Workshop 1: Crowd/community curation: challenges & credit attribution

Chair: Henning Hermjakob, EMBL-EBI, UK

Crowd sourcing and community annotation are regarded as a valuable complement to professional curators to improve the annotation and structuring of the vast and rapidly growing amount of biological and biomedical data. However, the annotation strategy based purely on voluntary contributions of many almost anonymous editors, so successful for Wikipedia, does often not work well for biomedical and biomolecular community resources. Highly specialised resources often have a limited number of potential editors, busy domain experts, who are under pressure to build their scientific careers through attributable scientific products, typically classic publications, and who see limited gain in contributing to community resources.

Professional curators are often not able to systematically reference and demonstrate the work they have done for a specific resource, because attribution of the content of large databases to specific curators is far less developed than for example author attribution on open source software development. In this workshop, we will discuss current approaches to community and professional curation, with a specific focus on incentives and attribution of contribution to specific authors.

Presentations and perspectives, panelists/presenters:

  • Henning Hermjakob, EMBL-EBI, Cambridge, UK
  • Xiao Si Zhe and Chris Hunter, Gigascience
  • Todd Taylor, RIKEN Center for Integrative Medical Sciences, Japan
  • Elvira Mitraka, University of Maryland School of Medicine, USA
  • Jennifer Polson, Anders Garlid, Tevfik Umut Dincer, University of California at Los Angeles, USA
  • Chunlei Wu, The Scripps Research Institute, USA
  • Thomas Lemberger, EMBO

The first part of the workshop will consist of short presentations from submitted abstracts, followed by a panel discussion.

Workshop 2: Data visualization & annotation

Chairs: Rama Balakrishnan, Stanford University, USA and Monica Munoz-Torres, Lawrence Berkeley National Laboratory, USA

Explaining the most intricate biological processes often requires a degree of detail beyond the scope of equations and algorithms; in fact, most biological knowledge is represented visually as illustrations, graphs, and diagrams. Genomics data in particular require specialized forms of visualization to improve our understanding and increase our chances of extracting meaningful conclusions from our analyses. Furthermore, the heterogeneity and abundance of genomic data include widely varied sources, techniques for their obtention, and intrinsic experimental error. And even data obtained under similar conditions from two or more individuals are loaded with biological variation. So what is the best way to interpret the stories the data are telling us? Given the questions we wish to answer and the data we are generating, which tools would be most useful and effective? In this workshop we will explore the tools available for human interpretation of genomic data, specifically in the context of annotation.

Presentations and perspectives, panelists/presenters:

  • Lorna Richardson, IGMM, University of Edinburgh, United Kingdom
  • Justyna Szostak, PMI Research & Development, Switzerland

The workshop will include a brief introduction to a landscape of tools available - as updated as the constantly changing field allows-, brief presentations chosen from abstract submissions and invited speakers, as well as ample discussion to capture the contributions and questions from attendants. In the end, we expect participants to walk away with a toolset in hand that may benefit the progress of their own research.

Workshop 3: Biocuration in big data to knowledge: new strategy, process & framework

Chair: Francis Ouellette, Ontario Institute for Cancer Research, Canada

While data sets that are large continue to challenge how we manage and present the data. Big Data, or Data Science has recently been recognized as a discipline. We will discuss different approaches and ways to address the analysis, capture, curation, searching and sharing of Big Data in this workshop. The chair will be prodding panelists on their opinion of this important new topic, and out it can affect biocuration activities worldwide.

Workshop Agenda:
1. Introduction and perspectives from co-chairs: Francis Ouellette, Ontario Institute for Cancer Research, ON, Canada.
2. Perspectives from panelists, and questions from the chair:

  • Johanna McEntyre, EMBL-EBI
  • Michael Cherry, Stanford University, USA
  • Takashi Gojobori, King Abdullah University of Science and Technology, Saudi Arabia
  • Suzi Lewis, Berkeley Bioinformatics Open-source Projects
  • Raja Mazumder, The George Washington University, USA
3. Open discussion and question period (from chair and audience)
4. Closing comments.

