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Showing posts from 2017

Two new collaborations

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 Director…

eLife Labs guest blog

Check out our recent guest blog for eLife Labs: Connecting Biomedical Knowledge through the Monarch Initiative

Redefining disease: an update from the NIH Undiagnosed Disease Program

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 UDP. The artic…

Biocuration 2017 Conference Highlights

Several members of the Monarch Initiative convened upon sunny Palo Alto, CA for theInternational 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 Connected. …

Meeting of the Minds: Monarch All Hands Meeting 2017

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. A hallmark of t…

Open Data Day spotlight on PhenoPackets

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 to see…

Rare Disease Day 2017

Diagnosing diseases is a tricky business requiring a formidable breadth and depth of knowledge and the skill to apply that knowledge. Patient diagnosis becomes even more difficult for rare diseases: quality reference data may not exist and a physician might only see one such patient in her entire career. According to the National Institutes of Health, there are between 6,000 and 7,000 rare diseases affecting from 25 to 30 million Americans, making it likely that most, if not all, health care professionals have seen these patients in their practice but may not have known it. Oftentimes, a patient with a rare disease gets misdiagnosed as having a more common disease with a similar set of symptoms. In such cases, the misdiagnosis can lead to ineffective, or even harmful treatment; this is a danger even for patients who have rarer forms of a common disease.

Next Tuesday is Rare Disease Day, a day devoted to raising awareness of rare diseases, learning from the patients and families living…

What's in a (gene) name? That which we call a gene by any other name would confuse a researcher

If you had told me that I would spend my PhD years studying a gene called Falafel, I probably would not have believed you. Yet, that is exactly what happened to me (I was also briefly studying a gene called Bazooka). When working with fruit flies, researchers often come up with entertaining names for newly discovered genes; however, these same genes in mammals can be quite different. For instance, Falafel is called PP4r3 in humans. This discrepancy in gene names (also called gene symbols) can be confusing, and part of the Monarch mission is to ease cross-talk between interspecies genotype data. As a researcher, it can be hard to remember what a gene is called in different species, and this problem becomes more difficult if a gene name is changed. Thankfully, gene names are infrequently changed, and there are groups committed to ensuring that gene names are systematic and regulated. Recently, however, I was prompted to think of alternative names for MARCH7, a gene discovered by Monarc…

Request for feedback: help us improve our tools!

Hello, all!
Greetings from your new Monarch blogger! I’m Lilly, and I will be taking over this blog space to keep you updated about exciting developments being done at the Monarch Initiative. I recently completed my PhD in neuroscience from Oregon Health & Science University, and I am very excited to work with the Monarch team to further study the relationships between genes, phenotypes, and diseases.
During my PhD, I studied how the brain’s innate immune system responds after an injury. Interesting fact: our brain’s immune system is separated from the rest of our body by the blood brain barrier. While white blood cells (leukocytes) patrol our bodies for disease and foreign objects, glial cells defend the brain. Glial cells also have various other functions, including creating myelin (insulation for neurons), and glial cell malfunction can lead to numerous diseases, such as Multiple Sclerosis.
I researched how glial cells react to brain injury by performing experiments with the mod…