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https://ceur-ws.org/Vol-2285/ICBO2018-preface.pdf
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA
Preface
International Conference on Biological Ontology (ICBO 2018)
Ontologies for Health, Food, Nutrition and Environment: A Partnership with
BIG-Data and Analytics
Conference website: http://icbo2018.cgrb.oregonstate.edu
Oregon State University hosted the 9th International Conference on Biological Ontology
(http://icbo2018.cgrb.oregonstate.edu) ICBO 2018. The theme of ICBO 2018 was
“Ontologies for Health, Food, Nutrition and Environment: A Partnership with BIG-Data
and Analytics. ICBO 2018 was a marquee event celebrating the 150th anniversary of the
founding of Oregon State University (https://oregonstate.edu/150).
ICBO 2018 provided a venue for presenting and discussing research, development and
the usefulness of biomedical ontologies from a wide range of disciplines, including
human health and diseases, vectors, drugs, bio-chemicals, biodiversity, plants,
agriculture, food, and the environment. The conference was attended by over 130
participants from 10 countries representing significant areas of biology, medicine,
ecology, computer science, mathematics, text-mining, data analytics, and software and
tool development. ICBO 2018 was chaired by Dr. Pankaj Jaiswal (Oregon State
University), along with conference program co-chairs Dr. Christopher Mungall
(Lawrence Berkeley National Laboratory) and Dr. Melissa Haendel (Oregon State
University) who organized the conference program, with help from the Program
Committee members. The scientific presentations were organized into 13 workshops, 29
plenary talks and 29 posters and software demonstrations. The 29 plenary talks and
posters were selected after peer-review of more than 60 scientific articles. The ICBO
2018 conference abstracts are available online
(http://icbo2018.cgrb.oregonstate.edu/abstracts). Open access articles published online
are presented in this conference proceedings.
Three thought-provoking Keynote talks were presented. Dr. Kwan Liu-Ma (University of
California, Davis, USA) on “Visualization: A Powerful Tool for Data Exploration and
Storytelling”, Josh Clark (Big Medium Inc., USA) on “The Care and Feeding of
Algorithms” for design, analytics and user engagement, and Dr. Parag Chitnis (National
Institute of Food and Agriculture, USA) on “Changing Face of Agriculture: Data-driven
opportunities for nutrition and health”.
ICBO2018 August 7-10, 2018
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA
Four invited talks were presented by Niklaus Grunwald (USDA-ARS) on “Taxa,
metacoder, poppr, and vcfR: Four packages for parsing, visualization, and manipulation
of genetic, genomic and metagenomic data in R”; David LeBauer (TerraRef project) on
“Vocabularies, Ontologies, APIs, and Formats for Heterogeneous High Throughput Crop
Phenotyping Data”; Carolyn Lawrence (Iowa State University, USA) on “GO-MAP
Implements CAFA Tools: Improved Automated Gene Function Annotation for Plants”;
and Matthew Lange (University of California, Davis, USA) on “Designing and Building
the IC-FOODS Foundry: Community, Technology, and Standards for a Semantic Web of
Food”.
Thirteen workshops were held at the venue of ICBO 2018, including pre- and post-
conference events. Each workshop session included talks, demonstrations, hands-on
exercises and discussion forums relevant to their theme. The pre-conference POTATO
(Phenotype Ontologies Traversing All The Organisms) Workshop was aimed at aligning
phenotype ontologies using design patterns. Participants discussed data standards and
phenotype annotation tools for pattern-based ontology development (Dead Simple
Ontology Design Patterns; DOSDP) and the Ontology Development Kit (ODK) were
discussed. The two-day post-conference workshop “Deep Learning in the Life Sciences”
was an introductory, hands-on workshop on machine learning to train students and
researchers working on various biological datasets. The workshop was co-organized with
the Center for Genome Research and Biocomputing (https://cgrb.oregonstate.edu/) and
instruction was provided by experts from IBM.
The Gramene Pathway Curation Jamboree, which ran over four days of the conference,
was organized by Sushma Naithani (Oregon State University; Gramene database). In the
Jamboree, participants learned about the biocuration process, literature and data mining,
pathway analysis, and biocuration tools with particular emphasis on plant pathways using
the Reactome Curator Tool. The curation of plant pathways is an ongoing work of the
Plant Reactome database. The Pathway Jamboree report is available from Gramene
News.
The 2nd International Workshop on Oncology and Ontology (ONCONTO) was focused
on advancing the ontological representation of cancer and related entities to support both
broader research in the domain and personalized treatment approaches.
The workshop “Data Standards and Knowledge Sharing in Biodiversity: Tools and
Applications” focused on cutting-edge work in the area of biodiversity data
representation and semantics, including ontology-driven text-mining analysis and
normalization of free-text specimen descriptions.
We thank the conference sponsors: the International Society for Biocuration, the College
of Agricultural Sciences, Department of Botany and Plant Pathology, Department of
ICBO2018 August 7-10, 2018
Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), Corvallis, Oregon, USA
Environment and Molecular Toxicology, College of Engineering, and the Sponsored
Research Office at Oregon State University, and industry partners, Illumina Inc., Sanmita
Inc, and Sensiplicity LLC. The conference was partially supported by the grants to
Pankaj Jaiswal for the Gramene database (IPGA: Gramene - Exploring Function through
Comparative Genomics and Network Analysis; NSF-PGRP Award 1127112) and the
Planteome project (cROP: Common Reference Ontologies and Applications for Plant
Biology; NSF-PGRP Award 1340112), and an NIH conference grant to Melissa Haendel
and Peter Robinson (Forums for Integrative phenomics; NIH award 1U13CA221044).
ICBO 2018 concluded with a vote of thanks, and the announcement of ICBO 2019 to be
held at University at Buffalo, New York, USA.
Pankaj Jaiswal, Ph.D.
ICBO 2018, Conference Chair
Associate Professor
Dept. of Botany and Plant Pathology
2082 Cordley Hall
Oregon State University
Corvallis, OR, 97331
USA
email: jaiswalp@oregonstate.edu
ICBO2018 August 7-10, 2018