The following workshops and tutorials are being co-located with ICBO 2021 during the Joint Ontology Workshops of the Bolzano Summer of Knowledge.
Contact: James A. Overton, firstname.lastname@example.org
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.
Contact: Janna Hastings, email@example.com
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 biomedical domain, 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 biomedical research 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, firstname.lastname@example.org
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, email@example.com
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.
This workshop aims to explore and promote connections between work in ontologies and natural language processing techniques, with a focus on the domain of biomedicine. Work in both areas will benefit from this connection. A significant hurdle in NLP, especially as applications increasingly require full natural language understanding, is the appropriate representation of the semantics of a particular word, phrase, sentence, or document. Ontologies encode useful domain and terminological knowledge and provide an ideal logical framework on which to build such semantic representations. Applications abound throughout biomedicine for these technologies, including in cohort identification, reporting, quality assurance, data integration, and clinical decision support. Similarly, NLP techniques can be useful for ontology creation, use, and evaluation, for instance in support of automated methods for generating and evaluating definitions for ontology terms. This workshop will provide a forum to discuss the state of the art in using NLP and ontologies together; disseminate research in these areas; enhance awareness of the problems faced in combining NLP with biomedical ontologies, along with the potential benefits; facilitate discussions within the ICBO community which we hope will advance the field; and foster new collaborations.
This half-day workshop will consist of paper presentations followed by an open discussion session on work crossing the boundaries of NLP and biomedical ontologies. We invite and encourage submissions by researchers who make combined use of biomedical ontologies and NLP.
COB: A Core set of Open Biological and Biomedical Ontology (OBO) Foundry Terms
COB brings together key terms from a wide range of OBO projects into a single, small ontology that is meant to provide a shared upper layer of terms that can be reused across OBO ontologies, and thereby improve 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. We will provide instructions on how to align your ontology with COB and receive reports on bridging incoherencies. We will work together on terms in COB that are under active development, to ensure that the term definitions meet the needs of different OBO projects.
Contact: Cui Tao, firstname.lastname@example.org.
Workshop planned date: 10 September
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, metaanalysis 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.
Integrated Food Ontology Workshop (IFOW) – Building the farm to fork digital highway: Integrated food ontology development for agricultural, food science and public health domains.
Contact: Damion Dooley, email@example.com
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 recent research laboratory initiated ontologies like OBOFoundry members FoodOn, the Food Biomarker Ontology (FOBI), the Ontology for Nutritional Studies (ONS), the Ontology for Nutritional Epidemiology (ONE), and the Crop Dietary Nutrition Ontology (CDNO). 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? Encouraged by the success of the inaugural 2020 IFOW workshop, this second round will explore the evolution of food-related ontologies as they integrate ecological, agricultural, nutritional, dietary, public health, one health surveillance, food security, and trade domain vocabulary, and the use of curation, validation, mapping and visualization tools for food ontology maintenance.
Contact: Alexander D. Diehl, firstname.lastname@example.org
Date: 15 September, 15th, 10 am – 1 pm Eastern time
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 2021 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.
There will be four submission formats: (i) full research papers (10 pages), (ii) short papers (5 pages), (iii) extended abstracts (1-3 pages), and 1-page abstracts for posters. The paper format will be the same as the format used in ICBO 2021. All submissions will go through peer reviews by at least two reviewers. We will provide a late abstract deadline for short reports of late-breaking results as well. Authors submitting papers have the option of submitting separately to the new ICBO Publications Track hosted by the Journal of Biomedical Semantics.