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Cell lines are key experimental models to understand protein interactions and signaling pathways. With a large pool of such data coming from different cell lines of different origin -of normal and -pathological tissues, proper analysis requires segregating data pertaining to specific cell lines. The project envisaged brings together hierarchical trees of organs, mammalian cell lines and diseases in one platform. Certain specific terms from Cell Type (CL) ontology, Foundational Model of Anatomy (FMA) and DOID ontologies are mapped for searchability. Ontology is developed in both OBO and OWL.

Arathi Raghunath, Bharat Bhat, Jignesh Bhate, Usha Mahadevan

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

An open source ISA software suite and an extensible hierarchical data structure implemented by a growing number of international public resources. It caters to data as diverse as stem cell, toxicogenomics, environmental gene surveys, microbial diversity studies, and a variety of metabolomics and metagenomics-based studies. But it maintains cross-domain compatibility in the way the experimental context is described.

International collaborative effort

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.

ImmPort, the Immunology Database and Analysis Portal, is a one stop shop to access reference and experiment data for immunologists. ImmPort provides advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT.

Richard H. Scheuermann, et al.

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

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

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 BioAssay Ontology (BAO) is an NIH-funded project to develop standard terminologies and a formal, extensible, knowledge-based description of biological assays and assay data (the ontology). Biocuration is a component of the BAO project to systematically annotate biological assays such as those in PubChem with standardized terminology describing assay concepts defined in the ontology. The BAO project also develops software tools to query and explore data sets in the context of the ontology.

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