Models and Other Software

Data

Data Formats

Websites with data

AE Apollo-Encoded
SSO Requires (Single) Sign On
UIDS Available via the Universal Interface to Disease Simulators

About

The primary purpose of the MIDAS Digital Commons (MDC) is to support infectious disease epidemiologists who are developing computational models of biological phenomena. The scope of the MDC is primarily defined by the past and present research of the MIDAS research network as reflected in its 1000+ publications (listed and linked to in reverse chronologic order here).

At present, the MDC consists of (1) a collection of digital objects in the domain of infectious disease epidemiology (2) a compute platform for running experiments, and (3) a search function that makes the digital objects findable.

The digital objects include software, datasets, and data formats.

We intend that all digital objects conform to FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. To make datasets interoperable, we represent them whenever possible in Apollo-XSD syntax and label them as being AE (Apollo-Encoded) in the MDC.

Standard Identifiers

The MDC encourages the use of the following standard identifier systems when representing data and metadata:
  • Apollo Location Codes (for locations) SSO - Locations for specific time intervals, including intervals that start in the past and are still open at present (i.e., the identifier should be used to refer to the location today.
  • LOINC codes (for lab tests) - Applies universal code names and identifiers to medical terminology related to electronic health records.
  • NCBI Taxon identifiers (for host and pathogen taxa) - A curated classification and nomenclature for all of the organisms in the public sequence databases.
  • RxNorm codes (for drugs) - A standardized nomenclature for clinical drugs, is produced by the National Library of Medicine
  • SNOMED CT codes (for diagnoses) - A systematically organized computer processable collection of medical terms providing codes, terms, synonyms and definitions used in clinical documentation and reporting.
  • Vaccine Ontology identifiers (for vaccines) - describes the detailed classification and definitions of vaccine components and vaccine administration processes.

FAIR-o-meter

We track conformance to FAIR guidelines here.

Ontology

The Apollo-SV ontology represents our conceptualization of infectious disease epidemiology. You can find it here.

Web service

A programmatic interface to the MIDAS Digital Commons is available in the form of a RESTful Web service. The webservice conforms to the Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH), which enables users to harvest data from the Digital Commons in order to build value-added services. The MDC Web service is documented using the Swagger software library which describes the endpoint URLs, HTTP methods, required parameters, optional parameters, response syntaxes and input forms to test the API directly from a web browser. The Web service documentation is available here.

Submission Guidelines

If you have any digital objects that you'd like to submit to the commons, please contact Mike Wagner via email at mmw1@pitt.edu.

Funding

The MIDAS Digital Commons is funded by the National Institutes of Health (NIGMS) program for Models of Infectious Disease Agent Study (MIDAS) grant U24GM110707.

Disclaimer

By using the MIDAS Digital Commons you agree that no warranties of any kind are made by the University of Pittsburgh (University) with respect to the data provided in the MIDAS Digital Commons or any use thereof, and the University hereby disclaim the implied warranties of merchantability, fitness for a particular purpose and non-infringement. The University shall not be liable for any claims, losses or damages of any kind arising from the data provided in the MIDAS Digital Commons or any use thereof.

Please direct comments and questions to our development team.