GeneClinics: a hybrid text/data electronic publishing model using XML applied to clinical genetic testing

Abstract

GeneClinics is an online genetic information resource consisting of descriptions of specific inherited disorders ("disease profiles") as well as information on the role of genetic testing in the diagnosis, management, and genetic counseling of patients with these inherited conditions. GeneClinics is intended to promote the use of genetic services in medical care and personal decision making by providing health care practitioners and patients with information on genetic testing for specific inherited disorders. GeneClinics is implemented as an object-oriented database containing a combination of data and semistructured text that is rendered as HTML for publishing a given "disease profile" on the Web. Content is acquired from authors via templates, converted to an XML document reflecting the underlying database schema (with tagging of embedded data), and then loaded into the database and subjected to peer review. The initial implementation of a production system and the first phase of population of the GeneClinics database content are complete. Further expansion of the content to cover more disease, significant scaling up of rate of content creation, and evaluation redesign are under way. The ultimate goal is to have an entry in GeneClinics for each entry in the GeneTests directory of medical genetics laboratories-that is, for each disease for which clinical genetic testing is available.

Figure 1

Top-level GeneClinics biological data model. This modified entity-relationship diagram illustrates the relationship between phenotype and genotype in the GeneClinics database as well as the relationship among the biological entities. This is a simplified high-level diagram of a subset of the biological data model, focusing on elements pertinent to the electronic publishing model. It does not represent the full entity-relationship diagram.

Figure 2

Sample instantiation of the GeneClinics biologic data model, showing the sharing of a single locus, gene, normal allele, and normal product by two distinct diseases caused by two different mutations (a deletion and a duplication of a 1.5-mega-base segment of DNA). The two diseases are Charcot-Marie-Tooth type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP).

Figure 3

Fragments of the GeneClinics XML document type definition.

Figure 4

Overview of information flow in the GeneClinics electronic publishing model. This diagram shows the flow of information from the authors to the GeneClinics editorial staff and reviewers and, ultimately, to the readership. It also illustrates the necessary data format conversion.

Figure 5

Screen shot of the WordPerfect-based XML editor open to early onset Alzheimer disease.

Figure 6

Screen shot of the HTML-rendered GeneClinics content for early onset Alzheimer disease.