TaxonWorks (http://taxonworks.org) is an integrated workbench for taxonomists and biodiversity scientists. It is designed to capture, organize, and enrich data, share and refine it with collaborators, and package it for analysis and publication. It is based on PostgreSQL (database) and the Ruby-on-Rails programming language and framework for developing web applications (https://github.com/SpeciesFileGroup/taxonworks). The TaxonWorks community is built around an open software ecosystem that facilitates participation at many levels. TaxonWorks is designed to serve both researchers who create and curate the data, as well as technical users, such as programmers and informatics specialists, who act as data consumers. TaxonWorks provides researchers with robust, user friendly interfaces based on well thought out customized workflows for efficient and validated data entry. It provides technical users database access through an application programming interface (API) that serves data in JSON format. The data model includes coverage for nearly all classes of data recorded in modern taxonomic treatments primary studies of biodiversity, including nomenclature, bibliography, specimens and collecting events, phylogenetic matrices and species descriptions, etc. The nomenclatural classes are based on the NOMEN ontology (https://github.com/SpeciesFileGroup/nomen).
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TaxonWorks: An experience of migrating large datasets into the new cybertaxonomic infrastructure
TaxonWorks (http://taxonworks.org) in an integrated, open-source, cybertaxonomic web application serving taxonomists and biodiversity scientists. It is designed to facilitate efficient data capture, storage, manipulation, and retrieval. It integrates a wide variety of data types used by biodiversity scientists, including, but not limited to, taxonomy (with validation based on codes of zoological, botanical, bacterial, and viral nomenclature), specimen data, bibliographies, media (images, PDFs, sounds, videos), morphology (character/trait matrices), distribution, biological associations. Available TaxonWorks web interfaces currently provide various data entry forms for simple and advanced querying of the database. TaxonWorks has integrated batch uploader functionality. But, for larger datasets, specialized migration scripts were used. Several projects, historically build in 3i (http://dmitriev.speciesfile.org), MX (http://mx.phenomix.org), SpeciesFiles (http://software.speciesfile.org), and other databases, have been or are being migrated into TaxonWorks. Of the projects moving into TaxonWorks, it is worth mentioning several: 3i World Auchenorrhyncha Database, LepIndex, Universal Chalcidoidea Database, Orthoptera SpeciesFile, Plecoptera SpeciesFile, Illinois Natural History Survey Insect Collection database, and several others. An experience of the data migration will be shared during the presentation.
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- Award ID(s):
- 1639601
- PAR ID:
- 10126842
- Date Published:
- Journal Name:
- Biodiversity Information Science and Standards
- Volume:
- 3
- ISSN:
- 2535-0897
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Large systematic revisionary projects incorporating data for hundreds or thousands of taxa require an integrative approach, with a strong biodiversity-informatics core for efficient data management to facilitate research on the group. Our original biodiversity informatics platform, 3i (Internet-accessible Interactive Identification) combined a customized MS Access database backend with ASP-based web interfaces to support revisionary syntheses of several large genera of leafhopers (Hemiptera: Auchenorrhyncha: Cicadellidae). More recently, for our National Science Foundation sponsored project, “GoLife: Collaborative Research: Integrative genealogy, ecology and phenomics of deltocephaline leafhoppers (Hemiptera: Cicadellidae), and their microbial associates”, we selected the new open-source platform TaxonWorks as the cyberinfrastructure. In the scope of the project, the original “3i World Auchenorrhyncha Database” was imported into TaxonWorks. At the present time, TaxonWorks has many tools to automatically import nomenclature, citations, and specimen based collection data. At the time of the initial migration of the 3i database, many of those tools were still under development, and complexity of the data in the database required a custom migration script, which is still probably the most efficient solution for importing datasets with long development history. At the moment, the World Auchenorrhyncha Database comprehensively covers nomenclature of the group and includes data on 70 valid families, 6,816 valid genera, 47,064 valid species as well as synonymy and subsequent combinations (Fig. 1). In addition, many taxon records include the original citation, bibliography, type information, etymology, etc. The bibliography of the group includes 37,579 sources, about 1/3 of which are associated with PDF files. Species have distribution records, either derived from individual specimens or as country and state level asserted distribution, as well as biological associations indicating host plants, predators, and parasitoids. Observation matrices in TaxonWorks are designed to handle morphological data associated with taxa or specimens. The matrices may be used to automatically generate interactive identification keys and taxon descriptions. They can also be downloaded to be imported, for example, into Lucid builder, or to perform phylogenetic analysis using an external application. At the moment there are 36 matrices associated with the project. The observation matrix from GoLife project covers 798 taxa by 210 descriptors (most of which are qualitative multi-state morphological descriptors) (Fig. 2). Illustrations are provided for 9,886 taxa and organized in the specialized image matrix and could be used as a pictorial key for