James Macklin
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View article: Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype Open
It is well-known that the use of vocabulary in phenotype treatments is often inconsistent. An earlier survey of biologists who create or use phenotypic characters revealed that this lack of standardization leads to ambiguities, frustrating…
View article: Maloja: simple and scalable Snakemake workflow orchestration in the cloud
Maloja: simple and scalable Snakemake workflow orchestration in the cloud Open
As sequencing technologies have matured, bioinformatics tasks have become more complex, computationally demanding, and data intensive. Workflow management software has been developed to aid in simplifying the replicable chaining of complex…
View article: I Know Something You Don’t Know: The annotation saga continues…
I Know Something You Don’t Know: The annotation saga continues… Open
Over the past 20 years, the biodiversity informatics community has pursued components of the digital annotation landscape with varying degrees of success. We will provide an historical overview of the theory, the advancements made through …
View article: Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure
Connecting the Dots: Aligning human capacity through networks toward a globally interoperable Digital Extended Specimen (DES) infrastructure Open
Thanks to substantial support for biodiversity data mobilization in recent decades, billions of occurrence records are openly available, documenting life on Earth and enabling timely research, awareness raising, and policy-making. Initiati…
View article: The founding charter of the Omic Biodiversity Observation Network (Omic BON)
The founding charter of the Omic Biodiversity Observation Network (Omic BON) Open
Omic BON is a thematic Biodiversity Observation Network under the Group on Earth Observations Biodiversity Observation Network (GEO BON), focused on coordinating the observation of biomolecules in organisms and the environment. Our foundin…
View article: Representation of Object Provenance for Research on Natural Science Objects: Samples, parts and derivatives in DINA-compliant collection data management
Representation of Object Provenance for Research on Natural Science Objects: Samples, parts and derivatives in DINA-compliant collection data management Open
Collection objects in natural science collections span a diverse set of object types of substantially different origin, physical composition, and relevance for different fields and methodologies of research and application. Object provenan…
View article: Campaigning for a Global Collections Network: Improving the digital representation and visibility of natural science collections from Latin America and the Caribbean
Campaigning for a Global Collections Network: Improving the digital representation and visibility of natural science collections from Latin America and the Caribbean Open
Global conservation of biodiversity is more important than ever before. The success of the Convention on Biological Diversity’s Post-2020 Global Biodiversity Framework and monitoring strategy will depend on the availability of reliable, in…
View article: Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet
Digital Extended Specimens: Enabling an Extensible Network of Biodiversity Data Records as Integrated Digital Objects on the Internet Open
The early twenty-first century has witnessed massive expansions in availability and accessibility of digital data in virtually all domains of the biodiversity sciences. Led by an array of asynchronous digitization activities spanning ecolo…
View article: Preliminary Findings of Usability Studies on an Ontology-Aware Taxon-by-Character Matrix Editor
Preliminary Findings of Usability Studies on an Ontology-Aware Taxon-by-Character Matrix Editor Open
Taxonomic treatments start with the creation of taxon-by-character matrices. Systematics authors recognized data ambiguity issues in published phenotypic characters and are willing to adopt an ontology-aware authoring tool (Cui et al. 2022…
View article: Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications
Authors’ attitude toward adopting a new workflow to improve the computability of phenotype publications Open
Critical to answering large-scale questions in biology is the integration of knowledge from different disciplines into a coherent, computable whole. Controlled vocabularies such as ontologies represent a clear path toward this goal. Using …
View article: Author-Driven Computable Data and Ontology Production for Taxonomists
Author-Driven Computable Data and Ontology Production for Taxonomists Open
It takes great effort to manually or semi-automatically convert free-text phenotype narratives (e.g., morphological descriptions in taxonomic works) to a computable format before they can be used in large-scale analyses. We argue that neit…
View article: Robust Integration of Biodiversity Data by Process- and State-based Representation of Object Histories and Modular Application Architecture
Robust Integration of Biodiversity Data by Process- and State-based Representation of Object Histories and Modular Application Architecture Open
