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PMID 18180765


  • Title

A collaborative knowledge base for cognitive phenomics

  • Reference

Sabb FW, Bearden CE, Glahn DC, Parker DS, Freimer N, Bilder RM. A collaborative knowledge base for cognitive phenomics. Molecular Psychiatry. 2008 Apr;13(4):350-60.

  • 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 representa- tion and sharing of empirical information about phenotypes important to neuropsychiatric research ( As a proof of concept, we focused on findings relevant to cognitive control, a neurocognitive construct considered important to multiple neuro-psychiatric 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.

  • Keywords

phenotype; cognition; heritability; genetics; cognitive control; informatics

  • Input Author



  • Introduction/Aims
A figure that details the phenomics strategy that looks a multi-variate and multi-level phenotypes
Refining cognitive and behavioral phenotypes is crucial for neuropsychiatry. Searching for genes and underlying biology of syndromes will be difficult unless the right phenotypes are being studied.
Current endophenotypes are poorly understood
Using informatics approaches to improve knowledge structure will help
Informatics tools get better as you get closer to the gene (BLAST and gene ontology), but are poor at the level of syndromes/symptoms/behavior (but see cognitive atlas project)
The aim of this paper was to develop a knowledgebase that focuses on these top levels to help examine and select relevant behavioral phenotypes for use in neuropsychiatric gwas studies

  • Method
A review paper/meta-analysis. see flow diagram for details.
Flow of methods and procedure for the review and analysis

Main procedure involved using PubMed to view literature and use to BLAST pubmed in order to find similar constructs as determined by co-occurrence in titles and abstracts in pubmed. These resulted in a set of papers which were reviewed by hand to determine what measurements were used in the particular manuscript and then these concepts and measurements were reviewed for findings in twin and family studies to determine heritability.

  • Results

Velocity of the use of the term cognitive control in the published literature over the last ten years in comparison to similar latent constructs (including working memory, response selction, task-switching)
Heatmap of pairwise searches of latent constructs. Jaccard value is a measure of co-occurence
Cognitive Control construct and related concepts and tasks. Thickness of circles represent literature size and distance from cognitive control label represents co-occurence frequency

Table of findings for heritability of construct

  • Discussion
    • Informatics tools can aid task selection by exposing interactions at the cognitive and behavioral level
    • Cognitive control is a latent construct being used more frequently in the literature, but likely represents a re-framing of previous tasks and concepts as the measurements do not differ from closely related constructs like working memory and response inhibition
    • Components of cognitive control are moderately heritable, but some indicators might be misused.