Integrating text--mining effort requires output standards

Abstract

AbstractWe recently released a plugin to Pathvisio to assist the curator with automatic integration of heterogeneous pathway knowledge. Pathway curation involves gathering this knowledge not only through discussions with peers, but also from biological databases and the scientific literature. Integrating this all into one pathway is challenging and to date still mainly a laborious manual process.More and more biological databases provide webservices (ie. REST or SOAP). The main objective of webservices is to provide an interface for other computer applications. Our plug-in uses these interfaces to gather binary relationships of a given pathway entity and present the relation in star shaped figures to the curator. The plug-in also uses functionality of Pathvisio to project and visualize research data on pathways. If research data exists, this can then be projected on to the suggested potential novel entities. The curator can then make an educated decision on extending pathways with database knowledge.Different text mining methods exist to process large quantities of available literature. Text mining results can be very valuable in pathway curation. Integrating them in a similar way as with biological databases is difficult. It requires a text-mining output standard. In our current plug-in we included text-mining support in our current version of the plug-in.We like to propose here a standard for text mining output. The output standard is a data object that captures the relationships found with text mining, the document identifiers, the sentences from where the results originate, the method used, and its metrics. Such an output standard would enable a user-oriented comparison of text mining results. Currently, text-mining results are mainly evaluated on their performance in finding relevant results. By enabling a text mining out standard, the results become available to the larger user community. The data is immediately accessible to a wide range of applications. If a text mining method supports our output standard, the pathway curation community can use it in Pathvisio through our plug-in.