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Showing posts from 2015

Save the Date: Symposium on Linking Disease Model Phenotypes to Human Conditions

Monarch is co-hosting a NIH Symposium titled “Linking Disease Model Phenotypes to Human Conditions” on September 10-11, 2015 at the Fishers Lane Auditorium, NIH, Rockville, MD. 
The purpose of the meeting is to convene a colloquium on the current status of Phenomics and its role in closing the gap that exists between biomedical research and clinical medical practice. The wealth of whole organism, cellular, and molecular data generated in the research laboratory must be translated into clinically relevant knowledge that enables the physician to make the best possible treatment decisions. Phenomics is gaining momentum due to the availability of the complete genomes for many organisms as well as higher throughput methods to genetically modify model organism genomes and observe and record phenotypes. Disease models comprise some of the most important tools of biomedical research. The efficacy of the use of disease models is based upon the principles of evolutionary conservation between sp…

Why the Human Phenotype Ontology?

We've often been asked, why should we use the Human Phenotype Ontology to describe patient phenotypes, rather than a more widely-used clinical vocabulary such as ICD or SNOMED? Here are the answers to some of these frequently asked questions:

1. We should use what other big NIH projects, like ClinVar, are using.

ClinVar is using HPO terms to describe phenotypes. This is done in collaboration with MedGen, which has imported HPO terms. Here is an example:

There are now many bioinformatics tools that use the HPO to empower exome diagnostics. The Monarch team has published two of these recently

1) Exomiser (Robinson et al., 2014 Genome Res.) => For discovering new disease genes via model organism data, several successful use cases at UDP and elsewhere

2) PhenIX (Zemojtel et al., 2014 Science Translational Medicine) => For clinical diagnostics of “difficult” cases. This paper was on Russ Altman's year in review at AMIA this year.

Also, a num…

What NLM should think about

Monarch replied to the 2015 Request for Information  “Soliciting Input into the Deliberations of the Advisory Committee to the NIH Director (ACD) Working Group on the National Library of Medicine (NLM)”. The RFI sought input regarding the strategic vision for the NLM to ensure that it remains an international leader in biomedical data and health information. 
Below are the Monarch consortium's thoughts. Our comments are primarily informed by our work on the development of information resources in support of translational biomedical informatics.
Dr. Melissa Haendel Dr. Peter Robinson Dr. Chris Mungall Dr. Harry Hochheiser Dr. David Eichmann Dr. Michel Dumontier

Training The Biomedical Informatics Research Training Program is perhaps the single most valuable contribution to the research community, providing considerable value to all of the NLM’s constituencies. At a time when informatics positions are going unfilled and demand is expected to continue to grow, the NLM funded training…

How to annotate a patient's phenotypic profile

How to annotate a patient's phenotypic profile using PhenoTips and the Human Phenotype Ontology PurposeWe have observed that performance of computational search algorithms within and across species improves if a comprehensive list of phenotypic features is recorded. It is helpful if the person annotating thinks of the set of annotations as a query against all known phenotype profiles. Therefore, the set of phenotypes chosen for the annotation must be as specific as possible, and represent the most salient and important observable phenotypes. Towards this end, Monarch has been asked to provide guidance on how to create a quality patient profile using the Human Phenotype Ontology (HPO). Below we detail our annotation guidelines for use in the PhenoTips application, our partner organization. 

The guidelines can also be considered more generically so as to be applicable to any annotation effort using HPO or even using other phenotype ontologies. The annotations should be limited to th…