Framework for a protein ontology

BMC Bioinformatics

Volumn 8, Issue SUPPL. 9, 2007, Pages

  Natale, Darren A ^a   Arighi, Cecilia N ^a   Barker, Winona C ^a   Blake, Judith ^b   Chang, Ti Cheng ^a   Hu, Zhangzhi ^a   Liu, Hongfang ^c   Smith, Barry ^d   Wu, Cathy H ^a  

^a GEORGETOWN UNIVERSITY MEDICAL CENTER   (United States)

^b JACKSON LABORATORY   (United States)

^c GEORGETOWN UNIVERSITY   (United States)

^d UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE SPLICING; BIOMEDICAL ONTOLOGIES; BONE MORPHOGENETIC PROTEINS; EVOLUTIONARY RELATIONSHIPS; INITIAL DEVELOPMENT; POST-TRANSLATIONAL MODIFICATIONS; PROTEOLYTIC CLEAVAGE; TRANSFORMING GROWTH FACTOR BETA;

GENES;

PROTEINS;

BONE MORPHOGENETIC PROTEIN; GENE PRODUCT; RNA; TRANSFORMING GROWTH FACTOR BETA; PROTEIN;

ALTERNATIVE RNA SPLICING; AMINO ACID SEQUENCE; BIOMEDICINE; CONFERENCE PAPER; EVOLUTION; GENETIC VARIABILITY; GENOMICS; HUMAN; INFORMATION PROCESSING; MEDICAL RESEARCH; NONHUMAN; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN STRUCTURE; PROTEOMICS; SIGNAL TRANSDUCTION; ARTICLE; CHEMISTRY; CLASSIFICATION; COMPUTER INTERFACE; DATA BASE; GENETICS; INFORMATION RETRIEVAL; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; INFORMATION STORAGE AND RETRIEVAL; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; USER-COMPUTER INTERFACE;

EID: 38449100150     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-S9-S1     Document Type: Conference Paper

References (45)