Biodiversity data is obtained by a variety of methodological approaches—including observation surveys, environmental sampling and biological object collection—employing diverse sample processing protocols and data transformations. While co…
View article: Data Standards for the Phenology of Plant Specimens
Data Standards for the Phenology of Plant Specimens Open
Phenological data (i.e., data on growth and reproductive events of organisms) are increasingly being used to study the effects of climate change, and biodiversity specimens have arisen as important sources of phenological data. However, ph…
View article: Technical Considerations for a Transactional Model to Realize the Digital Extended Specimen
Technical Considerations for a Transactional Model to Realize the Digital Extended Specimen Open
Technological innovations over the past two decades have given rise to the online availability of more than 150 million specimen and species-lot records from biological collections around the world through large-scale biodiversity data-agg…
View article: Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study Open
Producing findable, accessible, interoperable and reusable (FAIR) data cannot be accomplished solely by data curators in all disciplines. In biology, we have shown that phenotypic data curation is not only costly, but it is burdened with i…
View article: Update on the Brassicaceae species checklist
Update on the Brassicaceae species checklist Open
Here we present a revised species checklist for the Brassicaceae, updated from Warwick SI, Francis, A, Al-Shehbaz IA (2006), Brassicaceae: Species checklist and database on CD-ROM, Plant Systematics and Evolution 259: 249─25. This update o…
View article: Towards a unified data infrastructure to support European and global microbiome research: a call to action
Towards a unified data infrastructure to support European and global microbiome research: a call to action Open
High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data for…
View article: Towards a unified data infrastructure to support European and global microbiome research: a call to action
Towards a unified data infrastructure to support European and global microbiome research: a call to action Open
Summary High‐quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard …
View article: Even Simple Habitat Ontologies are Hard to Use
Even Simple Habitat Ontologies are Hard to Use Open
An essential component in describing, delimiting, and understanding the evolutionary context of a taxon is characterizing the habitats in which the taxon is found. We report on a simple habitat ontology that we have developed, and on our o…
View article: Digitization of US Herbaria - How close did we get to the 2020 goal?
Digitization of US Herbaria - How close did we get to the 2020 goal? Open
A discussion session held at a National Science Foundation-sponsored Herbarium Networks Workshop at Michigan State University in September of 2004 resulted in a rallying objective: make all botanical specimen information in United States c…
View article: DINA—Development of open source and open services for natural history collections & research
DINA—Development of open source and open services for natural history collections & research Open
The DINA Consortium (DINA = “ DI gital information system for NA tural history data”, https://dina-project.net) is a framework for like-minded practitioners of natural history collections to collaborate on the development of distributed, o…
View article: Additional file 1 of Microbiome definition re-visited: old concepts and new challenges
Additional file 1 of Microbiome definition re-visited: old concepts and new challenges Open
Additional file 1.
View article: Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes
Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes Open
To use published phenotype information in computational analyses, there have been efforts to convert descriptions of phenotype characters from human languages to ontologized statements. This postpublication curation process is not only slo…
View article: Using Wikidata and Metaphactory to Underpin an Integrated Flora of Canada
Using Wikidata and Metaphactory to Underpin an Integrated Flora of Canada Open
We are using Wikidata and Metaphactory to build an Integrated Flora of Canada (IFC). IFC will be integrated in two senses: First, it will draw on multiple existing flora (e.g. Flora of North America, Flora of Manitoba, etc.) for content. S…
View article: Ecobiomics: Environmental metagenomic biomonitoring
Ecobiomics: Environmental metagenomic biomonitoring Open
Land use disturbances are having enormous adverse impacts on the biodiversity and integrity of natural and managed ecosystems around the world. Adverse impacts on biodiversity are compromising ecosystem services and processes, reducing eco…
View article: DINA: Open Source and Open Services - A modern approach for natural history collection management systems and research
DINA: Open Source and Open Services - A modern approach for natural history collection management systems and research Open
The DINA Consortium (“ DI gital information system for NA tural history data”, https://dina-project.net ) was formed in order to provide a framework for like-minded large natural history collection-holding institutions to collaborate throu…