scholarly journals Semantic Annotation for Biological Information Retrieval System

2015 ◽  
Vol 2015 ◽  
pp. 1-11 ◽  
Author(s):  
Mohamed Marouf Z. Oshaiba ◽  
Enas M. F. El Houby ◽  
Akram Salah
Keyword(s):  
Query Expansion ◽  
Retrieval System ◽  
Biological Process ◽  
Semantic Annotation ◽  
Information Retrieval System ◽  
Cellular Component ◽  
Biological Information ◽  
Molecular Function ◽  
Problem Finding ◽  
Biological Domain

Online literatures are increasing in a tremendous rate. Biological domain is one of the fast growing domains. Biological researchers face a problem finding what they are searching for effectively and efficiently. The aim of this research is to find documents that contain any combination of biological process and/or molecular function and/or cellular component. This research proposes a framework that helps researchers to retrieve meaningful documents related to their asserted terms based on gene ontology (GO). The system utilizes GO by semantically decomposing it into three subontologies (cellular component, biological process, and molecular function). Researcher has the flexibility to choose searching terms from any combination of the three subontologies. Document annotation is taking a place in this research to create an index of biological terms in documents to speed the searching process. Query expansion is used to infer semantically related terms to asserted terms. It increases the search meaningful results using the term synonyms and term relationships. The system uses a ranking method to order the retrieved documents based on the ranking weights. The proposed system achieves researchers’ needs to find documents that fit the asserted terms semantically.

scholarly journals Transcriptomic inspection revealed a possible pathway regulating the formation of the high-quality brush hair in Chinese Haimen goat ( Capra hircus )

2018 ◽  
Vol 5 (1) ◽  
pp. 170907 ◽  
Author(s):  
Dejun Ji ◽  
Bo Yang ◽  
Yongjun Li ◽  
Miaoying Cai ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Biological Process ◽  
Kegg Pathway ◽  
Cellular Component ◽  
Biological Information ◽  
Capra Hircus ◽  
Molecular Function ◽  
High Quality ◽  
Type Iii ◽  
Kegg Pathways ◽  
Kegg Pathway Analysis

The high-quality brush hair, or Type III brush hair, is coarse hair but with a tip and little medulla, which uniquely grows in the cervical carina of Chinese Haimen goat ( Capra hircus ). To unveil the mechanism of the formation of Type III brush hair in Haimen goats, transcriptomic RNAseq technology was used for screening of differentially expressed genes (DEGs) in the skin samples of the Type III and the non-Type III hair goats, and these DEGs were analysed by KEGG pathway analysis. The results showed that a total of 295 DEGs were obtained, mainly from three main functional types: cellular component, molecular function and biological process. These DEGs were mainly enriched in three KEGG pathways, such as protein processing in endoplasmic reticulum, MAPK, and complement and coagulation cascades. These DEGs gave hints to a possible mechanism, under which heat stress possibly initiated the formation. The study provided some useful biological information, which could give a new view about the roles of certain factors in hair growth and give hints on the mechanism of the formation of the Type III brush hair in Chinese Haimen goat.

An Improved VSM Based Information Retrieval System and Fuzzy Query Expansion

2005 ◽  
pp. 537-546 ◽  
Author(s):  
Jiangning Wu ◽  
Hiroki Tanioka ◽  
Shizhu Wang ◽  
Donghua Pan ◽  
Kenichi Yamamoto ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Query Expansion ◽  
Retrieval System ◽  
Information Retrieval System ◽  
Fuzzy Query

CP Poly(A) RNA Binding Immunity via Outside-in Glycosyltransfer with MT of BTRC-Activating L12535 and PIN1 Subnetworks for Cognition in PFC|CD14

