Biodiversity Information Science and Standards :
Conference Abstract
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Corresponding author: Hong Cui (hongcui@email.arizona.edu)
Received: 27 Sep 2021 | Published: 27 Sep 2021
This is an open access article distributed under the terms of the CC0 Public Domain Dedication.
Citation:
Vieglais D, Richard SM, Cui H, Davies N, Deck J, Gan Q, Kansa EC, Kansa SW, Kunze J, Mandel D, Meyer C, Orrell TM, Ramdeen S, Snyder R, Walls RL, Zhou Y, Lehnert K (2021) Internet of Samples: Progress report. Biodiversity Information Science and Standards 5: e75797. https://doi.org/10.3897/biss.5.75797
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Material samples form an important portion of the data infrastructure for many disciplines. Here, a material sample is a physical object, representative of some physical thing, on which observations can be made. Material samples may be collected for one project initially, but can also be valuable resources for other studies in other disciplines. Collecting and curating material samples can be a costly process. Integrating institutionally managed sample collections, along with those sitting in individual offices or labs, is necessary to faciliate large-scale evidence-based scientific research. Many have recognized the problems and are working to make data related to material samples FAIR: findable, accessible, interoperable, and reusable.
The Internet of Samples (i.e., iSamples) is one of these projects. iSamples was funded by the United States National Science Foundation in 2020 with the following aims:
The initial sample collections that will make up the internet of samples include those from the System for Earth Sample Registration (SESAR), Open Context, the Genomic Observatories Meta-Database (GEOME), and Smithsonian Institution Museum of Natural History (NMNH), representing the disciplines of geoscience, archaeology/anthropology, and biology.
To achieve these aims, the proposed iSamples infrastructure (Fig.
The metadata modeling strategy adopted by the iSamples project is a metadata profile-based approach, where core metadata fields that are applicable to all samples, form the core metadata schema for iSamples. Each individual participating collectionis free to include additional metadata in their records, which will also be harvested by iSC and are discoverable through the iSC user interface or APIs (Application Programming Interfaces), just like the core. In-depth analysis of metadata profiles used by participating collections, including Darwin Core, has resulted in an iSamples core schema currently being tested and refined through use. See the current version of the iSamples core schema.
A number of properties require a controlled vocabulary. Controlled vocabularies used by existing records are kept, while new vocabularies are also being developed to support high-level grouping with consistent semantics across collection types. Examples include vocabularies for Context Category, Material Category, and Specimen Type (Table
Current controlled vocabulary terms for hasSpecimenCategories, hasMaterialCategories, and hasContextCategories for the iSamples project.
Specimen Type v2 | Material Category v.3 | ContextCategory v.20210703 |
decision graph of specimen type terms | decision graph of material terms | decision graph of sampled feature terms |
Aggregation Analytical Preparation Anthropogenic aggregation Artifact Biome aggregation Experiment product Fossil Liquid or gas sample Organism part Organism product Other solid object Whole organism |
Anthropogenic material Anthropogenic metal Biogenic non-organic material Dispersed media Gaseous material Liquid water Mineral Mixed soil sediment rock Non-aqueous liquid material Organic material Particulate Rock Sediment Soil Water ice |
Active human occupation site Atmosphere Earth interior Experiment setting Extraterrestrial environment Glacier environment Laboratory or curation environment Lake river or stream bottom Marine water body Marine water body bottom Site of past human activities Subaerial surface environment Subsurface fluid reservoir Terrestrial water body |
iSample project members are also active in the TDWG Material Sample Task Group and the global consultation on Digital Extended Specimens. Many members of the iSamples project also lead or participate in a sister research coordination network (RCN), Sampling Nature. The goal of this RCN is to develop and refine metadata standards and controlled vocabularies for the iSamples and other projects focusing on material samples. We cordially invite you to participate in the Sampling Nature RCN and help shape the future standards for material samples. Contact Sarah Ramdeen (sramdeen@ideo.columbia.edu) to engage with the RCN.
iSamples system design, material samples, Sampling Nature RCN, sample material, specimen type, sampled feature, metadata profiles
Dave Vieglais
TDWG 2021