determination of species and taxa of a higher rank. For the phylogenetic analysis, a dataset was constructed for 730 terminal taxa and >160,000 nucleotide positions obtained using anchored hybrid enrichment of genomic DNA for a sample of leafhoppers from the subfamily Deltocephalinae and outgroups. The probe kit targets leafhopper genes, as well as some bacterial genes (endosymbionts and plant pathogens transmitted by leafhoppers). The maximum likelihood analyses of concatenated nucleotide and amino acid sequences as well as coalescent gene tree analysis yielded well-resolved phylogenetic trees (Cao et al. 2022). Raw sequence data have been uploaded to the Sequence Read Archive on GenBank. Occurrence and morphological data, as well as diagnostic images, for voucher specimens have been incorporated into TaxonWorks. Data in TaxonWorks could be exported in raw format, get accessed via Application Programming Interface (API), or be shared with external data aggregators like Catalogue of Life, GBIF, iDigBio.more » « less
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TaxonWorks is an open-source workbench for biodiversity researchers. With several years of development behind it, we highlight its present status, and discuss if and when it makes sense to release a version 1.0, i.e. software completed to specific stage. TaxonWorks' scope is broad; it seeks to touch nearly all areas that might be of interest to taxonomists, i.e. those who integrate everything that is known about a taxon into a single resource. Its role as a software platform is placed in a broader context, where many instances of TaxonWorks each can support multiple research projects. Instances may be supported by individuals or organizations. A suite of technical tools including containerization and unit tests facilitate collaboration at many different levels. TaxonWorks is a research tool, mechanisms for analyzing the results of data curation including its application programing interface are described. The long-term development of TaxonWorks is supported by an endowment to the Species File Group. Its source is available on Github.more » « less
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Grant-supported digitization projects over the past 20 years at the Illinois Natural History Survey (INHS) have yielded over 1,000,000 occurrence records (representing over 2.7 million specimens), one of the most successful digitization efforts within the United States. However, receiving multiple grants at the cutting edge has led to numerous projects left at various stages of completeness, several relational databases, orphaned data, and specimens at various stages of curation. TaxonWorks (taxonworks.org), an integrated web-based workbench developed by the Species File Group and supported by the INHS and the National Science Foundation, has provided the digital infrastructure to unify multiple workflows, projects, databases, and even historical accession books into one easy to access, open-source platform. We demonstrate the practical utility of this platform and summarize past, present, and future efforts at the INHS towards integrating all our data within TaxonWorks.more » « less
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TaxonWorks is an integrated web-based application for practicing taxonomists and biodiversity specialists. It is focused on promoting collaboration between researchers and developers. TaxonWorks has a modular structure that enables various components of the application to target specific needs and requirements of different groups of users. Specific areas of interest may include nomenclature-related tasks (Yoder and Dmitriev 2021) designed to help assemble and validate scientific name checklists of a target group of organisms; and collection management tasks, including interfaces to create, filter, and edit collecting events, collection objects, and loans. This presentation focuses on matrix-related tools integrated into TaxonWorks. A matrix, which could either be used for phylogenetic analysis or to build an identification key, is structured as a table where columns represent numerous characters that could be used to describe a set of entities, taxa or specimens (presented as rows of the table). Each cell of the table may contain observations for specific character/entity combinations. TaxonWorks does not generate a table for each a particular matrix—all observations are stored as graphs. This structure allows building of a matrix of an unlimited size as well as reuse of individual observations in multiple matrices. For matrix columns, TaxonWorks supports a variety of different kinds of characters or descriptors: qualitative, presence/absence, quantitative, sample, gene, free text, and media. Each character may have specific properties, for example a qualitative descriptor may have numerous characters states, and a quantitative descriptor may have a measurement unit defined. For an entity in a matrix row, TaxonWorks supports either collection objects (specimens) or taxa as Operational Taxonomic Units (OTU). OTUs could either be linked to nomenclature or be stand alone entities (e.g., representing undescribed species). The matrix, once built, could serve several purposes. A matrix based on qualitative and quantitative characters could be used to build an interactive key (Fig. 1), construct standardized natural language descriptions for each entity, and determine a diagnosis (a minimal set of characters that separate one entity from all others). It could also be exported and used for phylogenetic analysis or to build an interactive key in an external application. TaxonWorks supports export files in several formats, including Nexus, TNT, NeXML. Application Programming Interfaces (API) are also available. A matrix based on media descriptors could be used as a pictorial identification tool (Fig. 2).more » « less
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3897/biss.3.37159
