The following workshops and tutorials are being co-located with ICBO during the Joint Ontology Workshops of the Bolzano Summer of Knowledge.
*** Registration for workshops is open at https://summerofknowledge.inf.unibz.it/registration/ ***
COB: A Core set of Open Biological and Biomedical Ontology (OBO) Foundry Terms
Contact: Randi Vita, email@example.com
COB will be held from Monday, August 31- Wednesday, September 2, 8:00am – 12:00pm PDT each day.
The Open Biological and Biomedical Ontology (OBO) project is a collective of ontology developers that are committed to collaboration and adherence to shared principles. The OBO Foundry mission is to develop a family of interoperable ontologies that are both logically well-formed and scientifically accurate. Participants voluntarily adhere to and contribute to the development of an evolving set of principles including open use, collaborative development, non-overlapping and strictly-scoped content, and common syntax and relations. The OBO Foundry provides services to the community such as hosting persistent URLs and ontology files, recording metadata for all ontologies in the OBO registry, as well as supporting discussion forums and regular calls between participants. We have developed a set of key top-level ontology terms that unify the many OBO Foundry ontologies, termed COB. COB simplifies the identification of terms, organizes terms, and helps users navigate across OBO projects. It includes logic that links OBO ontologies together, allowing interoperability problems to be detected and corrected. It also allows users to see related ontology terms from multiple ontologies at the same time. This helps users understand how OBO ontologies and their terms are related, as well as aiding developers to ensure interoperability. The purpose of this workshop is to continue active development of COB, taking advantage of the ICBO meeting to gather together, in person, representatives from the diverse OBO Foundry ontologies. As COB is still in development, we are eager to obtain feedback from the ontology community. We want to collect actionable suggestions on how OBO ontologies work or do not work for users, and what users most want to see included in COB.
Contact: Cui Tao, firstname.lastname@example.org.
September 19th, 9am CT
Drugs and vaccines have contributed to dramatic improvements in public health worldwide. Over the last decade, there have been efforts in the biomedical ontology community that represents various areas associated with drugs including vaccines that extend existing health and clinical terminology systems (e.g., SNOMED, RxNorm, NDF-RT, and MedDRA), vernacular medical terminologies, and their applications to research and clinical data. This workshop will provide a platform for discussing innovative solutions as well as the challenges in the development and application of biomedical ontologies to representing and analyzing drugs and vaccines, their administration, immune responses induced, adverse events, and similar topics. The workshop will cover two main areas: (i) ontology representation of drugs and vaccines, and (ii) applications of the ontologies in real-world situations – administration, adverse events, etc. Examples of biomedical subject matter in the scope of this workshop: drug components (e.g., drug active ingredients, vaccine antigens, and adjuvants), administration details (e.g., dosage, administration route, and frequency), gene immune responses and pathways, drug-drug or drug-food interactions, and adverse events. Both research and clinical subjects will be covered. We will also focus on computational methods used to study these, for example, literature mining of vaccine/drug-gene interaction networks, meta-analysis of host immune responses, and time event analysis of the pharmacological effects. This workshop is expected to support a deeper understanding of vaccine and drug mechanisms and effects using ontologies. More specific topics will be selected based on attendees’ submissions and interests.
Contact: Damion Dooley, email@example.com
Sept 16, 23, 30, Oct 7
Controlled vocabulary standardization efforts covering agricultural and food domains are evolving since their inception decades ago thanks to the mandates and continued support of institutional caretakers. Popular examples are FoodEx2, the European Food Safety Authority (EFSA) food classification and description system, the Global Language of Business GS1 product categorization scheme, the EUROFIR promoted LanguaL food composition thesaurus, the UN Food and Agriculture Organization’s AGROVOC SKOS-based vocabulary, and its support of the International Network of Food Data Systems (INFOODS) vocabulary for food nutrition testing. These vocabularies are used in a growing interconnected food database landscape but suffer from format issues like textual or spreadsheet formats, unresolvable identifiers, and inconsistent category semantics. Ontologies are new entrants into the food domain, bringing a wave of Semantic Web technology and philosophy to bear on the issue of data sharing and modeling of food-related activity and research which are becoming critical in the face of rapid change to our environment and anthroposphere. Examples range from BBC’s Food Ontology, driving its culinary media universe, to recently published research laboratory initiated ontologies like OBOFoundry members FoodOn, the Food Biomarker Ontology (FOBI), and the Ontology for Nutritional Studies (ONS), and related ontologies like the Medical Action Ontology (MAxO) and the Environmental Conditions, Treatments and Exposures ontology (ECTO) that are under development. Underpinning these mid-level, model-focused ontologies are environmental, chemical, biological, anatomical, disease and phenotype ontologies. Academic, agricultural and public health agencies are considering the benefits and complexities of adopting ontology in their research and data management and reporting infrastructure. How can ontologies interface to legacy datasets and online databases described by existing vocabularies? What vocabulary, tool ecosystem and data models are needed to correlate agricultural treatments, nutritional data, eating patterns, biomarkers, pathogens, and phytochemical levels with disease and health phenotypes? This workshop seeks to define the coverage of the different ecological, agricultural, nutritional, dietary, public health, one health surveillance, food security, and trade domains that food-related ontologies are modeling, and the use of data translation tools for bringing legacy data into the ontology fold.
