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 .

As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest, such as: genes genotypes gene variants (including SNPs, SNVs, QTLs, CNVs, and other rearrangements big and small) models (including cell lines, animal strains, species, breeds, as well as targeted mutants) pathways orthologs phenotypes publications We import data from a variety of data sources in formats including databases, spreadsheets, delimited text files, XML, JSON, and Web APIs, on a monthly schedule, which is placed into a Postgres database (hosted by the NIF ). Our curation team semantically maps each resource into our data model, primarily using ontologies . This involves both typing relevant columns, mappings between columns (such as be...

Last week, I had the pleasure of teaching at the National Centre for Rare Diseases hosted by the Istituto Superiore di Sanità and Dr. Domenica Taruscio. This rare disease registry course is in its second year, and is focused on exposing the maintainers of rare disease registries various aspects of registry planning and management. I was very impressed with the specific way in which this course was run. The week started with a discussion of the different types of registries (aims, study design, data sources), management sustainability, and clinical outcomes analysis. This was followed by an innovative collaborative learning exercise in the afternoon, where the participants were broken up into three groups. The collaborative learning focused on positive interdependence, individual accountability, face-to-face interaction, group processing and exercise of small-group interpersonal skills - all skills needed to realize a quality registry resource in addition to simply being a quality ...

We'll be heading to American Society for Human Genetics 2014 conference in San Diego, October 18-22. Please check out our work in the following sessions: 170. PhenomeCentral: An integrated portal for sharing patient phenotype and genotype data for rare genetic disorders. Mon Oct 20 5:30p. Concurrent Platform Session C: From Bytes To Phenotypes. Hall B1, Ground Level, Convention Center Michael Brudno will present the new data sharing portal PhenomeCentral , which facilitates the identification of phenotypically similar patients, utilizing the Human Phenotype Ontology (HPO) for linking patient phenotypes. Monarch contributes the API for the Annotation Sufficiency metric, actively develops on the HPO, and has provided user testing and documentation. Cases from our work with the NIH Intramural Undiagnosed Disease Program (UDP) have been deposited into PhenomeCentral. 1499T. Standardized phenotyping enables rapid and accurate prioritization of disease-associated and previou...

This week Monarch team members co-chaired and attended a National Institutes of Environmental Health Science (NIEHS) workshop on Development of a Framework for an Environmental Health Science Language ( agenda & report ). From Love Canal to Chernobyl, from the Clean Water Act to pending regulation of dietary supplements, what we breathe and what we eat is known to contribute to human health outcomes. Consistent capture, transmission, and analysis of these data for comprehensive use in multiple research and clinical environments depends upon standardization and integration of the data across multiple disciplines. Because we need to compare phenotypes based upon both genotypes and environmental variables over time, Monarch is very interested in understanding ways to represent and integrate these data. We currently have a great diversity of model and human environmental data: reagents targeting specific gene products, physiological perturbations such as exposure to light, drug tre...