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Data Models for Biological Databases

The following is a list of published data models for biological databases. The majority of data models on this list are for relational databases. However, I have also included XML and object models where the focus is on data storage and not data manipulation. I have not attempted to judge the quality of the data models at all: the only criteria for inclusion on this list is the existence of a website or publication that includes the data model. If you know of a data model that I have missed, please e-mail me (melanie_renee_nelson at yahoo dot com).

Data models for sequence data

• The Ensembl schema [html, ensembl.org ]
• The BioSQL schema [html, open-bio.org ]

Data models for biological function data

• The aMaze data model [html, amaze.ulb.ac.be] and publication [html, ncbi.nlm.nih.gov]

Data models for gene expression array data

• MAGE-ML and the MAGE-OM website [html, mged.org] and publication [html, genomebiology.com]
• The Stanford microarray database schema [ html, stanford.edu]
• The Longhorn Array Database website [html, longhornarraydatabase.org] and publication [html, biomedcentral.com]
• The Affymetrix Analysis Data Model [ html, affymetrix.com]

Data models for laboratory information management

• The SPINE (Structural Proteomics in the Northeast) data model overview [HTML, spine.nesg.org], MySQL database generation commands [text, spine.nesg.org], and original paper [ HTML, ncbi.nlm.nih.gov].
• The LabBase (an object-oriented LIMS database) user manual, which includesdiscussion of the data model [HTML, broad.mit.edu].

Data models for proteomics

• The PEDRo (Proteomics data management) website [HTML, pedro.man.ac.uk], which includes schemata [HTML, pedro.man.ac.uk], and The PEDRo publication [ HTML, ncbi.nlm.nih.gov]. HUPO (the Human Proteome Organization) is currently updating this data model. It will be renamed MIAPE (Minimum Information ot describe a Proteomics Experimet).

Data models for protein-protein interactions

• The HUPO (Human Proteome Organization) Proteomics Standards Initiative (PSI) committee has published an XML specification for protein-protein interactions [HTML, psidev.sourceforge.net]
• BIND (Biomolecular Interaction Newtowrk Database) [HTML, blueprint.org] provides its specification as an XML schema or DTD [HTML, blueprint.org]. The BIND group has published many papers, including on the specification [PDF, blueprint.org] and the database's functionality [PDF, blueprint.org].
• The latest Nucleic Acids Research update on DIP (The Database of Interacting Proteins) [HTML, nar.oupjournals.org] includes an overview of the data model.

Other biological data models

• The GMOD (Generic Model Organism Database) project [HTML, gmod.org] is working on developing a data model and tools that can be used to quickly develop an organism-specific database. This is an open source project. The current emphasis is on genetic and genomic information, but other areas are covered as well.

Primary author: Melanie Nelson
Last edited: 15 May 2004