ABOUT PPInterFinder

PPInterFinder is a web server that integrates text mining and information extraction techniques to mine information on Protein-Protein Interaction (PPI) from biomedical literature. The server is specific to human PPI and is more accurate to extract human PPI from biomedical literature. It uses two background modules namely, NAGGNER (http://www.biominingbu.org:8080/NAGGNER) for Named Entity Recognition (NER) and ProNormz (http://www.biominingbu.org/pronormz) for normalization. These two modules are highly specific to human proteins and have already been developed in the same lab. NAGGNER and ProNormz are available for biocuration purposes as two separate tools.

The input for PPInterFinder can be a biomedical abstract(s) or full text, and the corresponding output is the mined PPI information. The output sentence replaces the original protein names to the corresponding Entrez Gene’s official symbol and the confirmed relation keyword to its root word. For example, the root word for the group interacts, interacted, interacting and interaction is simply ‘interact’. The server provides three different options to upload the input; (i) PPInterFinder Format (ii) MEDLINE Format and (iii) XML Format. The MEDLINE and XML formats are recommended to be in the NCBI order as this differs between the databases. Samples inputs are available in the home page. Presence of some special character like Greek letters is not supported by the server.

Dr. Kalpana Raja Dr. Suresh Subramani Dr. Jeyakumar Natarajan
PhD Student PhD Student Associate Professor

Data Mining and Text Mining Laboratory,
Department of Bioinformatics,
School of Life Sciences,
Bharathiar University,
Coimbatore - 641 046,
Tamilnadu, INDIA


Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan. (2013)  PPInterFinder--a mining tool for extracting causal relations on human proteins from literature. Database (Oxford), bas052. PDF

Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Cejuela JM, Dubey P, Wu C.(2013) An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.Database (Oxford), bas056. PDF

Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan (2012)  PPInterFinder – A web server for mining human protein - protein interactions. In the Proceedings of BioCreative Workshop 2012, 4-5 Apr 2012, Washington DC, USA, 151-163. PDF


Supplementary Data 


This work has been carried out as a part of the Department of Information Technology (DIT) project entitled "Text Mining and Data Warehousing of Protein Kinases Relationships and Pathways" at Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India.