ترغب بنشر مسار تعليمي؟ اضغط هنا

The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments

82   0   0.0 ( 0 )
 نشر من قبل Rafael S. Gon\\c{c}alves
 تاريخ النشر 2019
  مجال البحث الهندسة المعلوماتية
والبحث باللغة English




اسأل ChatGPT حول البحث

The Center for Expanded Data Annotation and Retrieval (CEDAR) aims to revolutionize the way that metadata describing scientific experiments are authored. The software we have developed--the CEDAR Workbench--is a suite of Web-based tools and REST APIs that allows users to construct metadata templates, to fill in templates to generate high-quality metadata, and to share and manage these resources. The CEDAR Workbench provides a versatile, REST-based environment for authoring metadata that are enriched with terms from ontologies. The metadata are available as JSON, JSON-LD, or RDF for easy integration in scientific applications and reusability on the Web. Users can leverage our APIs for validating and submitting metadata to external repositories. The CEDAR Workbench is freely available and open-source.



قيم البحث

اقرأ أيضاً

We introduce GrapAL (Graph database of Academic Literature), a versatile tool for exploring and investigating a knowledge base of scientific literature, that was semi-automatically constructed using NLP methods. GrapAL satisfies a variety of use case s and information needs requested by researchers. At the core of GrapAL is a Neo4j graph database with an intuitive schema and a simple query language. In this paper, we describe the basic elements of GrapAL, how to use it, and several use cases such as finding experts on a given topic for peer reviewing, discovering indirect connections between biomedical entities and computing citation-based metrics. We open source the demo code to help other researchers develop applications that build on GrapAL.
In the materials design domain, much of the data from materials calculations are stored in different heterogeneous databases. Materials databases usually have different data models. Therefore, the users have to face the challenges to find the data fr om adequate sources and integrate data from multiple sources. Ontologies and ontology-based techniques can address such problems as the formal representation of domain knowledge can make data more available and interoperable among different systems. In this paper, we introduce the Materials Design Ontology (MDO), which defines concepts and relations to cover knowledge in the field of materials design. MDO is designed using domain knowledge in materials science (especially in solid-state physics), and is guided by the data from several databases in the materials design field. We show the application of the MDO to materials data retrieved from well-known materials databases.
105 - Jan Mikac 2008
In this paper, we propose an export architecture that provides a clear separation of authoring services from publication services. We illustrate this architecture with the LimSee3 authoring tool and several standard publication formats: Timesheets, SMIL, and XHTML.
We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample---a repository managed by the National Center for Biotechnology Info rmation (NCBI), and BioSamples---a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.4M sample metadata records in the two repositories are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the metadata. Most metadata field names and their values are not standardized or controlled. Even simple binary or numeric fields are often populated with inadequate values of different data types. By clustering metadata field names, we discovered there are often many distinct ways to represent the same aspect of a sample. Overall, the metadata we analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The significant aberrancies that we found in the metadata are likely to impede search and secondary use of the associated datasets.
Provenance is a critical ingredient for establishing trust of published scientific content. This is true whether we are considering a data set, a computational workflow, a peer-reviewed publication or a simple scientific claim with supportive evidenc e. Existing vocabularies such as DC Terms and the W3C PROV-O are domain-independent and general-purpose and they allow and encourage for extensions to cover more specific needs. We identify the specific need for identifying or distinguishing between the various roles assumed by agents manipulating digital artifacts, such as author, contributor and curator. We present the Provenance, Authoring and Versioning ontology (PAV): a lightweight ontology for capturing just enough descriptions essential for tracking the provenance, authoring and versioning of web resources. We argue that such descriptions are essential for digital scientific content. PAV distinguishes between contributors, authors and curators of content and creators of representations in addition to the provenance of originating resources that have been accessed, transformed and consumed. We explore five projects (and communities) that have adopted PAV illustrating their usage through concrete examples. Moreover, we present mappings that show how PAV extends the PROV-O ontology to support broader interoperability. The authors strived to keep PAV lightweight and compact by including only those terms that have demonstrated to be pragmatically useful in existing applications, and by recommending terms from existing ontologies when plausible. We analyze and compare PAV with related approaches, namely Provenance Vocabulary, DC Terms and BIBFRAME. We identify similarities and analyze their differences with PAV, outlining strengths and weaknesses of our proposed model. We specify SKOS mappings that align PAV with DC Terms.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا