A Molecular Biology Database Directory and Schema Library

Methodology and Notations



The Database Directory and Schema Library contains schemas represented in a common notation, as well in several alternative notations. Support for a common notation for representing schemas requires a concise and clear notation, as well as the ability to convert schemas from other notations to this common notation. For the Library, we are using the Object-Protocol Model (OPM) as the reference data model for representing schemas. Alternative representations for schemas are also provided using the
Entity-Relationship Model;
Relational Model;
ASN.1 data exchange notation.
The main reasons for employing OPM are listed below:
  1. OPM supports data modeling constructs shared by other well known semantic and object data models. In addition, OPM is unique in its support for derived constructs (views) which are important for representing alternative models.
  2. Using OPM allows taking advantage of existing OPM data management tools, including schema converters.
A data model can be judged for the conciseness and clarity of the schemas expressed with its constructs. OPM is a data model that follows the ODMG standard for object-oriented data models, and in addition supports construct for modeling scientific experiments (protocols) and constructs for specifying views (derived attributes and classes). Note that the ER model is less expressive than OPM, and that while the relational model can be used for expressing object structures, it requires substantially larger, and therefore less comprehensible, schemas than OPM or ER.
OPM documentation, examples, and links to databases developed with OPM can be found at the [ OPM Web Site], where you can also find OPM is associated with a suite of tools for constructing, maintaining and querying relational databases. OPM also provides tools for representing (publishing) OPM schemas in various formats (Html, Latex) and notations (diagrams, lists).