Tools, Data & Databases

The AMP-AD Knowledge Portal is a platform to access data, analytical results and tools generated within the National Institute of Aging’s AD Translational Research Program. All projects within this program operate as an open science collaboration and openly share resources early in the research life cycle for evaluation and reuse. The Portal is named for the first consortium to be initiated, the Accelerating Medicines Partnership in Alzheimer’s Disease Target Discovery and Preclinical Validation Project (AMP-AD). The majority of the content in the Portal is genomic data generated from human samples or experimental model systems, including the MODEL-AD Consortium. In addition to this, the Portal also contains bioinformatic analytical results including some generated by teams within individual projects and some generated through multi-team working groups. Bioinformaticians can download these resources for use in their own research. You will need a Synapse account to access the data in the AMP AD Knowledge Portal. The AMP-AD Knowledge Portal is funded by the National Institute on Aging. It is developed and maintained by Sage Bionetworks.

Full description: Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression

GeneWeaver is a database and suite of tools for the discovery of convergent relations among heterogeneous functional genomics studies of biological processes and disease related functions. It consists of a collection of integrated micro-services for the aggregation and integration of multi-species functional genomics data from curated resources, published experiments and aggregated evidence from genomic data resources. Its analysis services are built on statistical scalable combinatorial algorithms to allow users to develop custom workflows to perform set operations to compare and contrast diverse data sets. The system is accessed either through a user-friendly browser interface or an API. All analyses are repeatable on the original instance of user-selected data. A curation interface allows users to manage the storage of gene sets from literature and to perform annotation of gene sets to controlled vocabularies and ontologies.

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO currently contains over 13,000 terms and over 156,000 annotations to hereditary diseases. The HPO project and others have developed software for phenotype-driven differential diagnostics, genomic diagnostics, and translational research. The HPO is a flagship product of the Monarch Initiative, an NIH-supported international consortium dedicated to semantic integration of biomedical and model organism data with the ultimate goal of improving biomedical research. The HPO, as a part of the Monarch Initiative, is a central component of one of the 13 driver projects in the Global Alliance for Genomics and Health (GA4GH) strategic roadmap.

Image Echelon is a tool to quantify images where meaningful differences are discernible by eye, but difficult to quantify using traditional methods. It was developed to quantify neuronal fasciculation in microscopy images, but can be used to rank images based on any qualitative criteria. Classical methods ask observers to score an image in isolation along a scale (e.g., 1-5), which can be difficult to control between observers, especially in a highly variable data set. Image Echelon asks observers to compare two images and pick a “winner” and a “loser” along some criteria, an easier and more reliable task.

The International Mouse Strain Resource (IMSR) provides an online searchable web-based catalog of mouse resources available globally, including inbred, mutant, and genetically engineered mice, cryopreserved embryos and gametes, and ES cell lines. The IMSR website provides, for each strain or cell line, links for ordering, links to the repositories’ strain description, and links to phenotype and disease model data at Mouse Genome Informatics (MGI). Searches can be performed using one or many parameters, including the strain/stock designation, the strain repository or MGI ID, the state in which the strain/resource is maintained and the strain type. Genetic search parameters include the symbol or name of the phenotypic allele or gene of interest carried in the strain, and repository parameters include the name of one or more specific repositories, or the selection of all repositories in a geographical regional location.

The Mouse Genome Database (MGD) is the international community mouse database which supports basic, translational and computational research by providing integrated data on the genetics, genomics, and biology of the laboratory mouse. MGD serves as the source for biological reference data sets related to mouse genes, gene functions, phenotypes and disease models with an increasing emphasis on the association of these data to human biology and disease. MGD is the authoritative source of mouse gene and strain nomenclature as well as annotations for mouse gene function, phenotypes and human disease models.

We developed the Mouse Mutant Resource Database (https://mmrdb.jax.org) to host annotated variant calls and sample metadata and to facilitate data sorting, filtering, querying, and sharing. The database employs an algorithm for variant prioritization. The algorithm makes the following assumptions about causative variants: they will be rare (<3%) in the database, the allele ratio of the variant in the sample will fall within expectations for the sample genotype (>0.9 homozygous; 0.2–0.8 heterozygous), and the chromosomal position of the variant will be in agreement with chromosomal linkage data. We optimized the algorithm iteratively by reanalyzing exome data sets with previously confirmed, known mutations.

MouseMine is a powerful data warehouse providing comprehensive API (application programming interface) access to MGI data, as well as a forms-based user interface. MouseMine contains core data from MGI, including the mouse genome feature and allele catalogs, disease and phenotype annotations, expression data, publications, etc. Users can select from predefined query templates or construct custom queries and reports, iteratively refine searches, and save/reuse lists of results.

QTL Viewer is an interactive web-based analysis tool that will allow users to replicate the analyses reported for a study (For example the viewer at http://churchill-lab.jax.org/qtl/islet/DO378 represents the data published in the paper Keller, et al. Genetic Drivers of Pancreatic Islet Function, PMID 29567659). It includes the ability to search various subsets of data from a study such as phenotypes or expression data and then visualize data with profile, correlation, LOD, effect, mediation and SNP association plots.

SARNAclust is the first unsupervised method to identify and deconvolve multiple RNA sequence/structure motifs simultaneously. SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism. For full details see: https://doi.org/10.1371/journal.pcbi.1006078 Dotu I, Adamson SI, Coleman B, Fournier C, Ricart-Altimiras E, Eyras E, et al. (2018) SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data. PLoS Comput Biol 14(3): e1006078.