Projects

Projects

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Projects in which I am involved. I coordinate some of them, on some others I am an active participant. All of them have produced software and papers; supervising students has been part of my role in some of them. 

 

 

 

“The Living Document”, The Elsevier Grand Challenge, semi finalist, 10 selected out of 70 candidates.

Project description: The Living Document was initially conceptualized within the publishing workflow in life sciences; it evolved into a semantic document knowledge management framework for which we aim to facilitate three aspects central to the semantic web vision: organize, share and discover. All these within the serendipity that is natural to the Semantic Web. This project has now two subprojects:

Subproject: The Living Document in Life Sciences,

 

http://190.158.253.249:8080/LDProject/web/index.html

 

This project aims to study how to use tags, automatic and manually produced, for facilitating knowledge discovery across digital libraries.

Subproject: TAGS4LAB,

 

http://tags4lab.sourceforge.net

 

This project aims to study how to manage knowledge across laboratory notebooks (both paper and electronic- based). Central to this project is the use of principles from folksonomies, semantic web and HCI.

Responsibilities: project leader and coordinator

Dates: August 2008- August 2009

Collaborators: University of Bremen, Bremen, Germany. International Tropical Agriculture Center, CIAT,  Cali, Colombia. ScietifiKa, Granada, Spain. 

 


 

 

“Open architecture for Accessible Services Integration and Standardization” OASIS

Project description: OASIS aims to facilitate interoperability across service providers, mobile devices (wearable devices, phones, palm, etc) smart home technology and medical care providers for elderly and disabled population.

Responsibilities: co-coordination of activities related to the design and development of ontologies, ontology interoperability and methodological aspects of the project. 

Dates: April 2008 to April 2011.  Present position

University of Bremen, Bremen, Germany

Principal Investigator: John Bateman

 


 

 

“Laboratory Information Management System” (LIMS)

Project description: this project involved the use of wireless technology for data capture for biological investigation in functional plant genomics, the definition of ontologies and metadata for the annotation of biological investigations in functional plant genomics, and the generation of a web-based publishing mechanism that could interoperate (exchange information) with CIAT partners worldwide

Responsibilities: project coordination and software architecture designer, liaison officer for technical matter with software partners responsible for the development. Design and requirements definition. Development of metadata and ontologies for LIMS

Dates: 2006-2007

International Tropical Agriculture Center, CIAT, Cali, Colombia

 


 

 

GUI4EASY

Project description: The main aim of this project is to study how to best design effective GUIs. We have addressed two scenarios: the manipulation of OWL ontologies by non-ontology experts in a WEB based environment, and the manipulation of biological annotations as well as the definition of workflows in bioinformatics in a WEB based environment.

Subprojects: “OLS2OWL” (Ontology Look up service to OWL) 

Project description: the main aim of this project is to facilitate the definition of local repositories of OWL ontologies in Protégé. The software currently being implemented will facilitate the extraction of meaningful parts of ontologies, improving reusability

Responsibilities: project coordination, software design. UML and rapid prototyping techniques were used.

Dates: 2008-Present

Subprojects: MAP2OWL

Project description: the main aim of this project was to simplify the development of ontologies by using conceptual maps –allowing non-experts to develop ontologies without knowing the complexity of the OWL language.

Responsibilities: project coordination, software design, supervision of two under-graduate students in their final year (thesis work).

Dates: 2007

This project was developed in collaboration with the Universidad Javeriana, Cali, Universidad de la Sabana, Bogotá, and the  International Tropical Agriculture Center, CIAT, Cali, Colombia. 

 


 

 

TicTAGtoe

Project description: This project aims to study how to provide cognitive support for integrated OMICs environments. TicTAGToe makes extensive use of ontologies, Folksonomies, Semantic Web query languages and knowledge representation formalisms. This idea was initiated at the European Bioinformatics Institute in UK and has continued as collaboration with Rafael Jimenez –original DASTY2 creator.  So far we have completed two subprojects:

- OntoDAS,

 

http://ontodas.nbn.ac.za/

 

Project description: The main aim of this project was to facilitate the constriction of ontology based queries against the Gene Ontology AMIGO MySQL database.

Responsibilities: project coordination, supervision of one master student assigned to this project. Reporting to the University of KwaZulu-Natal (Head of School, CompSci), Proteomics Services - EBI (Team leader) and NBN (CEO).

Dates: 2007

This project was developed for the UKZN at the EBI in collaboration with the NBN.

- DASTY2, there is now DASTY3 (we are working on the paper)

 

http://www.ebi.ac.uk/dasty

 

Project description: a WEB 2.0 client for visualizing protein sequence feature information using DAS.

Responsibilities: project coordination, supervision of one master student assigned to this project. Reporting to Proteomics services Team leader (EBI) and NBN (CEO).

Dates: 2007

This project was developed in collaboration with the Proteomics Group at the EBI, Hinxton, England and the National Bioinformatics Institute, NBN, Cape Town, South Africa.

- Tag4Gs

Project description: Tag4Genomes is a Web Google ToolKit based visualization and annotation system. Tag4Gs facilitates the visualization and annotation of Prokaryote Genomes by using principles from Folksonomies; Tag4Gs has been designed for both, end users and specialized ontology curators.

Responsibilities: project coordinator and designer.

Dates: Currently under development

- TAGSTY

Project description: TAGSTY aims to provide a collaborative annotation environment for the Distributed Annotation System, DAS. TAGSTY supports both, free and ontology based tagging.

Responsibilities: project coordinator and designer.

Dates: currently under development.

This project is currently being developed with the EBI Proteomics group (Rafael Jimenez), The University of Cape Town and The University of el Valle, Colombia

 


 

 

Medical Image Annotator (MIA)

Project description: The image annotator provides a community environment for the ontology-based annotation of radiological images. 

Responsibilities: Software design, ontology development, software beta tester.

Dates: from 12/12/07 to 01/04/08

Initially developed at I2R, Singapore. Project concluded

 


 

 

Lipid ontology

Project description: development of an ontology for lipids.

Responsibilities: assistance in design and ontology development.

Dates: from 12/01/07 to 01/06/08

 


 

 

Dengue ontology

Project description: development of an ontology for the description of Dengue.

Responsibilities: assistance in design and ontology development.

Dates: currently under development

 


 

Reasoning on biodiversity ontologies

Project description: ontologizing GBIF metadata.

Responsibilities: designer and ontology development.

Dates: from03/29/08, currently under development.