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Pablo Mendes, PhD Student
In this page I describe my experience in terms of projects I am working on (or have worked on), publications I have participated in, courses I have taken and places I have worked at. I tried to help you to find what you are looking for by enabling some time-saving controls. Click on a section title to hide/show its contents, use the quick navigation bar to jump to a section and use the checkboxes to highlight/dim subjects according to your interest.
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Projects
Cuebee - Knowledge Driven Query Formulation
Cuebee is a flexible, extensible application for querying the semantic web. It provides a friendly interface to guide users through the process of formulating complex queries. No technical knowledge of query languages or the semantic web is required. The system composes SPARQL queries and is able to query multiple servers in the background. Cuebee also supports easy plug-and-play of SPARQL Endpoints.
[ view poster ] [ project page ]
Cuebee is a flexible, extensible application for querying the semantic web. It provides a friendly interface to guide users through the process of formulating complex queries. No technical knowledge of query languages or the semantic web is required. The system composes SPARQL queries and is able to query multiple servers in the background. Cuebee also supports easy plug-and-play of SPARQL Endpoints.
[ view poster ] [ project page ]
Exparql - Exploring SPARQL query results in visual interfaces
Exparql is a sister project to Cuebee that composes a flexible, extensible toolkit for visualizing and exploring SPARQL Endpoints. It provides a set of javascript widgets that can display and interact with any dataset exposed as a SPARQL Endpoint. [ project page ]
Exparql is a sister project to Cuebee that composes a flexible, extensible toolkit for visualizing and exploring SPARQL Endpoints. It provides a set of javascript widgets that can display and interact with any dataset exposed as a SPARQL Endpoint. [ project page ]
Semantic Browser - Browse Pubmed through UMLS connected MeSH terms
We spot ontology terms in text and allow the user to navigate literature by following Semantic Trails as a series of simple and complex relationships connecting entities in documents across a corpus.
[ view video demo ]
We spot ontology terms in text and allow the user to navigate literature by following Semantic Trails as a series of simple and complex relationships connecting entities in documents across a corpus.
[ view video demo ]
TcruziKB - A parasite knowledge base
The association of experimental data with domain knowledge expressed in ontologies facilitates information aggregation, meaningful querying and knowledge discovery to aid in the process of analyzing the extensive amount of interconnected data available for genome projects. TcruziKB is an ontology-based system to describe and provide access to the data available for the project TcruziDB, a genome database for the parasitic agent Trypanosoma cruzi. TcruziKB uses Cuebee as its query interface and D2R Server as the relational-to-RDF mapper.
[ view video demo ]
The association of experimental data with domain knowledge expressed in ontologies facilitates information aggregation, meaningful querying and knowledge discovery to aid in the process of analyzing the extensive amount of interconnected data available for genome projects. TcruziKB is an ontology-based system to describe and provide access to the data available for the project TcruziDB, a genome database for the parasitic agent Trypanosoma cruzi. TcruziKB uses Cuebee as its query interface and D2R Server as the relational-to-RDF mapper.
[ view video demo ]
Cuadro - A Semantic Photo Sharing Community
Cuadro helps the user to describe the meaning of is or her photo contents, allowing for organizing and searching pictures based on the meaning of its contents, not only on filenames or contextless text tags.
Cuadro helps the user to describe the meaning of is or her photo contents, allowing for organizing and searching pictures based on the meaning of its contents, not only on filenames or contextless text tags.
Publications
Ramakrishnan C, Mendes PN, Gama RATS, Ferreira GCN, Sheth AP, "Joint Extraction of Compound Entities and Relationships from Biomedical Literature," WI2008 IEEE/WIC/ACM International Conference on Web Intelligence (WI-08), Sydney Australia, Dec. 9-12, 2008.
Ramakrishnan C, Mendes PN, Wang S, Sheth AP, "Unsupervised Discovery of Compound Entities for Relationship Extraction," EKAW 2008 - 16th International Conference on Knowledge Engineering and Knowledge Management Knowledge Patterns, Acitrezza, Catania, Italy, 9-29 tp 10-3, 2008. 10.1007/978-3-540-87696-0
Mendes PN, McKnight B, Sheth AP, Kissinger JC, "TcruziKB: Enabling Complex Queries for Genomic Data Exploration," International Conference on Semantic Computing, vol. 0, no. 0, pp. 432-439, 2008 IEEE International Conference on Semantic Computing, 2008.10.1109/ICSC.2008.93
Dávila AMR, Mendes PN, Wagner G, Tschoeke DA, Cuadrat RRC, Liberman F, Matos L, Satake T, Ocaña KACS, Triana O, Cruz SMS, Jucá HCL, Cury JC, Silva FN, Geronimo GA, Ruiz M, Ruback E, Silva Jr. FP, Probst CM, Grisard EC, Krieger MA, Goldenberg S, Cavalcanti MCR, Moraes MO, Campos MLM and Mattoso M. ProtozoaDB: dynamic visualization and exploration of protozoan genomes. Nucl. Acids Res., 2007: p. gkm820.