Contact: Alexander D. Diehl, firstname.lastname@example.org
Friday, September 25th
The rapid advancement of experimental technologies for understanding cellular biology has led to challenges in keeping up with the volume and format of the data being produced and its distillation into new biological knowledge. Current high throughput methods such as single cell RNA sequencing and flow and mass cytometry are producing a large amount of data related to existing and novel cell types in health and disease. At the same time, experimental approaches such as microscopy, genomics, and metabolomics are expanding understanding of cellular functioning in relation to neighboring cells and the whole organism. Ontologies are being increasingly used as a tool for integrating and analyzing these diverse data types. The Cell Ontology (CL) and Cell Line Ontology (CLO) have long been established as reference ontologies in the OBO framework for representing cell type information, but additional ontologies such as the Gene Ontology, Protein Ontology, and the Ontology for Biomedical Investigation are also important for representing not only experimental data about cell types but also the methods used to produce that data. There is a continuing need for improve automated analysis techniques to link data about cells with appropriate ontologies. The CELLS 2020 workshop will focus on two themes: (i) challenges in the knowledge representation of newly-discovered and known cell types, and (ii) challenges in the knowledge representation of cells in disease states. This workshop will provide a venue for panel discussions of innovative solutions as well as the challenges in the development and application of biomedical ontologies to represent and analyze in vivo and in vitro cell- and cell line-related knowledge and data, including stem cell technologies. The workshop will cover the extension of CL and CLO for ontological representation of cell types and cell lines in new methodologies and experiments. It will also cover the applications and challenges in real-world use cases which may require other ontological adaptations beyond CL and CLO. Selected submissions will be featured in a BMC Bioinformatics thematic CELLS issue, as those from previous CELLS workshops have been.
The following accepted tutorials and workshops were postponed to the 2021 event.
Contact: James A. Overton, email@example.com
== UPDATE: THIS TUTORIAL HAS BEEN POSTPONED (Details to follow) ==
Numerous tools exist for building, managing and releasing ontologies. This tutorial aims to introduce participants to OBO Foundry best practices and provide hands-on training for specific ontology development tools. This first half of the workshop is targeted towards beginner-level ontology developers, teaching the basics about community ontology development, and using the Protégé ontology editor. The second half of the workshop is targeted towards broader skill levels, and will provide an opportunity for participants to learn to use the latest tools to support improved workflows, ontology management, and provenance and attribution.
Ontologies for Research in the Behavioural and Social Sciences (OntoBeSS)
Contact: Janna Hastings, firstname.lastname@example.org
== UPDATE: THIS WORKSHOP HAS BEEN POSTPONED TO 2021 ==
While the use of ontologies has become commonplace in the biomedical sciences, it has only recently started to take off within the social and behavioural sciences. Recent applications of ontologies within the social and behavioural sciences include the Human Behaviour Change Project and the Addiction Ontology (AddictO). Within the domain of biomedical informatics, the Ontology for Medically Related Social Entities is relevant. This workshop aims to provide a forum for the discussion of all aspects related to the use and development of ontologies for research in the social and behavioural sciences and for the description of social, behavioural and economic variables in studies involving humans or in population studies. Specific topics that are of interest include representations of population and personal attributes, behavioural and socioeconomic attributes, measurement, research methods and formal descriptions of social research studies, relating social theory and ontologies, and the development of a shared mid-level ontology for the social and behavioural ontologies. We will invite contributions detailing any aspect of theory or applications of ontologies within the social and behavioural sciences. An important additional objective of the workshop will be to form a community of practice and exchange around the development of ontologies for the social and behavioural sciences. We also seek to identify opportunities for collaboration on shared technical infrastructures and platforms, as currently no platform or portal exists for sharing and re-use of ontologies specifically for this domain.
Contact: Dr. Ing. Algergawy, email@example.com
== UPDATE: THIS WORKSHOP HAS BEEN POSTPONED TO 2021 ==
Biodiversity deals with heterogeneous data and concepts generated from a large number of disciplines in order to build a coherent picture of the extent of life on earth. The presence of such a myriad of data resources makes integrative biodiversity research increasingly important, as well as challenging given the variety of ways in which data and information are produced and made available. The Semantic Web approach enhances data discoverability, sharing, interoperability and integration through a formalized conceptual environment providing common formats, standards and terminological resources. This workshop aims to bring together computer scientists and biologists, working on Semantic Web approaches for biodiversity, ecology and related areas such as plant sciences, agronomy, agro-ecology or citizen science related to biodiversity. The goal is to exchange experiences, build a state of the art of realizations and challenges, and reuse and adapt solutions that have been proposed in other domains. The workshop focuses on presenting challenging issues and solutions for the design of high quality biodiversity information systems leveraging Semantic Web techniques.
Second International Workshop on Biomedical Ontologies & Natural Language Processing
Contact: Jonathan P. Bona, firstname.lastname@example.org
== UPDATE: THIS WORKSHOP HAS BEEN POSTPONED TO 2021 ==
Ontologies provide machine-interpretable semantic representations of biomedical information that can then be shared, queried, and reasoned about. Natural language processing techniques are increasingly being applied within the biomedical domain, allowing machines to automatically interpret and use the large amounts of unstructured textual data generated each day across the biomedical domain, including but not limited to that generated in the course of clinical care and research.