any disease caused by a virus.
alternate name: Viruses Infection

modeling method
type: DefinedTerm
description: The method or type of model used to achieve the purpose.
alternate name: Modeling Method

Population count
type: DefinedTerm
description: A count of simulated or physical individuals in a population.
alternate name: Population Count

scenario analysis
type: DefinedTerm
description: A method that tries to describe logical and internally consistent sequences of events to explore how the future might, could or should evolve from the past and present.
alternate name: Scenario Analysis

disease
type: DefinedTerm
description: A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
alternate name: Disease

modeling
type: DefinedTerm
description: Descriptors of the behavior of an outbreak
alternate name: Modeling

host organism
type: DefinedTerm
description: An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon.
alternate name: Host

health system capacity
type: DefinedTerm
description: Information about capacity, including hospital beds, PPE supplies, nursing home capacity, testing sites, therapeutics, etc.
alternate name: Health System Capacity

modeling purpose
type: DefinedTerm
description: The goal or purpose of a modeling study.
alternate name: Modeling Purpose

English
type: Language

Johns Hopkins University Infectious Disease Dynamics - COVID-19
type: Person
type: Agent

Apache 2.0
type: CreativeWork

GNU GPL v3
type: CreativeWork

National Institute of General Medical Sciences
type: Organization

MIDAS COORDINATION CENTER
type: Organization
location: PostalAddress
  street address: 5607 Baum Blvd
  address locality: Pittsburgh
  address region: PA
  address country: United States of America
  postal code: 15206

A scenario modeling pipeline for COVID-19 emergency planning
type: CreativeWork
description: An article containing the methods and features of the model.
license: CC BY 4.0
type: Entity
property value: DOI
license:
  name: CC BY 4.0
type: Agent

CC BY 4.0
type: CreativeWork

COVID-19 Minimal
type: CreativeWork
description: A minimal repository that contains everything needed to run the COVIDScenarioPipeline on fake data. The wiki contains information on how to get started with the model.
license: GNU GPL v3
type: Entity
property value: URL
license:
  name: GNU GPL v3
type: Agent
license:
  name: GNU GPL v3

R
type: ComputerLanguage
description: R is a programming language and software environment for statistical computing and graphics, widely used among statisticians and data miners.

Python
type: ComputerLanguage
description: Python is a high-level, interpreted programming language known for its readability and broad applicability in web development, data science, and automation.

about-property-structure
type: PropertyValue
description: The 'about' property contains mixed types: DefinedTerm objects represent subject matter/topics, while Place objects represent geographical scope or applicability