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Outline

Title
Abstract
Key Takeaways
Figures
Introduction
Biological Databases
Catpa: Design and Engineering
Specific Design Elements of Catpa
Subject Composition
Design and Evaluation of Catpa
Experimental Tasks
Experiment Procedure
Summary and Conclusion
References
All Topics
Biology
Bioinformatics

Design and evaluation of CATPA

Profile image of Mehmet DalkilicMehmet Dalkilic

2005, Proceedings of the 2005 ACM symposium on Applied computing - SAC '05

https://doi.org/10.1145/1066677.1066721
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29 pages

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Abstract

We present a new application for experimental biologists, the Curation Alignment Tool for Protein Analysis (CATPA), that allows for the efficient and effective creation, storage, management, and querying of experimentally curated protein families. As the number of discovered genomic and proteomic sequences outpaces our ability to understand them, the experimental biologist, who is our primary link in fundamentally and essentially understanding genomic and proteomic information, is left further behind in our race to automate and semi-automate information discovery.

Key takeaways
sparkles

AI

  1. CATPA enhances curation by allowing efficient management and querying of protein families.
  2. The system integrates both curation and annotation, addressing gaps in existing bioinformatics tools.
  3. CATPA utilizes a Java GUI and MySQL for user-friendly interaction and robust data management.
  4. An evaluation with 47 subjects demonstrated CATPA's superior efficiency over PFAAT in multiple tasks.
  5. Standardized vocabulary via Gene Ontology improves data sharing and search accuracy for biologists.
Figures (10)
Fig. 1. The spectrum of adding information from curation to annotation.
Fig. 1. The spectrum of adding information from curation to annotation.
Fig. 2. The ER Model for the CATPA architecture
Fig. 2. The ER Model for the CATPA architecture
‘ig. 3. The CATPA user interface. The alignment shows conserved regions (shaded). The
‘ig. 3. The CATPA user interface. The alignment shows conserved regions (shaded). The
Fig. 4. CATPA Interface: Browsing GO terms
Fig. 4. CATPA Interface: Browsing GO terms
Fig. 5. CATPA Interface: A curation
Fig. 5. CATPA Interface: A curation
Fig. 6. CATPA Interface: Querying results in CATPA. The workplace shows a point (with the mouse arrow) that when clicked moves to the residue in the alignment below.
Fig. 6. CATPA Interface: Querying results in CATPA. The workplace shows a point (with the mouse arrow) that when clicked moves to the residue in the alignment below.
Table I. Demographic composition of subjects
Table I. Demographic composition of subjects
Table Il. Demographic composition of subjects
Table Il. Demographic composition of subjects
Table III. Demographic composition of subjects
Table III. Demographic composition of subjects
Table IV. Subject verbal protocol comments and interpretations
Table IV. Subject verbal protocol comments and interpretations

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