Food packaging permeability and composition dataset dedicated to text-mining.
Ontology highlight
ABSTRACT:
SUBMITTER: Lentschat M
PROVIDER: S-EPMC8144675 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:This dataset is dedicated to text mining and is composed of partial n-Ary relation instances concerning food packaging composition and gas permeability. It was created from 31 tables derived from 10 English-language scientific articles in html format from several international journals hosted on the ScienceDirect website. This dataset includes two sets of data: manual table annotation results and automatic data extraction results. The tables were first annotated by one annotator and cross-curated by three different annotators. The annotation task aimed to identify all table data dealing with packaging permeability measurements and compositions. An Ontological and Terminological Resource (OTR) was used for the annotation process. The annotation guidelines were drawn up through a collective iterative approach involving the annotators, and they may be accessed alongside the data. This dataset of n-Ary relations can be used in natural language processing (NLP) approaches implemented in experimental fields, especially for n-Ary relation extraction research. It can also be useful for training or evaluation of methods for the extraction of experimental data from tables and text in scientific documents, especially in experimental domains such as food packaging.
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Project description:The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate.
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Project description:BackgroundDecoding transcriptional regulatory networks and the genomic cis-regulatory logic implemented in their control nodes is a fundamental challenge in genome biology. High-throughput computational and experimental analyses of regulatory networks and sequences rely heavily on positive control data from prior small-scale experiments, but the vast majority of previously discovered regulatory data remains locked in the biomedical literature.ResultsWe develop text-mining strategies to identify relevant publications and extract sequence information to assist the regulatory annotation process. Using a vector space model to identify Medline abstracts from papers likely to have high cis-regulatory content, we demonstrate that document relevance ranking can assist the curation of transcriptional regulatory networks and estimate that, minimally, 30,000 papers harbor unannotated cis-regulatory data. In addition, we show that DNA sequences can be extracted from primary text with high cis-regulatory content and mapped to genome sequences as a means of identifying the location, organism and target gene information that is critical to the cis-regulatory annotation process.ConclusionOur results demonstrate that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated cis-regulatory data needed to catalyze advances in the field of gene regulation.
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