A collaborative knowledge base for cognitive phenomics

Abstract

The human genome project has stimulated development of impressive repositories of biological knowledge at the genomic level and new knowledge bases are rapidly being developed in a 'bottom-up' fashion. In contrast, higher-level phenomics knowledge bases are underdeveloped, particularly with respect to the complex neuropsychiatric syndrome, symptom, cognitive, and neural systems phenotypes widely acknowledged as critical to advance molecular psychiatry research. This gap limits informatics strategies that could improve both the mining and representation of relevant knowledge, and help prioritize phenotypes for new research. Most existing structured knowledge bases also engage a limited set of contributors, and thus fail to leverage recent developments in social collaborative knowledge-building. We developed a collaborative annotation database to enable representation and sharing of empirical information about phenotypes important to neuropsychiatric research (www.Phenowiki.org). As a proof of concept, we focused on findings relevant to 'cognitive control', a neurocognitive construct considered important to multiple neuropsychiatric syndromes. Currently this knowledge base tabulates empirical findings about heritabilities and measurement properties of specific cognitive task and rating scale indicators (n=449 observations). It is hoped that this new open resource can serve as a starting point that enables broadly collaborative knowledge-building, and help investigators select and prioritize endophenotypes for translational research.

Figure 1

Methods showing ‘procedures’ (boxes) and ‘products’ (octagons) used to empirically define ‘cognitive control’ via the most strongly associated literature terms and specific task indicators. See ‘Materials and methods’ for details.

Figure 2

‘Velocity’ of cognitive control concept and its subcomponents. Figure displays the publication frequency (number of unique PMID citations) for each term by year. X axis shows the years; y axis shows how many articles for each concept in each year expressed as a percentage of total number of articles over the 10-year span for that concept to normalize for differences in overall literature size.

Figure 3

Components of the construct ‘cognitive control’. Figure displays a graphical representation of the construct ‘cognitive control’ as defined by the literature and expert review of behavioral tasks. Circles represent concepts most closely associated in the literature with the term cognitive control. Thickness of the circles represents the size of each literature. Arrows show where the term cognitive control was linked directly with a behavioral task, without first being related to one of the four concepts. Thickness of these lines represents number of occurrences. Bubbles depict cognitive tasks associated with each cognitive concept as determined by expert review of the literature. Distances between bubble and concepts, as well as between concepts, represent the strength of association (that is, number of co-occurrences).

Figure 4

The neuropsychiatric phenomics approach contrasts with the traditional approach to psychiatric genetics studies, in which gene–syndrome relationships are assessed directly. The neuropsychiatric phenomics strategy involves analysis of multiple levels of intermediate traits, across multiple syndromal categories.