The Ontology for Biomedical Investigations

Abstract

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

Fig 1. Partial high-level structure of OBI classes.

OBI classes are shown in blue. Classes imported from BFO, IAO and other external ontologies are shown in orange, purple and dark red, respectively. Some example subclasses, such as device and processed specimen are included to illustrate the use of the class processed material.

Fig 2. Measuring glucose concentration in blood.

The large boxes represent instances of processes and their participants. The collecting specimen from organism process takes place first. In this process, a syringe is used to draw blood from the mouse. At the end of this process a tube contains the blood specimen. In a second process, this specimen is used in an analyte assay, which measures the concentration of glucose in the blood. A glucometer is used to make this measurement. The analyte role inheres in the glucose molecules scattered throughout the blood specimen. This planned process achieves the analyte measurement objective.

Fig 3. T cell epitope assays in the IEDB and OBI.

The left hand panel illustrates how an IEDB user can select from different T cell epitope characterization assays in the IEDB. The labels utilized are shorthand which in the context of the assay tree in the IEDB is sufficient for an immunologist user to understand what assays are being denoted. Each assay in the IEDB refers to a formal definition in OBI (right hand panel). While the IEDB only captures with assays in which epitope specific proliferation is measured, the type of assay utilized (in this example thymidine incorporation) is applied in many other studies and is more likely to be re-usable.

Fig 4. Ontology-based representation of phenotype data.

The genetically modified parasite, a genetically modified organism, is generated by a genetic transformation process (top section). Assays are performed to examine the genetically modified parasite for the cellular component the gene product is located in, effects on its molecular function, or the biological process it participates in during a specific lifecycle stage (bottom section). The representation is at the instance levels, i.e. not all assays will have the specified inputs and outputs. The class mentions are to indicate what is being instantiated. Ontology terms are indicated by using ontology name abbreviations as prefix. Relations are italicized. The data collected in the submission form are in bold font. Fields requiring ontology terms are in thick border box.

Fig 5

Panel (a) shows the assay selection panel in ISAcreator (editor and curation tool) which uses OBI terms. Panel (b) shows ISA ‘Protocol REF’ elements, which are annotated with subclasses of ‘OBI:planned process’. Panel (c) shows a glyph-based representation of the underlying mapping of ISA syntax element into OBI framework: circles correspond to Material or Data, which are ‘specified_input_of’ some ‘OBI:planned process’ either ‘OBI:material transformation’ or ‘OBI:data transformation’. The graph matches by the underlying RDF representation.