How are contradictory relation findings resolved in Pathway Studio?
Relations are supported by facts extracted from the literature using MedScan, a Natural Language Processing (NLP) tool developed by Ariadne. Extracted information is added in ResNet databases and can be access through the Pathway Studio interface.
The extracted facts (displayed as relations) reflect the content of the literature. Contradictory findings come from three major reasons:
1. The effect is biologically context-dependant. Different localizations (cell compartment, cell and tissue type, organ, etc.), disease states, treatments, physical parameters (temperature, pH, etc.) can explain contradictory findings in Pathway Studio.
2. Scientific documents are contradictory. Authors have divergent interpretations or points of view.
3. The finding is a result of a text mining error. Ariadne has invested six years of development effort to prepare, screen and perfect our text mining mechanism and error.
Pathway Studio provides an excellent environment to assist the researcher in resolving contradictory findings. The number of references supporting a relation is a good first indicator of the finding accuracy. Pathway Studio allows researchers to review each relation individually to understand the context in which it was described in the literature. This is a good practice for relations with a low number of supporting references that are of special interest to the researcher. Actually Pathway Studio does not resolve apparent contradictions but exposes the references so that researchers can investigate and contextualize them.
There are different options to access the literature and the number of references supporting a relation in Pathway Studio:
1. From the Graphical View, put your mouse on a relation and a pop-up window appears that displays the number of references and two extracted sentences. By clicking on ‘more..’ from this pop-up window, you can display all sentences supporting a relation and direct hyperlinks to PubMed abstract of all supporting references in the Preview Pane.
2. From the Graphical View, double click on a relation or right click on a relation and select Properties in the menu. From there you have access to even more information on references supporting a relation (Journal name, etc.).
3. From the Relation Table View, it is possible to sort relations by number of supporting references. Sentences, Medline reference and many other fields can be displayed in the table view.
4. From the Folders tab of the main pane, right click on a pathway file and select Preview in the menu (or put your mouse on a pathway file and click on ‘more..’ from the displayed pop-up window). From there you have access to information on the selected pathway. You can easily navigate in the Preview pane to review the number of references and all extracted sentences supporting each relations of the pathway.
Pathway Studio interface facilitates management of contradiction findings. Once a contradiction is resolved, the researcher can remove a relation from a table or graphical view and even delete it from the ResNet database.
You can refer to the following FAQ to see how to permanently delete a relation from the ResNet database: HOW CAN I PERMANENTLY DELETE A RELATION OR ENTITY FROM THE RESNET DATABASE?
