@conference {ICBO_2018_27, title = {ICBO_2018_27: Semantic Interoperability: Challenges and Opportunities in Cell Type Knowledge Representation}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {

The Human Cell Atlas (HCA) and the California Institute for Regenerative Medicine{\textquoteright}s Center of Excellence in Stem Cell Genomics (CESCG) are identifying novel cell types at a rapid pace using single cell RNA sequencing (scRNAseq). To maximize the scientific return on these discoveries, it will be critical that the data derived from these studies is translated into biological knowledge that is findable, accessible, interoperable and reproducible (FAIR). To achieve this objective, we are developing a provisional cell type ontology (pCL) where the data being gathered from experimental work is represented in a standard semantic format that can be exchanged, retrieved, and inferred over using standard approaches and tools.

}, keywords = {cell type, CL Ontology, GABAergic, glutamatergic, HCA, Interoperability, pCL, scRNAseq}, url = {http://icbo2018.cgrb.oregonstate.edu/}, author = {Richard Scheuermann and Brian Aevermann and Mohamed Keshk} } @conference {ICBO_2018_42, title = {ICBO_2018_42: ELIXIR Interoperability: Standardisation of identifiers, schemas, and ontologies for scientific communities}, booktitle = {International Conference on Biomedical Ontology (ICBO 2018)}, series = {Proceedings of the International Conference on Biological Ontology (2018)}, year = {2018}, month = {08/06/2018}, publisher = {International Conference on Biological Ontology}, organization = {International Conference on Biological Ontology}, abstract = {ELIXIR (https://www.elixir-europe.org) unites Europe{\textquoteright}s leading life science organisations in managing the increasing volume of data being generated by publicly funded research. ELIXIR operates in a Hub-Node model with the Hub coordinating the activities undertaken by the Nodes via five technical platforms: Compute, Data, Interoperability, Tools, and Training to build a sustainable and foundational framework for Life Science informatics communities. This is done by establishing strategic guidelines underlying scientific operations across ELIXIR{\textquoteright}s twenty-one Node members (as of May 2018). The ELIXIR Interoperability Platform (EIP) has been established to deal with the challenge of delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data across the different levels of complexity and variety of life science data types: across the datasets, data catalogues, data tools and services; across the multitude of biological disciplines and geographical or organisational boundaries. The EIP aims to make available the services and resources needed to make data FAIR. These strategies will be founded on FAIR Principles. Ontologies are a crucial component of the EIP strategy, with OBO Foundry Ontologies recognised as reference resource, and leveraged through resources such as Ontology Lookup Service, which provides additional user services for search and annotation. EIP is currently engaged in addressing specific community-derived use cases where incorporating ontological information is essential: rare disease, marine metagenomics, and plant informatics. These require reference ontologies such as Human Phenotype Ontology (HP), Disease Ontology (DO), Cell Ontology (CL), and UBERON.}, keywords = {Bioschemas, FAIR, identifiers, Interoperability, linked-data, Ontology}, url = {http://icbo2018.cgrb.oregonstate.edu/}, author = {Sirarat Sarntivijai and Nick Juty and Carole Goble and Helen Parkinson and Chris Evelo and Jerry Lanfear and Niklas Blomberg} }