Aguero F, Zheng W, Weatherly DB, Mendes P, Kissinger JC. TcruziDB: An integrated, post-genomics community resource for Trypanosoma cruzi. Nucleic Acids Research 34, 2006: D428-431.
Dávila AMR, Lorenzini DM, Mendes PN, Satake TS, Sousa GR, Campos LM, Mazzoni CJ, Wagner G, Pires PF, Grisard EC. GARSA: Genomic Analysis Resources for Sequence Annotation. Bioinformatics, 2005.
Guerreiro LTA, Souza SS , Wagner G, Souza EA, Mendes PN, Campos LM, Barros L, Pires PF, Campos MLM, Grisard EC, Dávila, AMR. Exploring the genome of Trypanosoma vivax through GSS and in silico comparative analysis. Omics, NY, USA, v. 9, n. 1, p. 116-128, 2005.
Dávila AMR, Berriman M, Grisard EC, Kissinger J, Hertz-Fowler C, Pires PF, Barros L, Baião F, Mattoso M, Costa V, Zaverucha G, Aggarwal G, Castro PAR, Oliveira PM, Souza SS, Bernardes JS, Lorenzini DM, Guerreiro LTA, Wagner G, Ocaña KACS, Ferreira YC, Rech DH, Mendes PN, Campos LM, Mazzoni CJ, Frohlich AAM , Steindel M, Cavalcanti MC, Campos MLM. The BiowebDB Consortium: an integrative Bioinformatics approach for comparative genomics of Kinetoplastida. In: International Conference on Bioinformatics and Computational Biology, 2004, Angra dos Reis, RJ. International Conference on Bioinformatics and Computational Biology Abstracts, 2004.
Nascimento T, Mendes PN, Dávila AMR, Campos MLM, Campos LM, Pires PF, Barros L. A comparison between GUS and CHADO schemas for Genomic Databases. In: International Conference on Bioinformatics and Computational Biology, 2004, Angra dos Reis, RJ. International Conference on Bioinformatics and Computational Biology Abstracts, 2004.
Courses
Spring 2007
| Course | Credit | Grade |
|---|---|---|
| CSCI6760 - Computer Networks | 4 | A- |
| CSCI8380 - Advanced Topics in Information Systems | 4 | A- |
| CSCI8950 - Machine Learning | 4 | B+ |
Fall 2006
| Course | Credit | Grade |
|---|---|---|
| CSCI6470 - Algorithms | 4 | A- |
| CSCI6550 - Artificial Intelligence | 4 | A- |
| CSCI6950 - Directed Study (Advisor: Dr. Kissinger) | 4 | A |
| CSCI8990 - Research Seminar | 4 | S |
Spring 2006
| Course | Credit | Grade |
|---|---|---|
| CSCI8351 - Semantic Web Services | 4 | A |
| CSCI6900 - AI and The Web | 4 | A |
| CSCI6950 - Directed Study (Advisor: Dr. Sheth) | 4 | A |
Fall 2005
| Course | Credit | Grade |
|---|---|---|
| CSCI8350 - Semantic Web | 4 | A |
| CSCI6050 - Software Engineering | 4 | A |
| CSCI6370 Database Management | 4 | A |
Experience
Knoesis Center, July 2007 to present
Activities:
- Collaboration with CSBL/UGA on a NIH grant proposal for a semantic microbial genome analysis system
- Collaboration with Dr. Shaojun Wang on semi-supervised CRFs for secondary protein structure prediction and RNA alignment
- Collaboration with Cartic Ramakrishnan and CCHMC on a grant proposal for Information Extraction from Scientific Literature
- Development of the Web Portal for the Knoesis center, managing two undergrad assistants.
- Management and maintenance of two Linux webservers
Yahoo! Inc., June 2008 to September 2008
- Group: Structured Web Search, Santa Clara, CA & Yahoo Research Barcelona
- Product: Search Monkey
- Supervisors: Kevin Haas & Peter Mika
Large Scale Distributed Systems Laboratory (LSDIS), August 2005 to July 2007.
Activities: Semantic Web and Web Services research applied to Social Media and Bioinformatics.
Laboratory for Genomics and Bioinformatics (LGB), January 2007 to July 2007.
Achievements: Cut in half the time to run the plate submission and blasting pipelines by reengineering and automating the processes.
Activities: Development and mantainance of several genome databases (Oracle, Java Swing, Perl),
Systems and Network Management (Linux and Windows) and other Bioinformatics tasks in general (Reading, Cleaning,
Processing, Searching, etc).
Kissinger Lab @ CTEGD, August 2005 to January 2007.
Achievements: Publication of TcruziDB.org
Activities: Development and mantainance of TcruziDB and ApiDB using the GUS Framework. Programming platform: Java, Perl, Oracle, Web Services and Processes (Axis, WSDL, BPEL).