Literature mining and ontology based analysis of host-Brucella gene-gene interaction network

Ilknur Karadeniz, Junguk Hur, Yongqun He, Arzucan Özgür

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Brucella is an intracellular bacterium that causes chronic brucellosis in humans and various mammals. The identification of host-Brucella interaction is crucial to understand host immunity against Brucella infection and Brucella pathogenesis against host immune responses. Most of the information about the inter-species interactions between host and Brucella genes is only available in the text of the scientific publications. Many text-mining systems for extracting gene and protein interactions have been proposed. However, only a few of them have been designed by considering the peculiarities of host-pathogen interactions. In this paper, we used a text mining approach for extracting host-Brucella gene-gene interactions from the abstracts of articles in PubMed. The gene-gene interactions here represent the interactions between genes and/or gene products (e.g., proteins). The SciMiner tool, originally designed for detecting mammalian gene/protein names in text, was extended to identify host and Brucella gene/protein names in the abstracts. Next, sentence-level and abstract-level co-occurrence based approaches, as well as sentence-level machine learning based methods, originally designed for extracting intra-species gene interactions, were utilized to extract the interactions among the identified host and Brucella genes. The extracted interactions were manually evaluated. A total of 46 host-Brucella gene interactions were identified and represented as an interaction network. Twenty four of these interactions were identified from sentence-level processing. Twenty two additional interactions were identified when abstract-level processing was performed. The Interaction Network Ontology (INO) was used to represent the identified interaction types at a hierarchical ontology structure. Ontological modeling of specific gene-gene interactions demonstrates that host-pathogen gene-gene interactions occur at experimental conditions which can be ontologically represented. Our results show that the introduced literature mining and ontology-based modeling approach are effective in retrieving and analyzing host-pathogen gene-gene interaction networks.

Original languageEnglish (US)
Article number01386
JournalFrontiers in Microbiology
Issue numberDEC
StatePublished - 2015
Externally publishedYes


  • Brucella
  • Host and pathogen gene name recognition
  • Host-pathogen interaction extraction
  • Interaction Network Ontology (INO)
  • SciMiner
  • Support vector machines (SVM)
  • Text mining

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)


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