Developing Libraries of Semantically-augmented Graphics As Visual Standards for Biomedical Information Systems

Overview

Journal J Biomed Inform

Publisher Elsevier

Specialty Medical Informatics

Date 2025 Feb 17

PMID 39961540

Authors

Melissa D Clarkson

Steven Roggenkamp

Landon T Detwiler

Affiliations

Soon will be listed here.

Abstract

Objective: Visual representations generally serve as supplements to information, rather than as bearers of computable information themselves. Our objective is to develop a method for creating semantically-augmented graphic libraries that will serve as visual standards and can be implemented as visual assets in intelligent information systems.

Methods: Graphics were developed using a composable approach and specified using SVG. OWL was used to represent the entities of our system, which include elements, units, graphics, graphic libraries, and library collections. A graph database serves as our data management system. Semantics are applied at multiple levels: (a) each element is associated with a semantic style class to link visual style to semantic meaning, (b) graphics are described using object properties and data properties, (c) relationships are specified between graphics, and (d) mappings are made between the graphics and outside resources.

Results: The Graphic Library web application enables users to browse the libraries, view information pages for each graphic, and download individual graphics. We demonstrate how SPARQL can be employed to query the graphics database and the APIs can be used to retrieve the graphics and associated data for applications. In addition, this work shows that our method of designing composable graphics is well-suited to depicting variations in human anatomy.

Conclusion: This work provides a bridge between visual communication and the field of knowledge representation. We demonstrate a method for creating visual standards that are compatible with practices in biomedical ontology and implement a system for making them accessible to information systems.

References

Birgfeld C, Luquetti D, Gougoutas A, Bartlett S, Low D, Sie K . A phenotypic assessment tool for craniofacial microsomia. Plast Reconstr Surg. 2011; 127(1):313-320. DOI: 10.1097/PRS.0b013e3181f95d15. View

Preiss B, Echave V, Preiss S, Kaltenbach M . UVAL-MED a universal visual associative language for medicine. Proc Annu Symp Comput Appl Med Care. 1994; :262-6. PMC: 2247965. View

Musen M . The Protégé Project: A Look Back and a Look Forward. AI Matters. 2016; 1(4):4-12. PMC: 4883684. DOI: 10.1145/2757001.2757003. View

Payne P, Starren J . Quantifying visual similarity in clinical iconic graphics. J Am Med Inform Assoc. 2005; 12(3):338-45. PMC: 1090466. DOI: 10.1197/jamia.M1628. View

Le Mercier P, Bolleman J, de Castro E, Gasteiger E, Bansal P, Auchincloss A . SwissBioPics-an interactive library of cell images for the visualization of subcellular location data. Database (Oxford). 2022; 2022. PMC: 9216577. DOI: 10.1093/database/baac026. View

Nagaosa Y, Mateus M, Hassan B, Lanyon P, Doherty M . Development of a logically devised line drawing atlas for grading of knee osteoarthritis. Ann Rheum Dis. 2000; 59(8):587-95. PMC: 1753220. DOI: 10.1136/ard.59.8.587. View

Schulz S, Jansen L . Formal ontologies in biomedical knowledge representation. Yearb Med Inform. 2013; 8:132-46. View

Houts P, Doak C, Doak L, Loscalzo M . The role of pictures in improving health communication: a review of research on attention, comprehension, recall, and adherence. Patient Educ Couns. 2005; 61(2):173-90. DOI: 10.1016/j.pec.2005.05.004. View

Lekschas F, Stachelscheid H, Seltmann S, Kurtz A . Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization. Bioinformatics. 2014; 31(5):794-6. DOI: 10.1093/bioinformatics/btu707. View

10.

Lamy J, Soualmia L, Kerdelhue G, Venot A, Duclos C . Validating the semantics of a medical iconic language using ontological reasoning. J Biomed Inform. 2012; 46(1):56-67. DOI: 10.1016/j.jbi.2012.08.006. View

11.

Rougny A, Toure V, Albanese J, Waltemath D, Shirshov D, Sorokin A . SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. Brief Bioinform. 2021; 22(5). PMC: 8425392. DOI: 10.1093/bib/bbab049. View

12.

Patel R, Hamanishi E, Provart N . A Human "eFP" Browser for Generating Gene Expression Anatograms. PLoS One. 2016; 11(3):e0150982. PMC: 4783024. DOI: 10.1371/journal.pone.0150982. View

13.

Adeola A, Oladimeji A . Developing a visual rating chart for the esthetic outcome of unilateral cleft lip and palate repair. Ann Maxillofac Surg. 2015; 5(1):55-61. PMC: 4555950. DOI: 10.4103/2231-0746.161060. View

14.

Moreno P, Fexova S, George N, Manning J, Miao Z, Mohammed S . Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 2021; 50(D1):D129-D140. PMC: 8728300. DOI: 10.1093/nar/gkab1030. View

15.

Krause K . A framework for visual communication at Nature. Public Underst Sci. 2016; 26(1):15-24. DOI: 10.1177/0963662516640966. View

16.

Katz M, Kripalani S, Weiss B . Use of pictorial aids in medication instructions: a review of the literature. Am J Health Syst Pharm. 2006; 63(23):2391-7. DOI: 10.2146/ajhp060162. View

17.

Wilkinson C, Carr A, Doherty M . Does increasing the grades of the knee osteoarthritis line drawing atlas alter its clinimetric properties?. Ann Rheum Dis. 2005; 64(10):1467-73. PMC: 1755237. DOI: 10.1136/ard.2004.033282. View

18.

Schreiber F, Czauderna T . Design considerations for representing systems biology information with the Systems Biology Graphical Notation. J Integr Bioinform. 2022; 19(2). PMC: 9377698. DOI: 10.1515/jib-2022-0024. View

19.

Gougoutas A, Singh D, Low D, Bartlett S . Hemifacial microsomia: clinical features and pictographic representations of the OMENS classification system. Plast Reconstr Surg. 2007; 120(7):112e-113e. DOI: 10.1097/01.prs.0000287383.35963.5e. View

20.

Griffon N, Kerdelhue G, Soualmia L, Merabti T, Grosjean J, Lamy J . Evaluating alignment quality between iconic language and reference terminologies using similarity metrics. BMC Med Inform Decis Mak. 2014; 14:17. PMC: 4007774. DOI: 10.1186/1472-6947-14-17. View