Workshop 4: International collaboration in biocuration: projects & data/expertise sharing

Chairs: Claire O'Donovan and Sandra Orchard, EMBL-EBI, UK

The manual curation of the information of data in biomedical resources is an expensive task. Sharing curation effort is a model already being adopted by several data resources including the Gene Ontology annotation effort and the IntAct molecular interaction database. In this workshop we will present examples of such efforts and will then like to open the floor for discussion on how to further develop such models and to explore how databases can make cost savings by sharing infrastructure and tool development to ensure that the data generated by public funding can have a greater longevity and minimise redundant development of resources by multiple disparate groups.

Presentations and perspectives, panelists/presenters:

  • Sandra Orchard, EMBL-EBI, UK
  • Rama Balakrishnan, Stanford University, USA
  • Claire O'Donovan, EMBL-EBI, UK
  • Yuling Li, California Institute of Technology, USA

Workshop format: ~45 minutes short talks, ~45 minutes open floor discussion

Workshop 5: Genotype-2-phenotype: Curation challenges in translational & reverse translational informatics

Chair: Stanley Laulederkind and Shur-Jen Wang, Medical College of Wisconsin, USA

This workshop will focus on curation of diseases in model organisms and in human populations. The process of gathering the data and presenting the information in various databases will be discussed. The advantages and disadvantages of comparing animal models of disease with human disease will be debated.

Presentations and perspectives, panelists/presenters:

  • Elvira Mitraka, University of Maryland/IGS, USA
  • Hong Sun, Shanghai Center for Bioinformation Technology, China
  • Stacia Engel, Stanford University, USA
  • Li Ni, The Jackson Laboratory, USA
  • Stanley Laulederkind, Medical College of Wisconsin, USA

Workshop format: ~45 minutes short talks, ~45 minutes open floor discussion

Workshop 6: Money for biocuration: strategies, ideas & funding

Chairs: Renate Kania and Ulrike Wittig, Heidelberg Institute for Theoretical Studies, Germany

Even though funding research infrastructures becomes more widespread, maintaining and growing existing databases is problematic, even for well-established databases. The recognition of the importance of curation still lags behind that of data generation and this is also reflected by funding policies. In this workshop we will discuss what the International Society for Biocuration (ISB), assisted by us curators, could do to improve the situation. Would it for example be appropriate to generate a letter of recommendation to increase funders awareness of the importance of biocuration, or publish a comment article advocating explicit funding for biocuration? Or what other kind of action(s) could be helpful? Additionally alternative business models besides licensing like e.g. pay-per use or crowd funding, are planned to be discussed.

To get an overview about the current financial situation of ISB members databases, we would like you to participate in this survey. The statistics of the survey will be presented at the workshop.

Presentations and perspectives, panelists/presenters:

  • Donghui Li, Carnegie Institution & TAIR, USA
  • Alex Bateman, EMBL-EBI, UK
  • Ulrike Wittig, Heidelberg Institute for Theoretical Studies, Germany
  • Renate Kania, Heidelberg Institute for Theoretical Studies, Germany

Workshop format: short talks, discussion

Special Workshop: Biocuration in China: importance, road map & priority

Chairs: Weimin Zhu, Jingchu Luo and Zhang Zhang

Biocuration involves adding value to biomedical data by the processes of standardization, quality control and information transferring (also known as data annotation). It enhances data interoperability and consistency, and is critical in translating biomedical data into scientific discovery. Although China is becoming a leading scientific data producer, biocuration is still very new to the Chinese biomedical data community. Here we will discuss the importance, road map and priority of biocuration in China.

Workshop format: discussion on the following issues but not limited to:

  • Announcement of Establishment of "Big Data & Biocuration" Committee in Genetics Society of China
  • Chinese Translation of "Biocuration": 生物审编
  • Biocuration in China: promote biocuration, establish international advisory board, increase funding support in biocuration of domestic databases, etc.
  • Annual/Biennial Meeting of Chinese Biocuration Society