Issues in incorporation semantic integrity in molecular biological object-oriented databases

• Published in: Bioinformatics Vol. 11; no. 4; pp. 339 - 347
• Main Authors: Schweigert, Sabine, Herde, Patrick V.G., Sibbald, Peter R.
• Format: Journal Article
• Language: English
• Published: Washington, DC Oxford University Press 01.08.1995; Oxford
• Subjects: Biological and medical sciences; Biotechnology; Databases, Factual; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Biological; Molecular Biology; Semantics; Terminology as Topic; Missing data; Data analysis; Base mismatching; Nucleotide sequence; Semantics; Computerized processing; Object oriented; Database; Information retrieval; Review; Integrity
• ISSN: 1367-4803; 0266-7061; 1460-2059
• DOI: 10.1093/bioinformatics/11.4.339

Issues critical to ensuring semantic integrity in molecular biological data collections have been identified and include complexity, exceptions, missing data, changing models, holism and integration, delocalized data, interoperability and nomenclature. This combination is peculiar to biology and presents some interesting problems as a result. Little is known about semantic checking in object-oriented databases in general, but because such technology appears highly suitable for modeling biological data, it is appropriate to examine the ways in which object-oriented technology can support this functionality. It is concluded that object-oriented technology will support semantic checking even in a complex domain like biology. We propose 10 guidelines for future work including ways of treating exceptional cases and ‘positioning’ of constraints in a schema.