Biological data represent a unique informatics challenge but researchers around the world are developing innovative methods for linking biological data, making biological data accessible, standardizing, and sharing biological data. In this breakout session we will provide a look at several projects with innovative approaches to informatics challenges related to biological data and showcase the power of open science principles and emerging observation methods. We will also highlight the role that standards play in making all this possible.
Nicole Kearney: How the biodiversity community are making historic literature discoverable online
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Biodiversity Heritage Library (BHL) is the world’s largest online repository of biodiversity literature and archival materials. It is a global consortium of 500 libraries who have made over 59 million pages from their collections freely accessible online. Yet accessible does not equate to discoverable. Unlike contemporary scientific papers, the historical literature was not “born” with digital object identifiers (DOIs). This means historic articles sit outside the convenient linked infrastructure of modern publications, appearing in today’s reference lists as unlinked citations or not at all. The upshot of this is that our historic literature is falling into obscurity. This paper will detail the work the BHL is undertaking to bring the world’s historic literature into the modern linked network of scholarly research. It will also discuss the responsibility that comes with assigning DOIs retrospectively, what we are doing to promote best practice for out-of-copyright and orphaned content, and how DOIs are demonstrating that the historic literature is still hugely relevant today.
Marie-Elise Lecoq: The Living Atlases Community
The Atlas of Living Australia (ALA) has worked on a modular and open-source platform that provides information on all known species in Australia and contributes to the GBIF (Global Biodiversity Information Facility). Its modular and open-source architecture enables other institutions to re-use and modify the ALA platform for their thematics or national data portals. For several years, GBIF nodes and institutions have worked together to create an open-source community, named the Living Atlases community, around the ALA software. Today, we have more than 25 live data portals around the world based on the ALA framework. For two years, we have endeavoured to make this community more sustainable. First, we have organized a Community of Practice based on existing foundations such as the Apache or Linux communities. In addition, we have hired a technical coordinator and an administrative one that helped grow the community via better technical documentation on installing, maintaining data portals, and contributing to the main project. We have also developed tools that facilitate the installation and configuration of a Living Atlas data portal.
Nicky Nicolson: Specimen duplicate detection in aggregated biodiversity data
Plant specimens are considered easy to digitise, but they are often duplicated between separate institutions and duplicate specimens are independently curated and digitised. When these data are aggregated together into data portals, the duplicates are hidden. As the field values in these records may vary due to separate curation histories, these are not absolute (record-for-record) duplicates and it is necessary to use data-mining techniques for detection.
The GBIF network (www.gbif.org) mobilises c85 million records for plant specimens - this number will include many duplicated specimens. This talk outlines an automated process applied to GBIF mobilised data which identifies field collectors and their collecting activities (expeditions) and enables the detection of specimen duplicate sets. Resolution of these duplicates enables the sharing of curatorial information between separate institutions. A higher-level collector-oriented view of the specimens also helps users understand and summarise a collection. The process is enabled by data standards for specimen metadata sharing and has implications for data standards development in collection description efforts.
Curtis Dyreson & Neil Cobb: Symbiota2: Promoting FAIRness in biodiversity databases and developing “Extended Specimen” pathways
This talk discusses data management standards and practices in Symbiota2 from the values stored in a database to values in a knowledge graph. Symbiota2 a biodiversity collection management system that is a rewrite of Symbiota, one of the most popular biodiversity database applications. Symbiota2 is primarily used to store and manage specimen collection data. Data in Symbiota2 is stored and managed by a relational database. Some of the data can be exported formatted to the Darwin Core standard for integration with other datasets. Symbiota2 also provides web services to interact with the data at a more abstract level, documented using the OpenAPI standard. Finally, Symbiota2 produces a knowledge graph using the R2RML standard. An emerging focus will be to accommodate data created as part of the “Extended Specimen” phase of US collection digitization (e.g., genetics, traits, phylogenetics) and integrate specimen-based data with environmental data.
Megan Cromwell: Video Data Solutions: Standard Biological Data Quantification and Data Accessibility with Machine Learning Techniques
Video data are qualitative data that are time consuming to analyze, standardize, and archive in a user friendly manner. Over the last 12 years, the NOAA National Centers for Environmental Data Management has collaborated with the NOAA Office of Ocean Exploration and Research and their partners to systematically work through many of these challenges. We have learned that standard annotations offer a key to finding and reusing these data for scientific analysis. Machine Learning techniques are opening the doorway for annotating these data without the heavy human time commitment typically required. Partners from NOAA, Academia and non-Governmental Organizations (NGOs)have begun developing annotation methodologies through student crowd-sourced projects that will eventually resolve the many challenges associated with biological imagery annotation, for the benefit of data access and reuse.
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