ArticleJournal of biomedical semantics2012
Open semantic annotation of scientific publications using DOMEO.
Article in Journal of biomedical semantics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- An extensive review of tools for manual annotation of documents.Briefings in bioinformatics · 2021Review
- Measurement Recorder: developing a useful tool for making species descriptions that produces computable phenotypes.Database : the journal of biological databases and curation · 2020Article
- AnnoSys-implementation of a generic annotation system for schema-based data using the example of biodiversity collection data.Database : the journal of biological databases and curation · 2017Article
- The role of ontologies in biological and biomedical research: a functional perspective.Briefings in bioinformatics · 2015Article
- Biomedical imaging ontologies: A survey and proposal for future work.Journal of pathology informatics · 2015Article
- Benchmarking infrastructure for mutation text mining.Journal of biomedical semantics · 2014Article
- SEE: structured representation of scientific evidence in the biomedical domain using Semantic Web techniques.Journal of biomedical semantics · 2014Article
- Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications.Journal of biomedical semantics · 2014Article
- PAV ontology: provenance, authoring and versioning.Journal of biomedical semantics · 2013Article
- Article
- BioC: a minimalist approach to interoperability for biomedical text processing.Database : the journal of biological databases and curation · 2013Article
- On the reproducibility of science: unique identification of research resources in the biomedical literature.PeerJ · 2013Article
- An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.Database : the journal of biological databases and curation · 2013Article
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Authors and funding
3 authors.
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Abstract
backgroundOur group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model.
methodsThe Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO). Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies.Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms.
resultsWe report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org) and is scheduled for production deployment in the NIF's next full release.Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.