Protein annotation as term categorization in the gene ontology using word proximity networks

Verspoor, Karin; Cohn, Judith; Joslyn, Cliff; Mniszewski, Sue; Rechtsteiner, Andreas; Rocha, Luis M.; Simas, Tiago

doi:10.1186/1471-2105-6-s1-s20

Protein annotation as term categorization in the gene ontology using word proximity networks

Journal Article · Tue May 24 00:00:00 EDT 2005 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-6-s1-s20· OSTI ID:1626313

Verspoor, Karin ^[1]; Cohn, Judith ^[2]; Joslyn, Cliff ^[2]; Mniszewski, Sue ^[2]; Rechtsteiner, Andreas ^[2]; Rocha, Luis M. ^[3]; Simas, Tiago ^[4]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States); DOE/OSTI
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Indiana Univ., Bloomington, IN (United States). School of Informatics, Cognitive Science Program
Indiana Univ., Bloomington, IN (United States). Cognitive Science Program

Background: We participated in the BioCreAtIvE Task 2, which addressed the annotation of proteins into the Gene Ontology (GO) based on the text of a given document and the selection of evidence text from the document justifying that annotation. We approached the task utilizing several combinations of two distinct methods: an unsupervised algorithm for expanding words associated with GO nodes, and an annotation methodology which treats annotation as categorization of terms from a protein's document neighborhood into the GO. Results: The evaluation results indicate that the method for expanding words associated with GO nodes is quite powerful; we were able to successfully select appropriate evidence text for a given annotation in 38% of Task 2.1 queries by building on this method. The term categorization methodology achieved a precision of 16% for annotation within the correct extended family in Task 2.2, though we show through subsequent analysis that this can be improved with a different parameter setting. Our architecture proved not to be very successful on the evidence text component of the task, in the configuration used to generate the submitted results. Conclusion: The initial results show promise for both of the methods we explored, and we are planning to integrate the methods more closely to achieve better results overall.

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1626313

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: Suppl 1 Vol. 6; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (7)

Poset Ontologies and Concept Lattices as Semantic Hierarchies Joslyn, Cliff Lecture Notes in Computer Science https://doi.org/10.1007/978-3-540-27769-9_19	book	January 2004
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
Mapping gene ontology to proteins based on protein–protein interaction data Deng, Minghua; Tu, Zhidong; Sun, Fengzhu Bioinformatics, Vol. 20, Issue 6 https://doi.org/10.1093/bioinformatics/btg500	journal	April 2004
The Gene Ontology Categorizer Joslyn, C. A.; Mniszewski, S. M.; Fulmer, A. Bioinformatics, Vol. 20, Issue Suppl 1 https://doi.org/10.1093/bioinformatics/bth921	journal	July 2004
Ordered Sets: An Introduction Schröder, Bernd S. W. https://doi.org/10.1007/978-1-4612-0053-6	book	January 2003
Fuzzy Graphs and Fuzzy Hypergraphs Mordeson, John N.; Nair, Premchand S. Studies in Fuzziness and Soft Computing https://doi.org/10.1007/978-3-7908-1854-3	book	January 2000
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000

Cited By (12)

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters Funk, Christopher; Baumgartner, William; Garcia, Benjamin BMC Bioinformatics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2105-15-59	journal	February 2014
Overview of BioCreAtIvE: critical assessment of information extraction for biology Hirschman, Lynette; Yeh, Alexander; Blaschke, Christian BMC Bioinformatics, Vol. 6, Issue Suppl 1 https://doi.org/10.1186/1471-2105-6-s1-s1	journal	January 2005
Evaluation of BioCreAtIvE assessment of task 2 Blaschke, Christian; Leon, Eduardo Andres; Krallinger, Martin BMC Bioinformatics, Vol. 6, Issue S1 https://doi.org/10.1186/1471-2105-6-s1-s16	journal	May 2005
Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks Daraselia, Nikolai; Yuryev, Anton; Egorov, Sergei BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-243	journal	July 2007
Multi-label literature classification based on the Gene Ontology graph Jin, Bo; Muller, Brian; Zhai, Chengxiang BMC Bioinformatics, Vol. 9, Issue 1 https://doi.org/10.1186/1471-2105-9-525	journal	December 2008
Novel metrics for evaluating the functional coherence of protein groups via protein semantic network Zheng, Bin; Lu, Xinghua Genome Biology, Vol. 8, Issue 7 https://doi.org/10.1186/gb-2007-8-7-r153	journal	January 2007
Assessing the Impact of Case Sensitivity and Term Information Gain on Biomedical Concept Recognition Groza, Tudor; Verspoor, Karin PLOS ONE, Vol. 10, Issue 3 https://doi.org/10.1371/journal.pone.0119091	journal	March 2015
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks Abi-Haidar, Alaa; Kaur, Jasleen; Maguitman, Ana G. arXiv https://doi.org/10.48550/arxiv.0812.1029	text	January 2008
Distance Closures on Complex Networks Simas, Tiago; Rocha, Luis M. arXiv https://doi.org/10.48550/arxiv.1312.2459	preprint	January 2013
Roles for Text Mining in Protein Function Prediction Verspoor, Karin M. Methods in Molecular Biology https://doi.org/10.1007/978-1-4939-0709-0_6	book	January 2014
Distance closures on complex networks Simas, Tiago; Rocha, Luis M. Network Science, Vol. 3, Issue 2 https://doi.org/10.1017/nws.2015.11	journal	March 2015
Gene Function Prediction Based on the Gene Ontology Hierarchical Structure Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui PLoS ONE, Vol. 9, Issue 9 https://doi.org/10.1371/journal.pone.0107187	journal	September 2014

Similar Records

POSet Ontology Categorizer

Software · Tue Mar 01 00:00:00 EST 2005 · OSTI ID:1230863

Ontological Annotation with WordNet

Conference · Tue Jun 06 00:00:00 EDT 2006 · OSTI ID:908503

Automating Ontological Annotation with WordNet

Conference · Sat Jan 21 23:00:00 EST 2006 · OSTI ID:908203

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING
Biochemistry & Molecular Biology
Biotechnology & Applied Microbiology
Mathematical & Computational Biology

Protein annotation as term categorization in the gene ontology using word proximity networks

Citation Formats

References (7)

Cited By (12)

Similar Records

Related Subjects