Enhancing Workflow with a Semantic Description of Scientific Intent

Peer reviewedPreprin

EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature

This paper describes a set of guidelines for the citation of zoological and botanical specimens in the European Journal of Taxonomy. The guidelines stipulate controlled vocabularies and precise formats for presenting the specimens examined within a taxonomic publication, which allow for the rich data associated with the primary research material to be harvested, distributed and interlinked online via international biodiversity data aggregators. Herein we explain how the EJT editorial standard was defined and how this initiative fits into the journal's project to semantically enhance its publications using the Plazi TaxPub DTD extension. By establishing a standardised format for the citation of taxonomic specimens, the journal intends to widen the distribution of and improve accessibility to the data it publishes. Authors who conform to these guidelines will benefit from higher visibility and new ways of visualising their work. In a wider context, we hope that other taxonomy journals will adopt this approach to their publications, adapting their working methods to enable domain-specific text mining to take place. If specimen data can be efficiently cited, harvested and linked to wider resources, we propose that there is also the potential to develop alternative metrics for assessing impact and productivity within the natural science

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

From XML to XML: The why and how of making the biodiversity literature accessible to researchers

We present the ABLE document collection, which consists of a set of annotated volumes of the Bulletin of the British Museum (Natural History). These follow our work on automating the markup of scanned copies of the biodiversity literature, for the purpose of supporting working taxonomists. We consider an enhanced TEI XML markup language, which is used as an intermediate stage in translating from the initial XML obtained from Optical Character Recognition to the target taXMLit. The intermediate representation allows additional information from external sources such as a taxonomic thesaurus to be incorporated before the final translation into taXMLit

Extraction and parsing of herbarium specimen data: Exploring the use of the Dublin core application profile framework

Herbaria around the world house millions of plant specimens; botanists and other researchers value these resources as ingredients in biodiversity research. Even when the specimen sheets are digitized and made available online, the critical information about the specimen stored on the sheet are not in a usable (i.e., machine-processible) form. This paper describes a current research and development project that is designing and testing high-throughput workflows that combine machine- and human-processes to extract and parse the specimen label data. The primary focus of the paper is the metadata needs for the workflow and the creation of the structured metadata records describing the plant specimen. In the project, we are exploring the use of the new Dublin Core Metadata Initiative framework for application profiles. First articulated as the Singapore Framework for Dublin Core Application Profiles in 2007, the use of this framework is in its infancy. The promises of this framework for maximum interoperability and for documenting the use of metadata for maximum reusability, and for supporting metadata applications that are in conformance with Web architectural principles provide the incentive to explore and add implementation experience regarding this new framework

Collaborative platforms for streamlining workflows in Open Science

Despite the internet’s dynamic and collaborative nature, scientists continue to produce grant proposals, lab notebooks, data files, conclusions etc. that stay in static formats or are not published online and therefore not always easily accessible to the interested public. Because of limited adoption of tools that seamlessly integrate all aspects of a research project (conception, data generation, data evaluation, peer-reviewing and publishing of conclusions), much effort is later spent on reproducing or reformatting individual entities before they can be repurposed independently or as parts of articles.

We propose that workflows - performed both individually and collaboratively - could potentially become more efficient if all steps of the research cycle were coherently represented online and the underlying data were formatted, annotated and licensed for reuse. Such a system would accelerate the process of taking projects from conception to publication stages and allow for continuous updating of the data sets and their interpretation as well as their integration into other independent projects.

A major advantage of such workflows is the increased transparency, both with respect to the scientific process as to the contribution of each participant. The latter point is important from a perspective of motivation, as it enables the allocation of reputation, which creates incentives for scientists to contribute to projects. Such workflow platforms offering possibilities to fine-tune the accessibility of their content could gradually pave the path from the current static mode of research presentation into
a more coherent practice of open science

Show Me The Data: An Evaluation Of Data Access In The JRS Grant Portfolio

In order to be useful for biodiversity conservation and sustainable development, biodiversity information must be not only available, but also accessible.The JRS Biodiversity Foundation contracted an independent study to assess the level to which data produced by JRS-funded projects were discoverable online, and the ease with which those data could be viewed or downloaded. Only about half of the expected data products were viewable or discoverable online, and in many cases data were not clearly connected with project results. Data accessibility was not dependent on the country in which the project was located, and hasn't changed over time. Interviews with grantees helped to identify challenges to and enabling conditions for creating sharable data products. JRS is actively responding to the findings of this study through new planning tools to support future grantees and a data sharing policy that explicitly supports open access to data and data publication to well-recognized and secure repositories

An open-access platform for camera-trapping data

In southern Mexico, local communities have been playing important roles in the design and collection of wildlife data through camera-trapping in community-based monitoring of biodiversity projects. However, the methods used to store the data have limited their use in matters of decision-making and research. Thus, we present the Platform for Community-based Monitoring of Biodiversity (PCMB), a repository, which allows storage, visualization, and downloading of photographs captured by community-based monitoring of biodiversity projects in protected areas of southern Mexico. The platform was developed using agile software development with extensive interaction between computer scientists and biologists. System development included gathering data, design, built, database and attributes creation, and quality control. The PCMB currently contains 28,180 images of 6478 animals (69.4% mammals and 30.3% birds). Of the 32 species of mammals recorded in 18 PA since 2012, approximately a quarter of all photographs were of white-tailed deer (Odocoileus virginianus). Platforms permitting access to camera-trapping data are a valuable step in opening access to data of biodiversity; the PCMB is a practical new tool for wildlife management and research with data generated through local participation. Thus, this work encourages research on the data generated through the community-based monitoring of biodiversity projects in protected areas, to provide an important information infrastructure for effective management and conservation of wildlife