Ontologies provide a common platform of controlled vocabulary for researchers who need to share information across a particular domain, inclusive of machine-interpretable definitions of basic concepts in the domain and relations among them. The need for ontologies that provide a systematic arrangement of available data and allow cross talk across various related domains is gaining momentum. In this backdrop, we have developed a comprehensive ontology on primary and established cell lines-both normal and pathologic. It covers around 400 cell lines. This ontology has been built to include the major domains in the field of biology like anatomy, bio-molecules, chemicals and drugs, pathological conditions and genetic variations around the cell lines. An extensive network of relations has been built across these concepts to enable different combination of queries. The ontology covers all cell lines from major sources like ATCC, DSMZ, ECACC, ICLC etc. and is built in OWL format.

Usha Mahadevan

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

The Plant Ontology is a controlled vocabulary (ontology) that describes plant anatomical and morphological structures and growth and developmental stages for all plants. The goal of the PO is to establish a semantic framework for meaningful cross-species queries across gene expression and phenotype datasets from plant genomics and genetics experiments.

A web-based environment that discovers ontological structure from empirical data.

Elissa Chesler, Erich Baker, Michael Langston, Jeremy Jay

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

Medical annotator & dictionary

The eagle-i project is building a searchable network of research resources at research institutions nationwide. We are developing an application ontology for indexing and querying, and this effort is being guided by discussions within the ontology community aimed at promoting interoperability. We will be inventorying laboratories, services, instruments, services, reagents, organisms, persons, protocols, human studies (metadata), tissue/biological sample repositories and training opportunities. The eagle-i application ontology is being used to drive our data tool and search applications, and is available in beta form from google code: http://code.google.com/p/eagle-i/

Melissa Haendel, Carlo Torniai

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

Chemical biology resource providing biological activities of small molecules and substances.

The Drug Interaction Knowledge Base (DIKB) is a clinically-oriented, evidence-based, knowledge base designed to support pharmacoepidemiology and clinical decision support. The DIKB contains quantitative and qualitative assertions about drug mechanisms and pharmacokinetic drug-drug interactions for over 90 drugs; primarily psychotropics and HMG-CoA reductase inhibitors (statins).

Richard D Boyce

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

Kino is an integrated suite of tools that enables scientists to annotate biological related web-based documents. It can annotate documents by accessing NCBO ontologies. Kino consists of an NCBO integrated front-end that allows the convenient annotation and submission of web documents through a browser plug in, and an annotation aware back-end, capable of providing faceted search capabilities. These annotations have a variety of uses, ranging from extended search capabilities to advanced data mining. Annotated documents are indexed using a faceted indexing and search engine that provides fine-grained search capabilities to the scientists. Thus, Kino is a comprehensive architecture for annotating and indexing Biological oriented documents that should be of great use for the biological and biomedical community.

Amit Sheth, Ajith Ranabahu, Maryam Panahiazar