103 research outputs found
Semantics for Data in Agriculture: A Community-Based Wish List
The paper reports on activities carried within the Agrisemantics Working Group of the Research Data Alliance (RDA). The group investigated on what are the current problems research and practitioners experience in their work with semantic resources for agricultural data and elaborated the list of requirements that are the object of this paper. The main findings include the need to broaden the usability of tools so as to make them useful and available to the variety of profiles usually involved in working with semantics resources; the need to online platform to lift users from the burden of local installation; and the need for services that can be integrated in workflows. We further analyze requirements concerning the tools and services and provide details about the process followed to gather evidence from the community
Automated Georeferencing of Antarctic Species
Many text documents in the biological domain contain references to the toponym of specific phenomena (e.g. species sightings) in natural language form "In Garwood Valley summer activity was 0.2% for Umbilicaria aprina and 1.7% for Caloplaca sp. ..."
While methods have been developed to extract place names from documents, and attention has been given to the interpretation of spatial prepositions, the ability to connect toponym mentions in text with the phenomena to which they refer (in this case species) has been given limited attention, but would be of considerable benefit for the task of mapping specific phenomena mentioned in text documents.
As part of work to create a pipeline to automate georeferencing of species within legacy documents, this paper proposes a method to: (1) recognise species and toponyms within text and (2) match each species mention to the relevant toponym mention. Our methods find significant promise in a bespoke rules- and dictionary-based approach to recognise species within text (F1 scores up to 0.87 including partial matches) but less success, as yet, recognising toponyms using multiple gazetteers combined with an off the shelf natural language processing tool (F1 up to 0.62).
Most importantly, we offer a contribution to the relatively nascent area of matching toponym references to the object they locate (in our case species), including cases in which the toponym and species are in different sentences. We use tree-based models to achieve precision as high as 0.88 or an F1 score up to 0.68 depending on the downsampling rate. Initial results out perform previous research on detecting entity relationships that may cross sentence boundaries within biomedical text, and differ from previous work in specifically addressing species mapping
39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition
In this paper, we report on the outputs and adoption of the Agrisemantics
Working Group of the Research Data Alliance (RDA), consisting of a set of
recommendations to facilitate the adoption of semantic technologies and methods
for the purpose of data interoperability in the field of agriculture and
nutrition. From 2016 to 2019, the group gathered researchers and practitioners
at the crossing point between information technology and agricultural science,
to study all aspects in the life cycle of semantic resources:
conceptualization, edition, sharing, standardization, services, alignment, long
term support. First, the working group realized a landscape study, a study of
the uses of semantics in agrifood, then collected use cases for the
exploitation of semantics resources-a generic term to encompass vocabularies,
terminologies, thesauri, ontologies. The resulting requirements were
synthesized into 39 "hints" for users and developers of semantic resources, and
providers of semantic resource services. We believe adopting these
recommendations will engage agrifood sciences in a necessary transition to
leverage data production, sharing and reuse and the adoption of the FAIR data
principles. The paper includes examples of adoption of those requirements, and
a discussion of their contribution to the field of data science
Recommended from our members
Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires
Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using baseline human antibody repertoire sequences. Our analysis shows that human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data. We find that mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in baseline human antibody repertoires. In addition, high frequency mutations in baseline human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that baseline human antibody repertoires may be useful as predictive tools to guide mAb development in the future.
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Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the AgBioData Consortium
Over the last several decades, there has been rapid growth in the number and
scope of agricultural genetics, genomics and breeding (GGB) databases and
resources. The AgBioData Consortium (https://www.agbiodata.org/) currently
represents 44 databases and resources covering model or crop plant and animal
GGB data, ontologies, pathways, genetic variation and breeding platforms
(referred to as 'databases' throughout). One of the goals of the Consortium is
to facilitate FAIR (Findable, Accessible, Interoperable, and Reusable) data
management and the integration of datasets which requires data sharing, along
with structured vocabularies and/or ontologies. Two AgBioData working groups,
focused on Data Sharing and Ontologies, conducted a survey to assess the status
and future needs of the members in those areas. A total of 33 researchers
responded to the survey, representing 37 databases. Results suggest that data
sharing practices by AgBioData databases are in a healthy state, but it is not
clear whether this is true for all metadata and data types across all
databases; and that ontology use has not substantially changed since a similar
survey was conducted in 2017. We recommend 1) providing training for database
personnel in specific data sharing techniques, as well as in ontology use; 2)
further study on what metadata is shared, and how well it is shared among
databases; 3) promoting an understanding of data sharing and ontologies in the
stakeholder community; 4) improving data sharing and ontologies for specific
phenotypic data types and formats; and 5) lowering specific barriers to data
sharing and ontology use, by identifying sustainability solutions, and the
identification, promotion, or development of data standards. Combined, these
improvements are likely to help AgBioData databases increase development
efforts towards improved ontology use, and data sharing via programmatic means.Comment: 17 pages, 8 figure
Abundances of the elements in the solar system
A review of the abundances and condensation temperatures of the elements and
their nuclides in the solar nebula and in chondritic meteorites. Abundances of
the elements in some neighboring stars are also discussed.Comment: 42 pages, 11 tables, 8 figures, chapter, In Landolt- B\"ornstein, New
Series, Vol. VI/4B, Chap. 4.4, J.E. Tr\"umper (ed.), Berlin, Heidelberg, New
York: Springer-Verlag, p. 560-63
Wasting Breath in Hamlet
This is the final version. Available on open access from Palgrave via the DOI in this recordThis chapter draws on instances of disordered breathing in
Hamlet in order to examine the cultural signifcance of sighs in the early
modern period, as well as in the context of current work in the feld
of medical humanities. Tracing the medical history of sighing in ancient
and early modern treatises of the passions, the chapter argues that sighs,
in the text and the performance of the tragedy, exceed their conventional
interpretation as symptoms of pain and disrupt meaning on the page and
on stage. In the light of New Materialist theory, the air circulating in
Hamlet is shown to dismantle narratives of representation, posing new
questions for the future of medical humanities
Chemical vapour deposition synthetic diamond: materials, technology and applications
Substantial developments have been achieved in the synthesis of chemical
vapour deposition (CVD) diamond in recent years, providing engineers and
designers with access to a large range of new diamond materials. CVD diamond
has a number of outstanding material properties that can enable exceptional
performance in applications as diverse as medical diagnostics, water treatment,
radiation detection, high power electronics, consumer audio, magnetometry and
novel lasers. Often the material is synthesized in planar form, however
non-planar geometries are also possible and enable a number of key
applications. This article reviews the material properties and characteristics
of single crystal and polycrystalline CVD diamond, and how these can be
utilized, focusing particularly on optics, electronics and electrochemistry. It
also summarizes how CVD diamond can be tailored for specific applications,
based on the ability to synthesize a consistent and engineered high performance
product.Comment: 51 pages, 16 figure
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