back to NS210b Class page
A collaborative knowledge base for cognitive phenomics
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.
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 (www.Phenowiki.org). 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.
phenotype; cognition; heritability; genetics; cognitive control; informatics
- Input Author
- 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
Main procedure involved using PubMed to view literature and use PubAtlas.org 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.
- 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.