Dataset Information

Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.

ABSTRACT:

Background

Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging schema.org could benefit biomedical research resource providers, but it can be challenging to apply schema.org standards to biomedical research outputs. We created an online browser-based tool that empowers researchers and repository developers to utilize schema.org or other biomedical schema projects.

Results

Our browser-based tool includes features which can help address many of the barriers towards schema.org -compliance such as: The ability to easily browse for relevant schema.org classes, the ability to extend and customize a class to be more suitable for biomedical research outputs, the ability to create data validation to ensure adherence of a research output to a customized class, and the ability to register a custom class to our schema registry enabling others to search and re-use it. We demonstrate the use of our tool with the creation of the Outbreak.info schemaâ€"a large multi-class schema for harmonizing various COVID-19 related resources.

Conclusions

We have created a browser-based tool to empower biomedical research resource providers to leverage schema.org classes to make their research outputs more FAIR.

SUBMITTER: Cano M

PROVIDER: S-EPMC9176648 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.

Cano Marco M Tsueng Ginger G Zhou Xinghua X Hughes Laura D LD Mullen Julia L JL Xin Jiwen J Su Andrew I AI Wu Chunlei C

bioRxiv : the preprint server for biology 20220602

<h4>Background</h4>Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical research outputs are more readily accessible through open data efforts, finding relevant outputs remains a significant challenge. Schema.org is a metadata vocabulary standardization project that enables web content creators to make their content more FAIR. Leveraging schema.org could benefit biomedical research resou ...[more]

PMID: 35677074

Similar Datasets

Project description:PurposeSchema therapy was first applied to individuals with borderline personality disorder (BPD) over 20 years ago, and more recent work has suggested efficacy across a range of disorders. The present review aimed to systematically synthesize evidence for the efficacy and effectiveness of schema therapy in reducing early maladaptive schema (EMS) and improving symptoms as applied to a range of mental health disorders in adults including BPD, other personality disorders, eating disorders, anxiety disorders, and post-traumatic stress disorder.MethodsStudies were identified through electronic searches (EMBASE, PsycINFO, MEDLINE from 1990 to January 2016).ResultsThe search produced 835 titles, of which 12 studies were found to meet inclusion criteria. A significant number of studies of schema therapy treatment were excluded as they failed to include a measure of schema change. The Clinical Trial Assessment Measure was used to rate the methodological quality of studies. Schema change and disorder-specific symptom change was found in 11 of the 12 studies.ConclusionsSchema therapy has demonstrated initial significant results in terms of reducing EMS and improving symptoms for personality disorders, but formal mediation analytical studies are lacking and rigorous evidence for other mental health disorders is currently sparse.Practitioner pointsFirst review to investigate whether schema therapy leads to reduced maladaptive schemas and symptoms across mental health disorders. Limited evidence for schema change with schema therapy in borderline personality disorder (BPD), with only three studies conducting correlational analyses. Evidence for schema and symptom change in other mental health disorders is sparse, and so use of schema therapy for disorders other than BPD should be based on service user/patient preference and clinical expertise and/or that the theoretical underpinnings of schema therapy justify the use of it therapeutically. Further work is needed to develop the evidence base for schema therapy for other disorders.

Project description:BackgroundOntology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is a challenge to automated methods, which identify ontology terms in text. Classical approaches to word sense disambiguation use co-occurring words or terms. However, most treat ontologies as simple terminologies, without making use of the ontology structure or the semantic similarity between terms. Another useful source of information for disambiguation are metadata. Here, we systematically compare three approaches to word sense disambiguation, which use ontologies and metadata, respectively.ResultsThe 'Closest Sense' method assumes that the ontology defines multiple senses of the term. It computes the shortest path of co-occurring terms in the document to one of these senses. The 'Term Cooc' method defines a log-odds ratio for co-occurring terms including co-occurrences inferred from the ontology structure. The 'MetaData' approach trains a classifier on metadata. It does not require any ontology, but requires training data, which the other methods do not. To evaluate these approaches we defined a manually curated training corpus of 2600 documents for seven ambiguous terms from the Gene Ontology and MeSH. All approaches over all conditions achieve 80% success rate on average. The 'MetaData' approach performed best with 96%, when trained on high-quality data. Its performance deteriorates as quality of the training data decreases. The 'Term Cooc' approach performs better on Gene Ontology (92% success) than on MeSH (73% success) as MeSH is not a strict is-a/part-of, but rather a loose is-related-to hierarchy. The 'Closest Sense' approach achieves on average 80% success rate.ConclusionMetadata is valuable for disambiguation, but requires high quality training data. Closest Sense requires no training, but a large, consistently modelled ontology, which are two opposing conditions. Term Cooc achieves greater 90% success given a consistently modelled ontology. Overall, the results show that well structured ontologies can play a very important role to improve disambiguation.AvailabilityThe three benchmark datasets created for the purpose of disambiguation are available in Additional file 1.

Dataset Information

Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.

Background

Results

Conclusions

Publications

Schema Playground: A tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets