The human phenotype ontology (HPO) intends to offer a tool that will allow large-scale computational analysis of the human phenome. The HPO currently contains over 9500 terms, each of which describes an individual phenotypic anomaly. The terms are arranged in a directed acyclic graph and are connected by “is-a” edges, such that a term represents a more specific or limited instance of its parent term(s). All relationships in the HPO are is_a relationships, i.e. a simple class-subclass relationships. For instance, Abnormality of the feet is_a Abnormality of the lower limbs. The relationships are transitive, meaning that they are inherited up all paths to the root. Organ abnormality is the main subontology of the HPO and contains descriptions of clinical abnormalities. Additional subontologies are provided to describe inheritance patterns and onset/clinical course.

The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts.

NCBO

High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal.

Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz

The aim of the SKELETOME project is to develop a community-driven, ontology-based knowledge curation platform for the skeletal dysplasia domain.

Tudor Groza

Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta’s in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Dr. Paul Pavlidis

Gemma is a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize coexpression and differential expression results.

Dr. Paul Pavlidis

PID phenomer is a web-based integrated platform for collection, mapping, storage and visualization of observed phenotypic terms for primary immunodeficiency diseases (PIDs). It presents controlled vocabulary of ontology class structures and entities in downloadable formats such as Web Ontology Language (OWL) and Resource Description Framework (RDF) that facilitate global sharing and free exchange of PID data among other users' communities.

RCAI Immunoinformatics Research Unit

OntoMaton is a google spreadsheet application allowing for ontology search and tagging directly within google spreadsheets. More information can be found here: https://github.com/ISA-tools/OntoMaton

ISA team

The advent of genome-wide profiling technologies and their routine use in basic science and translational research is now promoting their application in the clinical setting. However, there are several potent informatics barriers that must be overcome before clinical sequencing can become routine. Good Laboratory Practice-based quality assurance metrics must be established to guarantee the accuracy required to make medical decisions. Genetic variants identified by sequencing must be systematically annotated and interpreted so that a clinical genomicist can decide which are medically actionable. Software applications and technologies are required to facilitate reporting of genomic results and to transmit these data to the electronic health record (EHR)

The International Fanconi Anemia Registry (IFAR) was started in 1982 at The Rockefeller University by Dr. Arleen Auerbach. The purpose of the IFAR is to study the nature, diagnosis, and treatment of individuals with Fanconi anemia (FA). The IFAR group is creating an ontology-driven application for data entry and analysis. This will enable more standardized and advanced genotyping and phenotyping which will also allow us to assess any correlations between the two.

Erica Sanborn, Agata Smogorzewska, Arleen Auerbach, Francis Lach, Edward Barbour, Shamim Mollah, Sajin Balakrishnan, Ummey Johra

A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

NCBO

The Epidemic Marketplace is a data integration platform where epidemiological data and related resources are stored, managed and made available, fostering collaboration.