TraitBank : practical semantics for organism attribute data

© IOS Press and The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Semantic Web 7 (2016): 577-588, doi:10.3233/SW-150190.Encyclopedia of Life (EOL) has developed TraitBank (http://eol.org/traitbank), a new repository for organism attribute (trait) data. TraitBank aggregates, manages and serves attribute data for organisms across the tree of life, including life history characteristics, habitats, distributions, ecological relationships and other data types. We describe how TraitBank ingests and manages these data in a way that leverages EOL’s existing infrastructure and semantic annotations to facilitate reasoning across the TraitBank corpus and interoperability with other resources. We also discuss TraitBank’s impact on users and collaborators and the challenges and benefits of our lightweight, scalable approach to the integration of biodiversity data.Support for TraitBank was provided by the Alfred P. Sloan Foundation, the Smithsonian Institution, the Marine Biological Laboratory, and the John D. and Catherine T. MacArthur Foundation

ENVIRONMENTS and EOL : identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioinformatics 31 (2015): 1872-1874, doi:10.1093/bioinformatics/btv045.The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.The Encyclopedia Of Life Rubenstein Fellows Program [CRDF EOL-33066-13/E33066], the LifeWatchGreece Research Infrastructure [384676-94/GSRT/ NSRF(C&E)] and the Novo Nordisk Foundation Center for Protein Research [NNF14CC0001]

WorldFAIR (D10.3) Agricultural biodiversity FAIR data assessment rubrics

The WorldFAIR Case Study on Agricultural Biodiversity (WP10) addresses the challenges of advancing interoperability and mobilising plant-pollinator interactions data for reuse. Previous efforts, reported in WorldFAIR Deliverable 10.1, ‘Agriculture-related pollinator data standards use cases report’ (Trekels et al., 2023), provided an overview of projects, good practices, tools, and examples for creating, managing and sharing data related to plant-pollinator interactions. It also outlined a work plan for conducting pilot studies. Deliverable 10.2 (Drucker et al., 2024) presented Agricultural Biodiversity Standards, Best Practices and Guidelines Recommendations. This deliverable presented results from six pilot studies that adopted standards and recommendations from the earlier report. The current report complements the efforts with Agricultural Biodiversity FAIR data assessment rubrics.We introduce a set of FAIR assessment tools tailored to the plant-pollinator interactions domain. These tools are designed to help researchers and institutions evaluate adherence to the FAIR principles. In the discovery phase, we found that a significant amount of data on plant-pollinator interactions is available as supplementary files of research articles, in a diversity of formats such as PDFs, Excel spreadsheets, and text files. The diversity of approaches and the lack of appropriate data vocabularies lead to confusion, information loss, and the need for complex data interpretation and transformation. Our proposed framework primarily targets researchers in this domain who wish to assess the FAIRness of the data they produce and take action to improve it. However, we believe it can also benefit data reviewers, data stewards, data repository managers and librarians dealing with plant-pollinator data. Our approach focuses on being as familiar as possible with the researcher's practices, language, and jargon. Ultimately, we aim to promote data publishing and reuse in the plant-pollinator interactions domain.We present a ‘Rubric for the assessment of Plant-Pollinator Interactions Data’ with examples from the data from the pilots developed in Deliverable 10.2 and in relation to the FAIR Implementation Profile (FIP) created by Work Package 10. We conduct ‘dataset assessments’ of available data from research projects surveyed in the discovery phase. Additionally, we describe in detail the ‘Automated FAIR-enabled Data Reviews’ generated by the Global Biotic Interactions (GLoBI) infrastructure, with examples from the pilots. We believe the tools described in this report will encourage data publishing and reuse in the plant-pollinator interactions domain. Moving from diverse approaches and siloed initiatives to widely available FAIR plant-pollination interactions data for scientists and decision-makers will enable the development of integrative studies that enhance our understanding of species biology, behaviour, ecology, phenology, and evolution

Social behavior and long-distance vocal communication in eastern American crows.

To examine the relationship between social organization and vocal behavior, I studied wild family groups of eastern American Crows, Corvus brachyrhynchos brachyrhynchos in Ann Arbor, Michigan. Some individuals tagged as nestlings acted as helpers at the nest in subsequent years. Helpers did not seem to gain inclusive fitness benefits, at least in the short term. Instead, ecological variables unrelated to group size were more important in nest success. Helpers could have been gaining parenting experience. Crows were partially migratory and group-territorial year round, though some individuals moved in and out of non-territorial summer flocks and roosting winter flocks. Males often remained with their parents longer than females, who may have been more likely to migrate and disperse. Caws recorded from wild and captive crows had a call-like structure, particularly in being harsh and graded. The repetitive, rhythmic, and complex organization of these caws into series, however, resembled vocalizations used by other songbirds in mating competition contexts. Some caw series types appeared to serve as general alarm signals, while unstructured cawing was clearly associated with predator mobbing. However, some caw series types are strongly associated with song-like contexts and one caw series type, doubled short caws, tracked seasonal changes in territorial bout frequency. Crows responded more strongly to playback of doubled cadence than to regular cadence, indicating a role for rhythm in repertoire size determination and supporting a hypothesis that doubled short caws are more territorial, or song-like, in function. Crows also responded slightly differently to caw series of similar cadence but different caw durations. Breeding pairs of crows responded more strongly to playback of strangers than did larger family groups. This result is consistent with a helper-reduced territoriality hypothesis: the presence of helpers lowers territorial response levels because they can usually passively deter intrusions or because the group's odds of success in a fight are great even if intruders engage them. Territoriality in a changing social milieu may provide selection pressure for song-like ritualization and elaboration of otherwise call-like signals.Ph.D.Biological SciencesEcologyZoologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/130328/2/9722061.pd

General Terms Design, Standardization

We describe a case study using a digital library resource to assist ecological research that involves computational approaches. Our purpose is to detail the approach and demonstrate the power of combining encyclopedic content presentation with harvestable data. While acknowledging the advantages and generality of this approach, we also consider the challenges faced before digital libraries can adequately support research in this way

Annotator 1

<p>Results from annotator 1, choosing all ecological interactions.</p

Annotator 3

<p>Results from annotator 3 choosing ecological interactions.</p

Species Associations

<p>Associations between species inferred from EOL text objects on all species pages. The first column is the Taxon ID for the subject of the taxon page. The second column is the Taxon ID for the taxon mentioned on the page.</p

Replacement Dictionary

<p>Dictionary file used by an algorithm to make EOL text objects easier for GNRD to read.</p