scholarly journals Identifying and Classifying Goals For Scientific Knowledge

2021 ◽  
Author(s):  
Mayla R Boguslav ◽  
Nourah M Salem ◽  
Elizabeth K White ◽  
Sonia M Leach ◽  
Lawrence E Hunter
Keyword(s):  
Natural Language Processing ◽  
Language Processing ◽  
Scientific Knowledge ◽  
Gold Standard ◽  
Source Code ◽  
Biomedical Literature ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Text Documents ◽  
Prenatal Nutrition

Motivation: Science progresses by posing good questions, yet work in biomedical text mining has not focused on them much. We propose a novel idea for biomedical natural language processing: identifying and characterizing the questions stated in the biomedical literature. Formally, the task is to identify and characterize ignorance statements, statements where scientific knowledge is missing or incomplete. The creation of such technology could have many significant impacts, from the training of PhD students to ranking publications and prioritizing funding based on particular questions of interest. The work presented here is intended as the first step towards these goals. Results: We present a novel ignorance taxonomy driven by the role ignorance statements play in the research, identifying specific goals for future scientific knowledge. Using this taxonomy and reliable annotation guidelines (inter-annotator agreement above 80%), we created a gold standard ignorance corpus of 60 full-text documents from the prenatal nutrition literature with over 10,000 annotations and used it to train classifiers that achieved over 0.80 F1 scores. Availability: Corpus and source code freely available for download at https://github.com/UCDenver-ccp/Ignorance-Question-Work. The source code is implemented in Python.

scholarly journals A Novel Metric to Quantify the Effect of Pathway Enrichment Evaluation With Respect to Biomedical Text-Mined Terms: Development and Feasibility Study (Preprint)

2021 ◽  
Author(s):  
Xuan Qin ◽  
Xinzhi Yao ◽  
Jingbo Xia
Keyword(s):  
Natural Language Processing ◽  
Text Mining ◽  
Drug Use ◽  
Natural Language ◽  
Language Processing ◽  
Entity Recognition ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Related Gene ◽  
Pathway Enrichment

BACKGROUND Natural language processing has long been applied in various applications for biomedical knowledge inference and discovery. Enrichment analysis based on named entity recognition is a classic application for inferring enriched associations in terms of specific biomedical entities such as gene, chemical, and mutation. OBJECTIVE The aim of this study was to investigate the effect of pathway enrichment evaluation with respect to biomedical text-mining results and to develop a novel metric to quantify the effect. METHODS Four biomedical text mining methods were selected to represent natural language processing methods on drug-related gene mining. Subsequently, a pathway enrichment experiment was performed by using the mined genes, and a series of inverse pathway frequency (IPF) metrics was proposed accordingly to evaluate the effect of pathway enrichment. Thereafter, 7 IPF metrics and traditional <i>P</i> value metrics were compared in simulation experiments to test the robustness of the proposed metrics. RESULTS IPF metrics were evaluated in a case study of rapamycin-related gene set. By applying the best IPF metrics in a pathway enrichment simulation test, a novel discovery of drug efficacy of rapamycin for breast cancer was replicated from the data chosen prior to the year 2000. Our findings show the effectiveness of the best IPF metric in support of knowledge discovery in new drug use. Further, the mechanism underlying the drug-disease association was visualized by Cytoscape. CONCLUSIONS The results of this study suggest the effectiveness of the proposed IPF metrics in pathway enrichment evaluation as well as its application in drug use discovery.

Enhancing Disability Determination Decision Process Through Natural Language Processing

2019 ◽  
Vol 4 (2) ◽  
pp. 15-28
Author(s):  
Eslam Amer
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Decision Process ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Disability Benefits ◽  
Disability Benefit ◽  
New Approach ◽  
Disability Determination

In this article, a new approach is introduced that makes use of the valuable information that can be extracted from a patient's electronic healthcare records (EHRs). The approach employs natural language processing and biomedical text mining to handle patient's data. The developed approach extracts relevant medical entities and builds relations between symptoms and other clinical signature modifiers. The extracted features are viewed as evaluation features. The approach utilizes such evaluation features to decide whether an applicant could gain disability benefits or not. Evaluations showed that the proposed approach accurately extracts symptoms and other laboratory marks with high F-measures (93.5-95.6%). Also, results showed an excellent deduction in assessments to approve or reject an applicant case to obtain a disability benefit.