2020 ◽  
Author(s):  
Lin Wang ◽  
Qingchun Chen ◽  
Haitao Feng ◽  
Minghu Jiang ◽  
Juxiang Huang ◽  
...  
Keyword(s):  
Immune Response ◽  
Network Inference ◽  
Rna Binding ◽  
Biological Process ◽  
Cellular Component ◽  
Innate Immune ◽  
Molecular Function ◽  
Ubiquitin Protein Ligase ◽  
The Common ◽  
Cluster Of Differentiation

Abstract Background: Ras suppressor protein 1 (L12535) and peptidylprolyl cis/trans isomerase NIMA-interacting 1 (PIN1) common molecular and knowledge subnetworks containing microtubule associated protein 1B-MAP1B_1 (upstream) related to cognition by references were identified in human left hemisphere, based on our established significant high expression beta-transducin repeat containing E3 ubiquitin protein ligase (BTRC)-activating downstream Gene (protein) reconstruction network inference (GRNInfer) and Database for Annotation, Visualization and Integrated Discovery (DAVID).Results: Our results show the common molecules exostosin-like glycosyltransferase 2 (EXTL2) interaction with MAP1B_1 both activating TERF1_1 with HSP90AB1 from BTRC-activating downstream GRNInfer database; The common biological process and molecular function of MAP1B_1, TERF1_1 as microtubule (MT) binding; HSP90AB1 as poly(A) RNA binding; BTRC, HSP90AB1, PIN1 as innate immune response from BTRC-activating downstream DAVID database; The common cellular component of EXTL2 at integral component of membrane; MAP1B_1, HSP90AB1, TERF1_1 at cytoplasm (CP); The common tissue distributions of L12535 and PIN1 in Prefrontal Cortex (PFC), PB cluster of differentiation (CD)14+Monocytes.Conclusions: We propose and mutual positively verify CP poly(A) RNA binding immunity via outside-in glycosyltransfer with MT of BTRC-activating L12535 and PIN1 subnetworks for cognition in PFC|CD14.

Towards a Possibilistic Information Retrieval System Using Semantic Query Expansion

2012 ◽  
pp. 216-242
Author(s):  
Bilel Elayeb ◽  
Ibrahim Bounhas ◽  
Oussama Ben Khiroun ◽  
Fabrice Evrard ◽  
Narjès Bellamine-BenSaoud
Keyword(s):  
Information Retrieval ◽  
Query Expansion ◽  
Retrieval System ◽  
Possibility Theory ◽  
Information Retrieval System ◽  
Test Collection ◽  
Expansion Process ◽  
Semantic Query ◽  
Linguistic Resources ◽  
Relevance Measure

This paper presents a new possibilistic information retrieval system using semantic query expansion. The work is involved in query expansion strategies based on external linguistic resources. In this case, the authors exploited the French dictionary “Le Grand Robert”. First, they model the dictionary as a graph and compute similarities between query terms by exploiting the circuits in the graph. Second, the possibility theory is used by taking advantage of a double relevance measure (possibility and necessity) between the articles of the dictionary and query terms. Third, these two approaches are combined by using two different aggregation methods. The authors also benefit from an existing approach for reweighting query terms in the possibilistic matching model to improve the expansion process. In order to assess and compare the approaches, the authors performed experiments on the standard ‘LeMonde94’ test collection.

scholarly journals Luppar: An Information Retrieval System for Closed Document Collections

2018 ◽  
Author(s):  
Fabiano Tavares Da Silva ◽  
José Everardo Bessa Maia
Keyword(s):  
Information Retrieval ◽  
Query Expansion ◽  
Retrieval System ◽  
Information Retrieval System ◽  
Local Context ◽  
Semantic Model ◽  
Context Analysis ◽  
Document Collections

This article presents Luppar, an Information Retrieval tool for closed collections of documents which uses a local distributional semantic model associated to each corpus. The system performs automatic query expansion using a combination of distributional semantic model and local context analysis and supports relevancy feedback. The performance of the system was evaluated in databases of different domains and presented results equal to or higher than those published in the literature.

