As a software developer at LBNL, I am involved in a number of data centric and ontology related projects. These include:- Creating ETL workflows for the National Microbiome Data Collaborative (https://microbiomedata.org).- Developing schemas using the Linked data Modeling Language (https://github.com/linkml/linkml) to integrate data from multiple sources.- Support and development of OBO Foundry (http://obofoundry.org/) ontologies.

Provided programming and database support for a wide range of research projects, such as:- Manage the programming of Jupyter notebooks and development for training modules- Extracting and cleaning data from complex EHR systems- Developing ontologies to model and integrate information- Developing methods for automated data-driven recruitment of patients to clinical trials

Developed biomedical ontologies and the applied of these ontologies to clinical and research data. Using these methods, I have successfully: - Integrated data from 99 National Dental PBRN practices for the purpose of studying tooth loss and longevity of restorations. - Integrated clinic data at Roswell Park with molecular marker results from genomic lab panels.I was involved in the development of web-based applications to allow researchers to explore and visualize these datasets. The technologies for this included: - Linux based server platform for hosting web-applications - Python Django framework for developing applications - Apache Superset for visualizing data - PostgreSQL to server as the relational database backend - GraphDB triple store to host integrated data

Directed efforts to integrate data from multiple data sources for research purposes. These data sources included Roswell Park’s: - Electronic medical record system (EMR) - REDCap data capture system - MOSAIQ radiation treatment database Managerial duties included: - Training programing staff on how to develop and execute SQL queries over large complex database systems (such as Roswell Park’s EMR) - Developing data models to allow non-technical staff to query data directly using the Genetegra software platform - Overseeing the development custom programs to merge and clean data from multiple sources (for example, bringing together data from Roswell Park’s REDCap and EMR systems) - Development of infrastructure to host platforms for the exploration of data using visualization - Deployment of an integrated system that brings together clinical data and molecular marker data so that this data can be queried in a single source - Initiating projects that use advanced computing methods, such as natural language processing and ontologies - Deployment of a prototype cBioportal server to explore genomic and clinical data I also played an active role in renewal of Roswell Park status as an NCI-designatedCancer Center.

During my time as a research scientist, I continued my work on the Oral Health and Disease Ontologies and the ImmPort Antibody Ontology (discussed below). I also played a key role in the implementation of a project sponsored by the National Dental PBRN (Practice Based Research Network) to analyze the dental records of 99 dental practices throughout the country. As part of my academic duties, I worked with doctoral students from the Indiana University Department of BioHealth Informatics who have an ontology component to their theses.

During my time as a postdoctoral researcher, I was a co-investigator developing two ontology projects. - Oral Health and Disease (https://github.com/wdduncan/ohd-ontology)The purpose of this ontology is to represent entities that are relevant to the diagnosis and treatment of dental maladies in a standardized way. My work for this project is centered on two tasks: (1) creating classes and relations to represent entities in the oral health domain; (2) extracting data from electronic dental record systems and re-representing this data using the classes defined in the ontology. - Antibody Ontology (https://bitbucket.org/wdduncan/antio/wiki/Home)The goal of this project is to provide advanced information technology support in the production, analysis, archiving, and exchange of scientific data for the diverse community of life science researchers supported by NIAID/DAIT. Within this project, my work is mainly focused on representing monoclonal antibodies and the targets that they recognize.

Worked as a research assistant developing the Ontology for Oral Health and Disease (https://github.com/oral-health-and-disease-ontologies/ohd-ontology). The purpose of this ontology is to represent entities that are relevant to the diagnosis and treatment of dental maladies in a standardized way. My work involved creating classes and relations to represent entities in the oral health domain, and extracting data from electronic dental record systems and re-representing this data using the classes defined in the ontology. Examples of work: - Develop classes and relations in Protégé to represent filling, crowns, veneers, inlays, onlays, implants, tooth decay, endontic procedures, and clinical findings. - Develop computer programs (written in LISP) to extract data from electronic dental record systems (e.g., Eaglesoft). This data is then translated into OWL statements using the LSW2 library (https://github.com/alanruttenberg/lsw2). - Extract relevant billing codes from documentation on Current Dental Terminology codes and re-represent these codes classes in the Ontology for Oral Health and Disease. - Import OWL ontologies (created using the process described above) into an OWLIM triple-store.This is done using the web interface provided by a Sesame web service (http://www.openrdf.org) running on an Apache/Tomcat web server. - Extract data from the OWLIM triple-store using SPARQL queries.The SPARQL queries are issued in a number of ways: (1) as part of LISP program using the LSW2 library; (2) via the Sesame web interface; (3) as part of an R program written for the purpose of creating data files that will undergo statistical analysis. As a teaching assistant, I taught critical thinking courses and assisted teaching courses in introduction to philosophy and research ethics.

Worked as a consultant (on site) for Mergent Financial in Charlotte, NC. My work focused mainly on developing PHP based web services and applications.Examples of work:- Converted existing web services written in Java to PHP.- Maintained and expanded functionality of an in-house content management system used by Mergent’s finance group for updating company web pages.- Worked on a Mergent product that allowed Mergent’s clients to access a wide range of financial information. My main contribution was to incorporate dynamic chart drawing.

Worked remotely (telecommuter) for General Software Systems, based in Fort Lauderdale, FL. Worked as telecommuter for General Software Systems based in Fort Lauderdale, FL. Developed a wide range of data driven desktop and web applications using HTML, Javascript, PHP, ASP, Vb.Net, C#, SQL Server, and MySQL. Examples of work:- Worked extensively for an on line mortgage company which both finances and builds houses. The web site used for collecting customer data and allowing customers to submit loans was written in classic ASP. The web site used by contractors to schedule their building projects was written in C#. The backend database was Sql Server for which I also wrote several stored procedures.- Developed web applications in Vb.Net for a large law firm which allows their clients to log in and check the status of their cases.- Wrote windows services in both C# and Vb.Net for the purpose of importing data into a Sql Server database.- Enhanced a car dealership’s web site written in PHP to allow its customers to submit payments on line.- Developed web site in PHP for the purpose of tracking and maintaining issuance of State of Florida reseller certification used for all retail merchandisers. Some tasks involved in this process were: developing user interfaces for entering and searching reseller data; designing tables in MySql to store reseller information; exporting reseller data to files in CSV, Pipe, and XML formats; allowing users to import data from the State of Florida stored in a tab delimited file; manipulating faxed in certificates and storing them as PNG files; and generating reports on various aspects concerning resellers’ data.

Wrote applications in VB and classic ASP to interact as a front end to a database. Maintained county web pages. Developed databases, and analyzed information system needs.Examples of work:- Wrote an application in VB 6 for the purpose of tracking taxes paid by companies that rent trucks.- Frequently updated county web site with such things as new job postings and news bulletins.- Developed a web application which allowed public to check the health code grades of any restaurant in the county.

Worked as part of development team writing windows based tax software using VB 6.Examples of work:- Developed user interfaces and custom dlls in VB 6 for the purpose of manipulating and maintaining customers’ files.- Maintained and enhanced program used for printing out customer invoices.- Worked on in house software used by accounting department.- Assisted users with setting up software for network use.- Helped users configure peripheral devices such as modems and printers to work with the software.

- Served in Desert Storm- Medals: Army Commendation, Army Achievement, Southeast Asia Service, and Kuwait Liberation - Honorable Discharge