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 experiment...

How to annotate a patient's phenotypic profile using PhenoTips and the Human Phenotype Ontology Purpose We 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 b...

We have added phenotype data from the International Mouse Phenotyping Consortium , who's goal is to discover functional insight for every mouse gene by generating and systematically phenotyping knockout mouse strains. This initially includes 890 mice affecting 763 genes with 222 unique phenotypes. IMPC data will be updated approximately monthly. IMPC data is presently accessible in the Monarch portal via Mouse gene pages (for example, Stk16 , Gpr107 , or Gpr22 ), or via phenotypic similarity comparison on disease pages (such as Sebastian Syndrome or Susceptibility to Malignant Hyperthermia 3 ). You can read more about our data sources here .

We have added ClinVar variant-disease associations into our database and first released into the Monarch Initiative portal in November, 2014. This new data accompanies previously incorporated ClinVar gene-disease associations (without the specificity of the variations). This initially includes 113,543 SNP, SNV, CNV (and other major rearrangements), linked to 13,591 genes and 11,154 diseases and phenotypes. The associations are also coupled to the original submitters and publications where the variations are reported. The data will be updated approximately monthly. You can read more about our data sources here .