Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery

Christopher J. Mungall, Nicole L. Washington, Jeremy Nguyen-Xuan, Christopher Condit, Damian Smedley, Sebastian Köhler, Tudor Groza, Kent Shefchek, Harry Hochheiser, Peter N. Robinson, Suzanna E. Lewis, Melissa Haendel

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites, for the purposes of cohort discovery and variant disease causal validation. This API can be used not only to search for matching patients, but also to match against public disease and model organism data. This public disease data enable matching known diseases and variant-phenotype associations using phenotype semantic similarity algorithms developed by the Monarch Initiative. The model data can provide additional evidence to aid diagnosis, suggest relevant models for disease mechanism and treatment exploration, and identify collaborators across the translational divide. The Monarch Initiative provides an implementation of this API for searching multiple integrated sources of data that contextualize the knowledge about any given patient or patient family into the greater biomedical knowledge landscape. While this corpus of data can aid diagnosis, it is also the beginning of research to improve understanding of rare human diseases.

Original languageEnglish (US)
Pages (from-to)979-984
Number of pages6
JournalHuman Mutation
Volume36
Issue number10
DOIs
StatePublished - Oct 1 2015

Fingerprint

Genetic Association Studies
Databases
Phenotype
Information Storage and Retrieval
Rare Diseases
Semantics
Research

Keywords

  • Informatics
  • Matchmaker Exchange
  • Model systems
  • Ontology
  • Phenotype
  • Rare disease

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Mungall, C. J., Washington, N. L., Nguyen-Xuan, J., Condit, C., Smedley, D., Köhler, S., ... Haendel, M. (2015). Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Human Mutation, 36(10), 979-984. https://doi.org/10.1002/humu.22857

Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. / Mungall, Christopher J.; Washington, Nicole L.; Nguyen-Xuan, Jeremy; Condit, Christopher; Smedley, Damian; Köhler, Sebastian; Groza, Tudor; Shefchek, Kent; Hochheiser, Harry; Robinson, Peter N.; Lewis, Suzanna E.; Haendel, Melissa.

In: Human Mutation, Vol. 36, No. 10, 01.10.2015, p. 979-984.

Research output: Contribution to journalArticle

Mungall, CJ, Washington, NL, Nguyen-Xuan, J, Condit, C, Smedley, D, Köhler, S, Groza, T, Shefchek, K, Hochheiser, H, Robinson, PN, Lewis, SE & Haendel, M 2015, 'Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery', Human Mutation, vol. 36, no. 10, pp. 979-984. https://doi.org/10.1002/humu.22857
Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, Köhler S et al. Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Human Mutation. 2015 Oct 1;36(10):979-984. https://doi.org/10.1002/humu.22857
Mungall, Christopher J. ; Washington, Nicole L. ; Nguyen-Xuan, Jeremy ; Condit, Christopher ; Smedley, Damian ; Köhler, Sebastian ; Groza, Tudor ; Shefchek, Kent ; Hochheiser, Harry ; Robinson, Peter N. ; Lewis, Suzanna E. ; Haendel, Melissa. / Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. In: Human Mutation. 2015 ; Vol. 36, No. 10. pp. 979-984.
@article{69ce9cbb589b451d84539f6e6bdbc631,
title = "Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery",
abstract = "The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites, for the purposes of cohort discovery and variant disease causal validation. This API can be used not only to search for matching patients, but also to match against public disease and model organism data. This public disease data enable matching known diseases and variant-phenotype associations using phenotype semantic similarity algorithms developed by the Monarch Initiative. The model data can provide additional evidence to aid diagnosis, suggest relevant models for disease mechanism and treatment exploration, and identify collaborators across the translational divide. The Monarch Initiative provides an implementation of this API for searching multiple integrated sources of data that contextualize the knowledge about any given patient or patient family into the greater biomedical knowledge landscape. While this corpus of data can aid diagnosis, it is also the beginning of research to improve understanding of rare human diseases.",
keywords = "Informatics, Matchmaker Exchange, Model systems, Ontology, Phenotype, Rare disease",
author = "Mungall, {Christopher J.} and Washington, {Nicole L.} and Jeremy Nguyen-Xuan and Christopher Condit and Damian Smedley and Sebastian K{\"o}hler and Tudor Groza and Kent Shefchek and Harry Hochheiser and Robinson, {Peter N.} and Lewis, {Suzanna E.} and Melissa Haendel",
year = "2015",
month = "10",
day = "1",
doi = "10.1002/humu.22857",
language = "English (US)",
volume = "36",
pages = "979--984",
journal = "Human Mutation",
issn = "1059-7794",
publisher = "Wiley-Liss Inc.",
number = "10",

}

TY - JOUR

T1 - Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery

AU - Mungall, Christopher J.

AU - Washington, Nicole L.

AU - Nguyen-Xuan, Jeremy

AU - Condit, Christopher

AU - Smedley, Damian

AU - Köhler, Sebastian

AU - Groza, Tudor

AU - Shefchek, Kent

AU - Hochheiser, Harry

AU - Robinson, Peter N.

AU - Lewis, Suzanna E.

AU - Haendel, Melissa

PY - 2015/10/1

Y1 - 2015/10/1

N2 - The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites, for the purposes of cohort discovery and variant disease causal validation. This API can be used not only to search for matching patients, but also to match against public disease and model organism data. This public disease data enable matching known diseases and variant-phenotype associations using phenotype semantic similarity algorithms developed by the Monarch Initiative. The model data can provide additional evidence to aid diagnosis, suggest relevant models for disease mechanism and treatment exploration, and identify collaborators across the translational divide. The Monarch Initiative provides an implementation of this API for searching multiple integrated sources of data that contextualize the knowledge about any given patient or patient family into the greater biomedical knowledge landscape. While this corpus of data can aid diagnosis, it is also the beginning of research to improve understanding of rare human diseases.

AB - The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites, for the purposes of cohort discovery and variant disease causal validation. This API can be used not only to search for matching patients, but also to match against public disease and model organism data. This public disease data enable matching known diseases and variant-phenotype associations using phenotype semantic similarity algorithms developed by the Monarch Initiative. The model data can provide additional evidence to aid diagnosis, suggest relevant models for disease mechanism and treatment exploration, and identify collaborators across the translational divide. The Monarch Initiative provides an implementation of this API for searching multiple integrated sources of data that contextualize the knowledge about any given patient or patient family into the greater biomedical knowledge landscape. While this corpus of data can aid diagnosis, it is also the beginning of research to improve understanding of rare human diseases.

KW - Informatics

KW - Matchmaker Exchange

KW - Model systems

KW - Ontology

KW - Phenotype

KW - Rare disease

UR - http://www.scopus.com/inward/record.url?scp=84941880519&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84941880519&partnerID=8YFLogxK

U2 - 10.1002/humu.22857

DO - 10.1002/humu.22857

M3 - Article

VL - 36

SP - 979

EP - 984

JO - Human Mutation

JF - Human Mutation

SN - 1059-7794

IS - 10

ER -