TraitBank: Practical semantics for organism attribute data

Parr, Cynthia; Schulz, Katja; Hammock, Jennifer; Wilson, Nevin; Leary, Patrick; Rice, Jeremy J.; Corrigan, Robert J.

doi:10.3233/sw-150190

Cited by 41 publications

(51 citation statements)

References 41 publications

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“…For example, IsoBank could assign integrative taxonomic information system (https://www. ITIS.gov) serial numbers to organismal submissions that are then linked to a geographic distribution, evolutionary, or ecological relationships (12)(13)(14). We envision a database revolving around three primary informational subunits-user, sample, and analytical-each of which will be associated with core metadata terms, which could be further classified where required (Fig.…”

Section: Data Storage and Metadata Structurementioning

confidence: 99%

Why we need a centralized repository for isotopic data

Pauli

Newsome

Cook

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Section: Data Storage and Metadata Structurementioning

confidence: 99%

Why we need a centralized repository for isotopic data

Pauli

Newsome

Cook

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…We create archives of VertNet, including the trait content, on a periodic basis, and put those on CyVerse, as part of our routine processes, where they are assigned DOIs (35–39). These are harvestable for use by other resources such as TraitBank (60; http://eol.org/info/516) upon publication. The most recent archives include trait content.…”

Section: Acknowledgementsmentioning

confidence: 99%

The importance of digitized biocollections as a source of trait data and a new VertNet resource

et al. 2016

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For vast areas of the globe and large parts of the tree of life, data needed to inform trait diversity is incomplete. Such trait data, when fully assembled, however, form the link between the evolutionary history of organisms, their assembly into communities, and the nature and functioning of ecosystems. Recent efforts to close data gaps have focused on collating trait-by-species databases, which only provide species-level, aggregated value ranges for traits of interest and often lack the direct observations on which those ranges are based. Perhaps under-appreciated is that digitized biocollection records collectively contain a vast trove of trait data measured directly from individuals, but this content remains hidden and highly heterogeneous, impeding discoverability and use. We developed and deployed a suite of openly accessible software tools in order to collate a full set of trait descriptions and extract two key traits, body length and mass, from >18 million specimen records in VertNet, a global biodiversity data publisher and aggregator. We tested success rate of these tools against hand-checked validation data sets and characterized quality and quantity. A post-processing toolkit was developed to standardize and harmonize data sets, and to integrate this improved content into VertNet for broadest reuse. The result of this work was to add more than 1.5 million harmonized measurements on vertebrate body mass and length directly to specimen records. Rates of false positives and negatives for extracted data were extremely low. We also created new tools for filtering, querying, and assembling this research-ready vertebrate trait content for view and download. Our work has yielded a novel database and platform for harmonized trait content that will grow as tools introduced here become part of publication workflows. We close by noting how this effort extends to new communities already developing similar digitized content.Database URL: http://portal.vertnet.org/search?advanced=1

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“…; Reichman, Jones & Schildhauer ; Parr et al . ), and ultimately, impedes discovery and advancement of knowledge towards a unified foundation for ecological science (Madin et al . and references therein).…”

Section: Introductionmentioning

confidence: 99%

Towards a thesaurus of plant characteristics: an ecological contribution

et al. 2016

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Ecological research produces a tremendous amount of data, but the diversity in scales and topics covered and the ways in which studies are carried out result in large numbers of small, idiosyncratic data sets using heterogeneous terminologies. Such heterogeneity can be attributed, in part, to a lack of standards for acquiring, organizing and describing data. Here, we propose a terminological resource, a Thesaurus Of Plant characteristics (TOP), whose aim is to harmonize and formalize concepts for plant characteristics widely used in ecology. 2. TOP concentrates on two types of plant characteristics: traits and environmental associations. It builds on previous initiatives for several aspects: 1) characteristics are designed following the entity-quality model (a characteristic is modelled as the “Quality” of an “Entity” ”) used in the context of Open Biological Ontologies; 2) whenever possible, the Entities and Qualities are taken from existing terminology standards, mainly the PO (Plant Ontology) and PATO (Phenotypic Quality Ontology) ontologies, and 3) whenever a characteristic already has a definition, if appropriate, it is reused and referenced. The development of TOP, which complies with semantic web principles, was carried out through the involvement of experts from both the ecology and the semantics research communities. Regular updates of TOP are planned, based on community feedback and involvement. 3. TOP provides names, definitions, units, synonyms and related terms for about 700 plant characteristics. TOP is available online (www.top-thesaurus.org), and can be browsed using an alphabetical list of characteristics, a hierarchical tree of characteristics, a faceted and a free-text search, and through an Application Programming Interface. 4. Harmonizing definitions of concepts, as proposed by TOP, forms the basis for better integration of data across heterogeneous data sets and terminologies, thereby increasing the potential for data reuse. It also allows enhanced scientific synthesis. TOP therefore has the potential to improve research and communication not only within the field of ecology, but also in related fields with interest in plant functioning and distribution

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TraitBank: Practical semantics for organism attribute data

Cited by 41 publications

References 41 publications

Why we need a centralized repository for isotopic data

Why we need a centralized repository for isotopic data

The importance of digitized biocollections as a source of trait data and a new VertNet resource

Towards a thesaurus of plant characteristics: an ecological contribution

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