Dataset Information

Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.

ABSTRACT: The detection of MicroRNA (miRNA) mentions in scientific literature facilitates researchers with the ability to find relevant and appropriate literature based on queries formulated using miRNA information. Considering most published biological studies elaborated on signal transduction pathways or genetic regulatory information in the form of figure captions, the extraction of miRNA from both the main content and figure captions of a manuscript is useful in aggregate analysis and comparative analysis of the studies published. In this study, we present a statistical principle-based miRNA recognition and normalization method to identify miRNAs and link them to the identifiers in the Rfam database. As one of the core components in the text mining pipeline of the database miRTarBase, the proposed method combined the advantages of previous works relying on pattern, dictionary and supervised learning and provided an integrated solution for the problem of miRNA identification. Furthermore, the knowledge learned from the training data was organized in a human-interpretable manner to understand the reason why the system considers a span of text as a miRNA mention, and the represented knowledge can be further complemented by domain experts. We studied the ambiguity level of miRNA nomenclature to connect the miRNA mentions to the Rfam database and evaluated the performance of our approach on two datasets: the BioCreative VI Bio-ID corpus and the miRNA interaction corpus by extending the later corpus with additional Rfam normalization information. Our study highlights and also proposes a better understanding of the challenges associated with miRNA identification and normalization in scientific literature and the research gap that needs to be further explored in prospective studies.

SUBMITTER: Dai HJ

PROVIDER: S-EPMC6391575 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.

Dai Hong-Jie HJ Wang Chen-Kai CK Chang Nai-Wen NW Huang Ming-Siang MS Jonnagaddala Jitendra J Wang Feng-Duo FD Hsu Wen-Lian WL

Database : the journal of biological databases and curation 20190101

The detection of MicroRNA (miRNA) mentions in scientific literature facilitates researchers with the ability to find relevant and appropriate literature based on queries formulated using miRNA information. Considering most published biological studies elaborated on signal transduction pathways or genetic regulatory information in the form of figure captions, the extraction of miRNA from both the main content and figure captions of a manuscript is useful in aggregate analysis and comparative anal ...[more]

PMID: 30809637

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Project description:The dialectical relationship between ecosystems and society is complex; therefore, holistic approaches are required to address this complexity. This view also stands out in the ecosystem services valuation field, where different scholars and global platforms have drawn attention to the need to incorporate plural valuation initiatives at decision-making. In this sense, through a comprehensive design, we conducted a multi-layered valuation of ecosystem services, and we highlighted multiple values in two areas of the province of Caldas, Colombia. We proposed a three-phase valuation process called Recognizing, Normalizing and Articulating values. Then, in cooperation with the regional environmental authority, we obtained different water-related ecosystem services values. Our results showed some warnings: first, we found mismatches between ecosystem services values; second, people assigned high values to ecosystems but the actual capacity of ecosystems to support ES is low. Finally, monetary values were marginal compared to social and ecological values. We conclude by saying that the more strata are assessed, the more values appear in the valuation scenarios, and those values could be conflicting. Our results have political implications, since they highlight the need to incorporate plural values as a fundamental tool for planning and land use in real scenarios where conflicts of interest and values are evident. Highlights • Plural valuation of ecosystem services is a field in construction and we add methodological insights.• We provided a multilayered-valuation of ecosystem services to elicit plural values related to water.• We used a pragmatic philosophy following a multimethod research design with a mixed-approach.• Water ecosystem services have different values and we proved in two areas from Colombia.• The more layers unfolded, the more values found according to our approach. Nature contributions to people; Plural valuation; Social participation; Integration: decision making.

Dataset Information

Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.

Publications

Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature.

Similar Datasets

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