Enhancing Disability Determination Decision Process Through Natural Language Processing

2022 ◽  
pp. 682-693
Author(s):  
Eslam Amer
Keyword(s):  
Natural Language Processing ◽  
Text Mining ◽  
Natural Language ◽  
Language Processing ◽  
Decision Process ◽  
Biomedical Text ◽  
Biomedical Text Mining ◽  
Disability Benefits ◽  
New Approach ◽  
Disability Determination

In this article, a new approach is introduced that makes use of the valuable information that can be extracted from a patient's electronic healthcare records (EHRs). The approach employs natural language processing and biomedical text mining to handle patient's data. The developed approach extracts relevant medical entities and builds relations between symptoms and other clinical signature modifiers. The extracted features are viewed as evaluation features. The approach utilizes such evaluation features to decide whether an applicant could gain disability benefits or not. Evaluations showed that the proposed approach accurately extracts symptoms and other laboratory marks with high F-measures (93.5-95.6%). Also, results showed an excellent deduction in assessments to approve or reject an applicant case to obtain a disability benefit.

scholarly journals Comparison of natural language processing tools for automatic gene ontology annotation of scientific literature

2018 ◽  
Author(s):  
Lucas Beasley ◽  
Prashanti Manda
Keyword(s):  
Gene Ontology ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Gold Standard ◽  
Scientific Literature ◽  
Biomedical Literature ◽  
Automated Annotation ◽  
Manual Curation ◽  
Gold Standard Reference

Manual curation of scientific literature for ontology-based knowledge representation has proven infeasible and unscalable to the large and growing volume of scientific literature. Automated annotation solutions that leverage text mining and Natural Language Processing (NLP) have been developed to ameliorate the problem of literature curation. These NLP approaches use parsing, syntactical, and lexical analysis of text to recognize and annotate pieces of text with ontology concepts. Here, we conduct a comparison of four state of the art NLP tools at the task of recognizing Gene Ontology concepts from biomedical literature using the Colorado Richly Annotated Full-Text (CRAFT) corpus as a gold standard reference. We demonstrate the use of semantic similarity metrics to compare NLP tool annotations to the gold standard.

scholarly journals Comparison of natural language processing tools for automatic gene ontology annotation of scientific literature

2018 ◽  
Author(s):  
Lucas Beasley ◽  
Prashanti Manda
Keyword(s):  
Gene Ontology ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Gold Standard ◽  
Scientific Literature ◽  
Biomedical Literature ◽  
Automated Annotation ◽  
Manual Curation ◽  
Gold Standard Reference

Manual curation of scientific literature for ontology-based knowledge representation has proven infeasible and unscalable to the large and growing volume of scientific literature. Automated annotation solutions that leverage text mining and Natural Language Processing (NLP) have been developed to ameliorate the problem of literature curation. These NLP approaches use parsing, syntactical, and lexical analysis of text to recognize and annotate pieces of text with ontology concepts. Here, we conduct a comparison of four state of the art NLP tools at the task of recognizing Gene Ontology concepts from biomedical literature using the Colorado Richly Annotated Full-Text (CRAFT) corpus as a gold standard reference. We demonstrate the use of semantic similarity metrics to compare NLP tool annotations to the gold standard.

LIS4: Lesk Inspired Sense Specific Semantic Similarity using WordNet

2021 ◽  
pp. 2150006
Author(s):  
Saravanakumar Kandasamy ◽  
Aswani Kumar Cherukuri
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Semantic Similarity ◽  
Language Processing ◽  
Gold Standard ◽  
Question Answering ◽  
Knowledge Based ◽  
Benchmark Datasets ◽  
Processing Information

Semantic similarity quantification between concepts is one of the inevitable parts in domains like Natural Language Processing, Information Retrieval, Question Answering, etc. to understand the text and their relationships better. Last few decades, many measures have been proposed by incorporating various corpus-based and knowledge-based resources. WordNet and Wikipedia are two of the Knowledge-based resources. The contribution of WordNet in the above said domain is enormous due to its richness in defining a word and all of its relationship with others. In this paper, we proposed an approach to quantify the similarity between concepts that exploits the synsets and the gloss definitions of different concepts using WordNet. Our method considers the gloss definitions, contextual words that are helping in defining a word, synsets of contextual word and the confidence of occurrence of a word in other word’s definition for calculating the similarity. The evaluation based on different gold standard benchmark datasets shows the efficiency of our system in comparison with other existing taxonomical and definitional measures.

scholarly journals INDRA-IPM: interactive pathway modeling using natural language with automated assembly

2019 ◽  
Vol 35 (21) ◽  
pp. 4501-4503 ◽  
Author(s):  
Petar V Todorov ◽  
Benjamin M Gyori ◽  
John A Bachman ◽  
Peter K Sorger
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Web Service ◽  
Language Processing ◽  
Source Code ◽  
Supplementary Information ◽  
Expression Data ◽  
Supplementary Data ◽  
Automated Assembly ◽  
Web Based

Abstract Summary INDRA-IPM (Interactive Pathway Map) is a web-based pathway map modeling tool that combines natural language processing with automated model assembly and visualization. INDRA-IPM contextualizes models with expression data and exports them to standard formats. Availability and implementation INDRA-IPM is available at: http://pathwaymap.indra.bio. Source code is available at http://github.com/sorgerlab/indra_pathway_map. The underlying web service API is available at http://api.indra.bio:8000. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems

Database ◽  
2018 ◽  
Vol 2018 ◽  
Author(s):  
Wasila Dahdul ◽  
Prashanti Manda ◽  
Hong Cui ◽  
James P Balhoff ◽  
T Alexander Dececchi ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Gold Standard
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