Ontology
- Why cell line ontology?
- Concepts and ontology details
- Mapping to other sources
- Search ability
- Access to ontology
- Developers
Databases provide a large source for information and filtering of data available into manageable clusters of specific requirements constitute an important part of efficient data analysis. A standardized ontology which can talk across different databases with different identifiers and help in retrieving relevant data is a genuine requirement for the scientific community. Also, selecting an appropriate study model for any given experiment is a challenging task. 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, a repository which allows one to cluster all cell lines with a specific set of properties is a major requirement. This ontology brings together hierarchical nodes of organs, cell lines and diseases in one platform, thus enabling ontology based navigation of cell lines.
The ontology is developed in OBO format using Obo edit version2.0 beta55. There are four major classes in the ontology, the four major attributes of a cell line one would want to query with-species, tissue of origin, disease association and the cell line name. Care is taken to fill all synonyms for a given cell line and will be regularly updated. Conscious effort is made to map the terms wherever possible to already existing ontologies in OBO foundry. The emphasis is to maintain a standard ontology that can cross talk with an existing ontology so that integration becomes easier and cross talk across databases possible.
To allow interoperability across ontologies/sources, for species ontology, NCBI taxonomy is referred for species, for tissues, anatomical entity of FMA ontology (Rosse C, Mejino JVL. 2003. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 36:478-500.) and for disease associations DOID ontology (http://bioportal.bioontology.org/ontologies/39857); both of these ontologies are in OBO foundry.
The “Cell type” ontology (http://bioportal.bioontology.org/ontologies/39004) in OBO foundry has an option for cell lines in experimentally modified cells that is yet to be updated. The present cell line ontology can be considered as an extension to the “Cell type” ontology.
The ontology is developed keeping in mind the search requirements. The ontology can be easily searched for the disease associations, tissues of origin and species of cell lines using the freely available OBO edit version2.0 beta55 tool. It is recommended that the version2.0 of OBO edit is used for best results.
Version 1.0 includes around 500 commonly used mammalian, bird and insect cell lines from sources like ATCC, HyperCLDB, PubMed etc. We intend to update this ontology regularly and include more features that would enable query for other features of cell lines like transgenic cell lines, embryonic cell lines, unique protein expressions, etc.
The ontology can be downloaded free (preferably opened with OBO edit tool to view hierarchies) at: http://bioportal.bioontology.org/ontologies/39927
The ontology was developed by Molecular Connections Pvt. Ltd., a Bioinformatics company doing business in the field of text mining for the past 10 years, established leaders in this field from India.
For any clarifications/comments on the ontology or for any collaboration please contact-
Dr. Usha Mahadevan; usha@molecularconnections.com
Dr. Arathi Raghunath; arathi@molecularconnectons.com
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