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Publications
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This page contains selected publications for which
I have electronic versions. These papers may be copyrighted
by the publishers and are placed here to facilitate
scientific dissemination of the work. The publications
are arranged by topic:
All of the database and software papers are oriented
toward biology applications or use examples from bioinformatics
for illustration. This page also includes some unpublished
papers that were written when I was at the Computational
Molecular Biology Group at Baylor College of Medicine.
There are some good (novel and/or practically useful)
ideas in them, and since there are many more people
interested in bioinformatics these days than have
experience in it, I'm putting the papers here for
people who would like to learn more about these topics.
XML DATABASES
- Designing XML Databases Prentice-Hall,
2002. (web
site)
How to design XML databases, database management
systems, and database systems. The book has several
examples from bioinformatics.
GRAPH DATABASES
- Graph Data Models for Genomics Unpublished
(pdf)
Describes graph data models for biology data.
This was the last paper I wrote on graph data models.
- Data Note System for Capturing Laboratory Data
Genomics, 43, pages 232-236, 1997. (pdf)
A graph database used to capture information
about experimental results. The investigator can
use a graphical user interface to design a schema,
and the system automatically generates data entry
and query forms.
- Graph Database Systems for Genomics (with
ER Bergeman, CB Lawrence) IEEE Engineering in Medicine
and Biology 11(6). Special issue on Managing Data
for the Human Genome Project. November 1995. (pdf)
Describes the design and application of graph
database systems used for the Human Genome Project.
- Querying a Genome Database Using Graphs
(with ER Bergeman, CB Lawrence) Third International
Conference on Bioinformatics and Genome Research,
World Scientific Publishing 1996. (pdf)
Introductory paper on representing genome data
using graphs, querying a genome database using simple
graph queries, and presenting the results via a
web interface.
- A Graph-Theoretic Data Model for Genome Mapping
Databases (with ER Bergeman, CB Lawrence) In
Proceedings of the Twenty-Sixth Annual Hawaii International
Conference on System Sciences. January 1995. (This
conference track became PSB) (pdf)
Overview of using graph databases to represent
genome data.
- Querying on a Persistent Graph Logic Programming
Language Unpublished (pdf)
Theoretical description of an algorithm representing
and querying data using graphs.
DATABASE INTEGRATION
- Graph Communication between Database System
Components Fourth International Conference on Bioinformatics
and Genome Research June 1995. (oral) (presentation
pdf)
- Conceptual Integration of Genome Databases
via Reduced Autonomy and Domain-Specific Data Models
Meeting on Interconnection of Molecular Biology
Databases, Cambridge, England. July 1995.(html,
presentation
pdf)
- Conceptual Models: Not Just for Design Anymore
Meeting on Interconnection of Molecular Biology
Databases, Stanford, CA. Aug 1994. (oral) (presentation
pdf)
- Integrating Genome and Biology Data (with
CB Lawrence) Unpublished (pdf)
This describes how to integrate biological data
from using graphs and motivates the integration
using biology. The approach is still useful and
is being used today. It is particularly relevant
in light of the work done by W3C on RDF and the
semantic web.
- Integrating Genome Data (ER Bergeman,
CB Lawrence) Unpublished (pdf)
Not only was this paper never published, it was
not completed either. I'm putting this out here
because it presents some of the issues involved
in database integration for biology databases. Unfortunately,
it is not dated as none of the issues described
have been reasonably addressed.
DATABASE DESIGN
- A Graph Conceptual Model for Developing Human
Genome Center Databases (with ER Bergeman, CB
Lawrence) Computers in Biology and Medicine 26 (3).
Special issue on Information Retrieval and Genomics.
1996. (included in 1997 IMIA Yearbook of Medical
Informatics, Schattauer Publishing, Stuttgart, FRG)
(pdf)
Overview of graph conceptual modeling and an
example of its application to object-oriented design.
- How to Design a Genome Database (with
ER Bergeman, CB Lawrence) First World Congress on
Computational Medicine and Public Health, World
Scientific Publishing. 1996. (pdf)
Phased database design process from the perspective
of the user, database, and interaction.
- Modeling Domains with a Complex Structure
(with ER Bergeman, CB Lawrence) Unpublished (pdf)
How constructs from domain modeling, conceptual
modeling, and semantic networks can be used to model
the complex relationships in biology processes.
- Application of Knowledge Base Design Techniques
to Genetic Markers Fourth International Conference
on Information and Knowledge Management (CIKM-95).
ACM Press. November 1995. (pdf,
presentation pdf,
external
abstract)
- Theories and Tools for Designing Application-Specific
Knowledge Base Data Models University of Michigan
Ph.D. dissertation, University Microfilms. April
1993. (pdf, ps)
SOFTWARE DEVELOPMENT
- Viewing Genome Data as Objects for Application
Development (ER Bergeman, M Graves, CB Lawrence.)
Third International Conference on Intelligent Systems
for Molecular Biology (ISMB-95). July 1995. (pdf)
Method for accessing graph data through an object-oriented
system.
- Software Analysis for Laboratory Data
(ER Bergeman, M Graves, CB Lawrence.) Unpublished
(pdf)
Pulls together ideas from several software engineering
methodologies which are useful for biology and shows
how to use them to develop a LIMS. Although this
work predates UML, most of the techniques were incorporated
into UML, so this paper now provides a rationale
and techniques for using UML to develop a LIMS.
- Using Tcl/Tk in Biology Research Application
Development (ER Bergeman, M Graves) Fifth Annual
Tcl/Tk Workshop 1997 (external
abstract)
Brief description of an approach to rapid prototyping
in biology research.
GENOME MAPPING
- A generalization of location useful for modeling
maps Unpublished (pdf)
Describes a useful mechanism for integrating
models of maps. Interesting for scientists trying
to model genome maps in organisms not yet sequenced.
Although I didn't realize it at the time, the same
approach will also work to integrate sequence annotations.
- Integrating Order and Distance Relationships
from Heterogeneous Maps First International
Conference on Intelligent Systems for Molecular
Biology (ISMB-93) (pdf)
Describes how to integrate relationships between
different kinds of genome maps. A knowledge base
was automatically generated from a formal specification
that allowed relationships from genetic, physical,
and radiation hybrid maps to be shared and integrated.
- A Conceptual Model for Genome Mapping Data
(with CB Lawrence) Department of Energy Human Genome
Program Contractor-Grantee Workshop IV 1994 (external
abstract)
Brief overview of using graph models for genome
mapping.
ASTRONOMY SATELLITE SCHEDULING
- Coarse-grained scheduling for astronomy satellites
(M Graves, B McCollum) SPIE Conference on Knowledge-Based
Artificial Intelligence Systems in Aerospace and
Industry, Orlando, FL, April 1994. (pdf)
- A Constraint-Logic Based Implementation of
the `Coarse-Grained' Approach to Data Acquisition
Scheduling of the International Ultraviolet Explorer
Orbiting Observatory (B McCollum, M Graves)
Third International Symposium on Artificial Intelligence,
Robotics, and Automation for Space (i-SAIRAS `94).
Jet Propulsion Laboratory Pub. 94-23, Pasadena,
CA, October 1994. (pdf)
- Scheduling the IUE Satellite with Constraint
Logic (B McCollum, M Graves) Robotic Telescopes:
Current Capabilities, Present Developments, and
Future Prospects for Automated Astronomy, GW Henry
and JA Eaton, eds. Provo: Astronomical Society of
the Pacific. 1995. (pdf)
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