ABSTRACT
Scientific articles contain a wealth of information about experimental methods and results describing biological designs. Due to its unstructured nature and multiple sources of ambiguity and variability, extracting this information from text is a difficult task. In this paper, we describe the development of the synthetic biology knowledge system (SBKS) text processing pipeline. The pipeline uses natural language processing techniques to extract and correlate information from the literature for synthetic biology researchers. Specifically, we apply named entity recognition, relation extraction, concept grounding, and topic modeling to extract information from published literature to link articles to elements within our knowledge system. Our results show the efficacy of each of the components on synthetic biology literature and provide future directions for further advancement of the pipeline.
Subject(s)
Data Mining , Synthetic Biology , Data Mining/methods , Natural Language ProcessingABSTRACT
The Synthetic Biology Knowledge System (SBKS) is an instance of the SynBioHub repository that includes text and data information that has been mined from papers published in ACS Synthetic Biology. This paper describes the SBKS curation framework that is being developed to construct the knowledge stored in this repository. The text mining pipeline performs automatic annotation of the articles using natural language processing techniques to identify salient content such as key terms, relationships between terms, and main topics. The data mining pipeline performs automatic annotation of the sequences extracted from the supplemental documents with the genetic parts used in them. Together these two pipelines link genetic parts to papers describing the context in which they are used. Ultimately, SBKS will reduce the time necessary for synthetic biologists to find the information necessary to complete their designs.
Subject(s)
Synthetic Biology , User-Computer Interface , Animals , Cell Line , Data Mining , HumansABSTRACT
The growing quantity of digital recorded music available in large-scale resources such as the Internet archive provides an important new resource for musical analysis. An e-Research approach has been adopted in order to create a very substantive web-accessible corpus of musical analyses in a common framework for use by music scholars, students and beyond, and to establish a methodology and tooling that will enable others to add to the resource in the future. The enabling infrastructure brings together scientific workflow and Semantic Web technologies with a set of algorithms and tools for extracting features from recorded music. It has been used to deliver a prototype system, described here, that demonstrates the utility of LINKED DATA for enhancing the curation of collections of music signal data for analysis and publishing results that can be simply and readily correlated to these and other sources. This paper describes the motivation, infrastructure design and the proof-of-concept case study and reflects on emerging e-Research practice as researchers embrace the scale of the Web.