scholarly journals Multi-Level Analyses of Genome-Wide Association Study to Reveal Significant Risk Genes and Pathways in Neuromyelitis Optica Spectrum Disorder

2021 ◽  
Vol 12 ◽  
Author(s):  
Ting Li ◽  
He Li ◽  
Yue Li ◽  
Shu-An Dong ◽  
Ming Yi ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Biological Process ◽  
Susceptibility Gene ◽  
Susceptibility Genes ◽  
Cellular Component ◽  
Molecular Function ◽  
Risk Genes ◽  
Kegg Pathways ◽  
Gene Sets ◽  
Genome Wide

BackgroundNeuromyelitis optica spectrum disorder (NMOSD) is an inflammatory disease of the central nervous system and it is understandable that environmental and genetic factors underlie the etiology of NMOSD. However, the susceptibility genes and associated pathways of NMOSD patients who are AQP4-Ab positive and negative have not been elucidated.MethodsSecondary analysis from a NMOSD Genome-wide association study (GWAS) dataset originally published in 2018 (215 NMOSD cases and 1244 controls) was conducted to identify potential susceptibility genes and associated pathways in AQP4-positive and negative NMOSD patients, respectively (132 AQP4-positive and 83 AQP4-negative).ResultsIn AQP4-positive NMOSD cases, five shared risk genes were obtained at chromosome 6 in AQP4-positive NMOSD cases by using more stringent p-Values in both methods (p < 0.05/16,532), comprising CFB, EHMT2, HLA-DQA1, MSH5, and SLC44A4. Fifty potential susceptibility gene sets were determined and 12 significant KEGG pathways were identified. Sixty-seven biological process pathways, 32 cellular-component pathways, and 29 molecular-function pathways with a p-Value of <0.05 were obtained from the GO annotations of the 128 pathways identified. In the AQP4 negative NMOSD group, no significant genes were obtained by using more stringent p-Values in both methods (p < 0.05/16,485). The 22 potential susceptibility gene sets were determined. There were no shared potential susceptibility genes between the AQP4-positive and negative groups, furthermore, four significant KEGG pathways were also identified. Of the GO annotations of the 165 pathways identified, 99 biological process pathways, 37 cellular-component pathways, and 29 molecular-function pathways with a p-Value of <0.05 were obtained.ConclusionThe potential molecular mechanism underlying NMOSD may be related to proteins encoded by these novel genes in complements, antigen presentation, and immune regulation. The new results may represent an improved comprehension of the genetic and molecular mechanisms underlying NMOSD.

Lexical Co-Occurrence and Contextual Window-Based Approach with Semantic Similarity for Query Expansion

2017 ◽  
Vol 13 (3) ◽  
pp. 57-78 ◽  
Author(s):  
Jagendra Singh ◽  
Rakesh Kumar
Keyword(s):  
Semantic Similarity ◽  
Query Expansion ◽  
Ad Hoc ◽  
Retrieval System ◽  
Hybrid Approach ◽  
Information Retrieval System ◽  
Query Reformulation ◽  
Baseline Method ◽  
Benchmark Datasets ◽  
Pseudo Feedback

Query expansion (QE) is an efficient method for enhancing the efficiency of information retrieval system. In this work, we try to capture the limitations of pseudo-feedback based QE approach and propose a hybrid approach for enhancing the efficiency of feedback based QE by combining corpus-based, contextual based information of query terms, and semantic based knowledge of query terms. First of all, this paper explores the use of different corpus-based lexical co-occurrence approaches to select an optimal combination of query terms from a pool of terms obtained using pseudo-feedback based QE. Next, we explore semantic similarity approach based on word2vec for ranking the QE terms obtained from top pseudo-feedback documents. Further, we combine co-occurrence statistics, contextual window statistics, and semantic similarity based approaches together to select the best expansion terms for query reformulation. The experiments were performed on FIRE ad-hoc and TREC-3 benchmark datasets. The statistics of our proposed experimental results show significant improvement over baseline method.

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