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Using annotations from controlled vocabularies to find meaningful associations

by Woei-jyh Lee, Louiqa Raschid, Padmini Srinivasan, Nigam Shah, Daniel Rubin - In Proc. 4th Int. Workshop on Data Integration in the Life Sciences , 2007
"... Abstract. This paper presents the LSLink (or Life Science Link) methodology that provides users with a set of tools to explore the rich Web of interconnected and annotated objects in multiple repositories, and to identify meaningful associations. Consider a physical link between objects in two repos ..."
Abstract - Cited by 8 (4 self) - Add to MetaCart
repositories, where each of the objects is annotated with controlled vocabulary (CV) terms from two ontologies. Using a set of LSLink instances generated from a background dataset of knowledge we identify associations between pairs of CV terms that are potentially significant and may lead to new knowledge. We

RNA polymerase III transcribes human microRNAs.

by Glen M Borchert , William Lanier , Beverly L Davidson - Nature Struct. Mol. Biol. , 2006
"... Prior work demonstrates that mammalian microRNA (miRNA or miR) expression requires RNA polymerase II (Pol II). However, the transcriptional requirements of many miRNAs remain untested. Our genomic analysis of miRNAs in the human chromosome 19 miRNA cluster (C19MC) revealed that they are intersperse ..."
Abstract - Cited by 201 (3 self) - Add to MetaCart
-free transcription assays showed that Pol III, but not Pol II, is associated with miRNA genomic sequence and sufficient for transcription. Moreover, the mature miRNA sequences of approximately 50 additional human miRNAs lie within Alu and other known repetitive elements. These findings extend the current view of mi

The OLAC metadata set and controlled vocabularies

by Steven Bird - In Proceedings of ACL/EACL Workshop on Sharing Tools and Resources for Research and Education , 2001
"... As language data and associated technologies proliferate and as the language resources community rapidly expands, it has become difficult to locate and reuse existing resources. Are there any lexical resources for such-and-such a language? What tool can work with transcripts in this particular forma ..."
Abstract - Cited by 14 (3 self) - Add to MetaCart
Initiative, and called OLAC – the Open Language Archives Community. The OLAC Metadata Set and the associated controlled vocabularies facilitate consistent description and focussed searching. We report progress on the metadata set and controlled vocabularies, describing current issues and soliciting input

PAnG- Finding Patterns in Annotation Graphs

by Philip Anderson, Louiqa Raschid, Andreas Thor, Maria Esther Vidal, Joseph Benik
"... Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences and health sciences, where concepts such as genes, proteins or clinical trials are annotated with controlled vocabulary terms from ontologies. We present a tool, PAnG (Patterns in Ann ..."
Abstract - Cited by 2 (1 self) - Add to MetaCart
Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences and health sciences, where concepts such as genes, proteins or clinical trials are annotated with controlled vocabulary terms from ontologies. We present a tool, PAnG (Patterns

The OLAC Metadata Set and Controlled Vocabularies

by Steven Bird Linguistic, Steven Bird, Gary Simons - In This volume , 2001
"... As language data and associated technologies proliferate and as the language resources community rapidly expands, it has become difficult to locate and reuse existing resources. Are there any lexical resources for such-and-such a language? What tool can work with transcripts in this particul ..."
Abstract - Add to MetaCart
on the Open Archives Initiative, and called OLAC -- the Open Language Archives Community. The OLAC Metadata Set and the associated controlled vocabularies facilitate consistent description and focussed searching. We report progress on the metadata set and controlled vocabularies, describing current

Finding cross genome patterns in annotation graphs

by Joseph Benik, Caren Chang, Louiqa Raschid, Maria-esther Vidal, Guillermo Palma, Andreas Thor - In Proceedings of Data Integration in the Life Sciences (DILS , 2012
"... Abstract. Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences where con-cepts such as genes and proteins are annotated with controlled vocabu-lary terms from ontologies. Scientists are interested in analyzing or min-ing these annotatio ..."
Abstract - Cited by 4 (3 self) - Add to MetaCart
Abstract. Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences where con-cepts such as genes and proteins are annotated with controlled vocabu-lary terms from ontologies. Scientists are interested in analyzing or min

KOBAS server: a web-based platform for automated annotation and pathway identification

by Jianmin Wu, Xizeng Mao, Tao Cai, Jingchu Luo, Liping Wei - Nucleic Acids Res , 2006
"... There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experi-ments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously demon ..."
Abstract - Cited by 54 (7 self) - Add to MetaCart
There is an increasing need to automatically annotate a set of genes or proteins (from genome sequencing, DNA microarray analysis or protein 2D gel experi-ments) using controlled vocabularies and identify the pathways involved, especially the statistically enriched pathways. We have previously

Exploiting Semantics from Ontologies and Shared Annotations to Find Patterns in Annotated Linked Open Data

by Guillermo Palma, Maria-esther Vidal, Louiqa Raschid, Andreas Thor
"... Abstract. Linked Open Data initiatives have made available a diversity of collections that domain experts have annotated with controlled vocabulary terms from ontologies. The challenge is to explore these rich and complex annotated datasets, together with the domain semantics captured within ontolog ..."
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Abstract. Linked Open Data initiatives have made available a diversity of collections that domain experts have annotated with controlled vocabulary terms from ontologies. The challenge is to explore these rich and complex annotated datasets, together with the domain semantics captured within

Link Prediction for Annotation Graphs using Graph Summarization

by Andreas Thor, Philip Anderson, Louiqa Raschid, Saket Navlakha, Samir Khuller, Xiao-ning Zhang
"... Abstract. Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences where genes or proteins are annotated with controlled vocabulary terms (CV terms) from ontologies. The W3C Linking Open Data (LOD) initiative and semantic Web technologies a ..."
Abstract - Cited by 9 (2 self) - Add to MetaCart
Abstract. Annotation graph datasets are a natural representation of scientific knowledge. They are common in the life sciences where genes or proteins are annotated with controlled vocabulary terms (CV terms) from ontologies. The W3C Linking Open Data (LOD) initiative and semantic Web technologies

Using reasoning to guide annotation with gene ontology terms in goat

by Michael Bada, Daniele Turi, Robin Mcentire, Robert Stevens - SIGMOD Record
"... High-quality annotation of biological data is central to bioinformatics. Annotation using terms from ontologies provides reliable computational access to data. The Gene Ontology (GO), a structured controlled vocabulary of nearly 17,000 terms, is becoming the de facto standard for describing the func ..."
Abstract - Cited by 21 (5 self) - Add to MetaCart
High-quality annotation of biological data is central to bioinformatics. Annotation using terms from ontologies provides reliable computational access to data. The Gene Ontology (GO), a structured controlled vocabulary of nearly 17,000 terms, is becoming the de facto standard for describing
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