Prokaryote Protein Localization Relation Extraction (PPLRE) Project

A Prokaryote Protein Localization Relation Extraction (PPLRE) Project was a research project to enhance PSORTdb with experimentally validated Prokaryote protein localizations from a PubMed snapshot.

• Context:
  • It is managed by the SFU Database and Data Mining Lab, SFU Natural Language Lab, and the SFU Brinkman Lab.
  • It developed an Information Extraction from Text System (PPLRE system).
• See: Complex Relation Extraction Task, PPLRE Data Examples.

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Notes

1. PPLRE Project Introduction
2. PPLRE Domain Description
3. PPLRE Research Topics
4. PPLRE High-level Design
   1. PPLRE High-level System Design
   2. PPLRE High-level Data Design
   3. PPLRE High-level Examples
5. PPLRE System Design
   1. PPLRE Annotator
   2. PPLRE Preprocessor
   3. PPLRE Relation Recognition Algorithms
6. PPLRE Data Design
   1. PPLRE Corpus
      1. PPLRE Curated Corpus
      2. PPLRE Corpus Stats
   2. PPLRE Structured Data
   3. PPLRE Data Examples
7. PPLRE Evaluation Task
   1. PPLRE Automated Evaluation System
   2. PPLRE Manual Evaluation System
8. PPLRE Resources
9. PPLRE Project Team and Milestones
10. PPLRE Open Issues
    1. PPLRE Curation Issues
    2. PPLRE Annotation Issues
11. PPLRE References

References

2010

• (Yu et al., 2010) ⇒ Nancy Y. Yu, James R. Wagner, Matthew R. Laird, Gabor Melli, Sébastien Rey, Raymond Lo, Phuong Dao, S. Cenk Sahinalp, Martin Ester, Leonard J. Foster, and Fiona S. L. Brinkman. (2010). “PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.” In: Bioinformatics, 26(13). doi:10.1093/bioinformatics/btq249

2007

• (Melli et al., 2007) ⇒ Gabor Melli, Martin Ester, and Anoop Sarkar. (2007). “Recognition of Multi-sentence n-ary Subcellular Localization Mentions in Biomedical Abstracts.” In: Proceedings of LBM-2007. (presentation)

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