To continue advancing towards our goals of improving patient health via integrated genomic and phenotypic data, the Monarch Initiative has begun two new, exciting collaborations. Dr. David Osumi-Sutherland and Dr. Helen Parkinson, Head of Molecular Archival Resources at EMBL-EBI, are delighted to announce the beginning of a new collaboration between the EBI and the Monarch Initiative. This collaboration will focus on integration of systematic phenotyping data from model organisms and biosamples, improvement of patient diagnosis using more deeply integrated model data, and improved rigor of semantic data integration for invertebrates, neural connectivity data, behavior, and molecular phenotypes. The Monarch team has collaborated with Drs. Parkinson and Osumi-Sutherland over many years on a variety of projects such as the International Mouse Phenotyping Consortium and the Global Alliance for Genomics and Health , and we are very excited to have funding from the NIH Office of the D

Check out our recent guest blog for eLife Labs: Connecting Biomedical Knowledge through the Monarch Initiative  https://elifesciences.org/labs/ca82fe43/connecting-biomedical-knowledge-through-the-the-monarch-initiative

There are approximately 30 million Americans living with a rare disease, and only about 5% of those diseases have a known treatment. To better understand rare diseases and conditions and to support the diagnosis of patients, the NIH Undiagnosed Diseases Program (UDP) was created in 2008. The UDP has worked with over 700 patients, of which, about 40% are children. Of these patients, between 25-50% of cases now have a diagnosis, although time to diagnosis has varied from one week to four years [1] . These numbers are lower for patients outside of the UDP: time to diagnosis is 4.8 years on average but can take up to 20 years [2] . Historically, the UDP has selectively accepted only about 100 new patients a year, focusing on the hardest-to-diagnose patients, with the goal of diagnosing and treating these patients to improve their livelihood. A recent article [3] by Boerkoel et al., co-written by several members of the Monarch Initiative , describes recent advances made at the NIH

Several members of the Monarch Initiative convened upon sunny Palo Alto, CA for the International Society for Biocuration (ISB) annual meeting . The meeting, held at Stanford University from March 26-29, 2017, brought together experts in the field of biocuration and included presentations, posters, and workshops on the topics of curating biological data, database creation and maintenance, community annotation, and education. Between brief, but glorious, moments of sun soaking (reminder: several of us are from rainy Portland), we enjoyed meeting our fellow biocurators and presenting talks and posters. Here’s a brief overview of the presentations from four Monarch team members, including links to the slides and posters in case you missed them! Melissa Haendel, Monarch co-PI, presented a talk titled “How Open is Open?” discussing the open science principles of FAIR TLC. Here, FAIR TLC stands for making data: Findable, Accessible, Interoperable, Reusable, Traceable, Licensed, and C

At the end of February, the global members of the Monarch Initiative convened at the Jackson Laboratory in Farmington, Connecticut for our annual All-Hands Meeting. This collaborative meeting allowed us to set goals for 2017, have hands-on working time for various projects, bond over an epic Hibachi meal, and compete in giant Jenga. Since the Monarch team works around the globe, the All-Hands Meeting was a unique chance for everyone to gather in the same room. As a new member to the team, I particularly enjoyed meeting the rest of my coworkers in person - instead of over video chat! The meeting was a big success, yet it ended on a dramatic note when several of our flights were canceled, resulting in three-hour-long taxi rides and an impromptu trip to Waffle House. In this post I will mention some of the highlights from the meeting as well as the goals we discussed for the upcoming year and how these goals fit into three main themes: ontologies, tools, and collaborations.  

To celebrate Open Data Day 2017 , I want to highlight one of the Monarch Initiative ’s innovative data sharing tools: the PhenoPacket . At Monarch we playfully refer to the PhenoPacket concept as a “bag of phenotypes” to describe patients. If you aren’t a researcher or clinician, you are probably wondering what a “phenotype” is. A phenotype can be simply defined as the patient signs and symptoms associated with a disease, or more technically defined as the physical manifestation of the combined effects of a person’s genes and their environment. PhenoPackets are a novel way to systematically organize and share the data associated with a patient’s phenotypes. Currently, data about a patient’s phenotypes is collected by doctors and researchers and can be found in publications, databases, electronic health records, clinical trials, and even social media. This wide variation in data creation leads to diverse data that is not standardized or in a central location, so it is very difficult