Framework for a protein ontology

Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti Cheng Chang, Zhangzhi Hu, Hongfang D Liu, Barry Smith, Cathy H. Wu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies - one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir.georgetown.edu/ pro).

Original languageEnglish (US)
Title of host publicationProceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics
Pages29-36
Number of pages8
DOIs
StatePublished - 2006
Externally publishedYes
EventTMBIO 2006: ACM 1st International Workshop on Text Mining in Bioinformatics, held in conjunction with the ACM 15th Conference on Information and Knowledge Management, CIKM 2006 - Arlington, VA, United States
Duration: Nov 10 2006Nov 10 2006

Other

OtherTMBIO 2006: ACM 1st International Workshop on Text Mining in Bioinformatics, held in conjunction with the ACM 15th Conference on Information and Knowledge Management, CIKM 2006
CountryUnited States
CityArlington, VA
Period11/10/0611/10/06

Fingerprint

Ontology
Proteins
Biological Ontologies
Genes
Molecular Sequence Annotation
Gene Ontology
Alternative Splicing
Post Translational Protein Processing
Foundries
Transforming Growth Factor beta
Proteomics
Specifications
Research

Keywords

  • GO
  • OBO
  • OBO foundry
  • Ontology
  • PANTHER
  • Pfam
  • PIRSF
  • Protein
  • SCOP

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Bioengineering
  • Computer Science(all)

Cite this

Natale, D. A., Arighi, C. N., Barker, W., Blake, J., Chang, T. C., Hu, Z., ... Wu, C. H. (2006). Framework for a protein ontology. In Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics (pp. 29-36) https://doi.org/10.1145/1183535.1183544

Framework for a protein ontology. / Natale, Darren A.; Arighi, Cecilia N.; Barker, Winona; Blake, Judith; Chang, Ti Cheng; Hu, Zhangzhi; Liu, Hongfang D; Smith, Barry; Wu, Cathy H.

Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics. 2006. p. 29-36.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Natale, DA, Arighi, CN, Barker, W, Blake, J, Chang, TC, Hu, Z, Liu, HD, Smith, B & Wu, CH 2006, Framework for a protein ontology. in Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics. pp. 29-36, TMBIO 2006: ACM 1st International Workshop on Text Mining in Bioinformatics, held in conjunction with the ACM 15th Conference on Information and Knowledge Management, CIKM 2006, Arlington, VA, United States, 11/10/06. https://doi.org/10.1145/1183535.1183544
Natale DA, Arighi CN, Barker W, Blake J, Chang TC, Hu Z et al. Framework for a protein ontology. In Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics. 2006. p. 29-36 https://doi.org/10.1145/1183535.1183544
Natale, Darren A. ; Arighi, Cecilia N. ; Barker, Winona ; Blake, Judith ; Chang, Ti Cheng ; Hu, Zhangzhi ; Liu, Hongfang D ; Smith, Barry ; Wu, Cathy H. / Framework for a protein ontology. Proceedings of TMBIO 2006: ACM First International Workshop on Text Mining in Bioinformatics. 2006. pp. 29-36
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