Protein-Protein Interaction Mention Recognition Task

A Protein-Protein Interaction Mention Recognition Task is a domain specific relation mention recognition task that requires the identification of Protein-Protein Interaction Relation Mentions.

• Context:
  • It can be solved by a Protein-Protein Interaction Mention Recognition System (that implements a Protein-Protein Interaction Mention Recognition Algorithm.
  • It can extract ProteinProteinInteraction(Protein, Protein) Relations.
• Example(s):
  • Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation. ⇒ Complex: Clb2–Cdc28; and Phosphorylation: Clb2=>Swe1, Cdc28=>Swe1, and Cdc5=>Swe1, a Protein-Protein Interaction Recognition Task.
• See: Network Analysis, Protein-Protein Interaction Task, Protein-Protein Interaction Relation Mention Extraction Task.

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References

• ID-Serve[1]

2008

• (Airola, 2008) ⇒ Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter and Tapio Salakoski. (2008). “A Graph Kernel for Protein-Protein Interaction Extraction.” In: Proceedings of BioNLP 2008

2007

• (Fundel et al., 2007) ⇒ Katrin Fundel, R. Kuffner, and R. Zimmer. (2007). “RelEx--relation extraction using dependency parse trees." Bioinformatics. 2007 Feb 1;23(3):365-71.

2006

• (Ananiadou and Tsuruoka, 2006) ⇒ Sophia Ananiadou and Yoshimasa Tsuruoka. (2006). “Text Mining in Biomedicine: an Overview of Techniques. Tutorial. EACL-2006. (presentation.pdf)
• (McCallum, 2006) ⇒ Andrew McCallum. (2006). “Information Extraction, Data Mining and Joint Inference. SIGKDD Proceedings (KDD-2006). (presentation.pdf)

2005

• (Ramani et al., 2005) ⇒ A. K. Ramani, Razvan C. Bunescu, Raymond Mooney and E. M. Marcotte. (2005). “Consolidating the Set of Known Human Protein-Protein Interactions in Preparation for Large-Scale Mapping of the Human Interactome." Genome Biology, volume 6, number 5, r40.

2003

• (Ding et al., 2003) ⇒ J. Ding, D. Berleant, J. Xu, and A. W. Fulmer. (2003). “Extracting Biochemical Interactions from MEDLINE Using a Link Grammar Parser.” In: Proc of the 15th IEEE International Conference on Tools with Artificial Intelligence (ICTAI'03).

2001

• (Blaschke and Valencia, 2001) ⇒ Christian Blaschke and A. Valencia. (2001). “Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study]." Comparative and Functional Genomics, 2:196-206.

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