Ignet

Documentation

Cite Ignet:

Ozgur A, Hur J, Xiang Z, Ong E, Radev D, and He Y. Ignet: A centrality and INO-based web system for analyzing and visualizing literature-mined networks. August 1-2, 2016, joint session ICBO+BioCreative, at the International Conference on Biomedical Ontologies (ICBO-2016) and BioCreative 2016, August 1-4, 2016, Oregon State University, Corvallis, OR, USA. 2-page proceeding paper (http://ceur-ws.org/Vol-1747/BP01_ICBO2016.pdf).

note: A journal article about Ignet is under preparation.

Our own publications as references for Ignet development:

Ignet was co-developed by three groups led by Dr. Oliver He at the University of Michigan, USA, Dr. Junguk Hur at the University of North Dakoda, USA, and Dr. Arzucan Özgür from Bogazici University, Turkey. The following papers published by us have been used as references as our Ignet development.

Erkan G, Ozgur A, Radev DR: Semi-supervised classification for extracting protein interaction sentences using dependency parsing. In: Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL), 2007: 228-237.
Ozgur A, Vu T, Erkan G, Radev DR. Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics 2008, 24(13):i277-285. PMID: 18586725. PMCID: PMC2718658.
Hur J, Schuyler AD, States DJ, Feldman EL. SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 2009, 25(6):838-40. PMID: 19188191. PMCID: PMC2654801.
Ozgur A, Xiang Z, Radev D, and He Y. Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics. 2011, 2(Suppl 2):S8. PMID: 21624163. PMCID: PMC3102897.
Hur J, Xiang Z, Feldman EL, He Y. Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network. BMC Immunology. 2011. 12(1):49. PMID: 21871085. PMCID: PMC3180695.
Hur J, Özgür A, Xiang Z, He Y. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Journal of Biomedical Semantics. 2012, 3:18. PMID: 23256563. PMCID: PMC3599673.
Hur J, Özgür A, Xiang Z, and He Y. Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. Journal of Biomedical Semantics. 2015, 6:2. PMID: 25785184. PMCID: PMC4362819.
Karadeniz İ, Hur J, He Y, Özgür A. Literature Mining and Ontology based Analysis of Host-Brucella Gene-Gene Interaction Network. Front Microbiol. 2015, 6:1386. PMID: 26696993. PMCID: PMC4673313.
Özgür A, Hur J, and He Y. The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Mining. 2016, 9:41. PMID: 28031747. PMCID: PMC5168857.
Hur J, Özgür A, He Y. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J Biomed Semantics. 2017, 8(1):12. PMID: 28288685. PMCID: PMC5348867.
Hur J, Özgür A, He Y. Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. J Biomed Semantics.. 2018, 9(1):17. PMID: 29880031.PMCID: PMC5991464.
Tiftikci M, Özgür A, He Y, Hur J. Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. BMC Bioinformatics.. 2019, 20(Suppl 21):707. PMID: 31865904. PMCID: PMC6927101.

More related information in Ignet:

Also, check the following pages in Ignet for more information:

The Help and Tutorial page for more information about how to use different Ignet features.
The Links page includes the links of data resource, ontologies, and programs used for our Ignet development.

VO-SciMiner, one related Web-based literature mining program developed by our team:

In addition to Ignet, we have also developed VO-SciMiner: a Vaccine Ontology (VO)-based SciMiner program that utilizes VO to ming vaccine-related gene-gene and vaccine-gene interactions. Brucella vaccines are used as the demonstration for this program development. See more information about VO-SciMiner in our paper: PMC3180695. This paper demonstrates the advantages of using ontology to support literature mining of gene interactions in a specific domain such as the vaccine domain.

We also plan to eventually incorporate some attractive and relevant features available in VO-SciMiner to Ignet for more domain specific literature mining, where the domain can be vaccines, cell types, pathways, etc.