1. Bard J Ontologies: Formalising biological knowledge for bioinformatics Bioessays 2003 25 501-506 12717820
2. Blake JA Bio-ontologies - fast and furious Nat Biotechnol 2004 22 773-774 15175701
3. Blake JA Bult CJ Beyond the data deluge: Data integration and bio-ontologies J Biomed Inform 2006 39 314-320 16564748
4. Open Biomedical Ontologies http://obo.sourceforge.net
5. Protein Ontology http://pir.georgetown.edu/pro
6. The OBO Foundry http://obofoundry.org/
7. Gene Ontology Consortium The Gene Ontology (GO) project in 2006 Nucleic Acids Res 2006 34 D322-326 1347384 16381878
8. Eilbeck K Lewis SE Mungall CJ Yandell M Stein L Durbin R Ashburner M The Sequence Ontology: A tool for the unification of genome annotations Genome Biol 2005 6 R44 1175956 15892872
9. Disease Ontology http://diseaseontology.sourceforge.net/
10. International Classification of Diseases (ICD) http://www.who.int/ classifications/icd/en/
11. SNOMED Clinical Terms http://www.snomed.org/
12. Bodenreider O The Unified Medical Language System (UMLS): Integrating biomedical terminology Nucleic Acids Res 2004 32 D267-270 308795 14681409
13. Proteomics Standards Initiative Protein Modification http://psidev.sourceforge.net/mod/
14. Garavelli JS The RESID Database of Protein Modifications as a resource and annotation tool Proteomics 2004 4 1527-1533 15174122
15. UniProt Consortium The Universal Protein Resource (UniProt) Nucleic Acids Res 2007 35 D193-197 1669721 17142230
16. Hermjakob H Montecchi-Palazzi L Bader G Wojcik J Salwinski L Ceol A Moore S Orchard S Sarkans U von Mering C Roechert B Poux S Jung E Mersch H Kersey P Lappe M Li Y Zeng R Rana D Nikolski M Husi H Brun C Shanker K Grant SG Sander C Bork P Zhu W Pandey A Brazma A Jacq B Vidal M Sherman D Legrain P Cesareni G Xenarios I Eisenberg D Steipe B Hogue C Apweiler R The HUPO PSI's molecular interaction format - a community standard for the representation of protein interaction data Nat Biotechnol 2004 22 177-183 14755292
17. Kushida T Takagi T Fukuda KI Event Ontology: A pathway-centric ontology for biological processes Pac Symp Biocomput 2006 11 152-163
18. Yamamoto S Asanuma T Takagi T Fukuda KI The molecule role ontology: An ontology for annotation of signal transduction pathway molecules in the scientific literature Comparative and Functional Genomics 2004 5 528-536
19. Joshi-Tope G Gillespie M Vastrik I D'Eustachio P Schmidt E de Bono B Jassal B Gopinath GR Wu GR Matthews L Lewis S Birney E Stein L Reactome: a knowledgebase of biological pathways Nucleic Acids Res 2005 33 D428-432 540026 15608231
20. Sidhu AS Dillon TS Chang E Protein Ontology: Data Integration using Protein Ontology Database Modeling in Biology: Practices and Challenges New York, Springer Inc Ma Z, Chen JY 2006 39-60
21. Sahoo SS Thomas C Sheth A York WS Tartir S Knowledge modeling and its application in life sciences: A tale of two ontologies Proceedings of the 15th International Conference on World Wide Web New York, ACM Press Carr L, De Roure D, Iyengar A, Goble CA, Dahlin M 2006 317-326 http://portal.acm.org/citation.cfm?id=1135826&jmp=abstract&coll= GUIDE&dl=GUI
22. Smith B Ceuster W Klagger B Kohler J Kumar A Lomax J Mungall C Neuhaus F Rector AL Rosse C Relations in Biomedical Ontologies Genome Biol 2005 6 R46 1175958 15892874
23. Burglin TR Cassata G Loss and gain of domains during evolution of cut superclass homeobox genes Int J Dev Biol 2002 46 115-123 11902672
24. Shimeld SM Characterization of AmphiF-spondin reveals the modular evolution of chordate F-spondin genes Mol Biol Evol 1998 15 1218-1223 9729886
25. Ceusters W Elkin P Smith B Referent tracking: The problem of negative findings Stud Health Technol Inform 2006 124 741-746 17108603
26. Mandal D Moitra PK Basu J Mapping of a spectrin-binding domain of human erythrocyte membrane protein 4.2 Biochem J 2002 364 841-847 1222634 12049649
27. Polakowska RR Eickbush T Falciano V Razvi F Goldsmith LA Organization and evolution of the human epidermal keratinocyte transglutaminase I gene Proc Natl Acad Sci USA 1992 89 4476-4480 49105 1350092
28. Korsgren C Lawler J Lambert S Speicher D Cohen CM Complete amino acid sequence and homologies of human erythrocyte membrane protein band 4.2 Proc Natl Acad Sci USA 1990 87 613-617 53315 2300550
29. Boeshans KM Mueser TC Ahvazi B A three-dimensional model of the human transglutaminase 1: Insights into the understanding of lamellar ichthyosis J Mol Model 2007 13 233-246 17024410
30. Andreeva A Howorth D Brenner SE Hubbard TJ Chothia C Murzin AG SCOP database in 2004: Refinements integrate structure and sequence family data Nucleic Acids Res 2004 32 D226-229 308773 14681400
31. Finn RD Mistry J Schuster-Bockler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R Eddy SR Sonnhammer EL Bateman A Pfam: Clans, web tools and services Nucleic Acids Res 2006 34 D247-251 1347511 16381856
32. Wu CH Nikolskaya A Huang H Yeh L-S Natale DA Vinayaka CR Hu Z Mazumder R Kumar S Kourtesis P Ledley RS Suzek BE Arminski L Chen Y Zhang J Cardenas JL Chung S Castro-Alvear J Dinkov G Barker WC PIRSF family classification system at the Protein Information Resource Nucleic Acids Res 2004 32 D112-114 308831 14681371
33. Mi H Lazareva-Ulitsky B Loo R Kejariwal A Vandergriff J Rabkin S Guo N Muruganujan A Doremieux O Campbell MJ Kitano H Thomas PD The PANTHER database of protein families, subfamilies, functions and pathways Nucleic Acids Res 2005 33 D284-288 540032 15608197
34. Bork P Sander C Valencia A Convergent evolution of similar enzymatic function on different protein folds: The hexokinase, ribokinase, and galactokinase families of sugar kinases Protein Sci 1993 2 31-40 8382990
35. Blake JA Eppig JT Bult CJ Kadin JA Richardson JE Mouse Genome Database Group. The Mouse Genome Database (MGD): Updates and enhancements Nucleic Acids Res 2006 34 D562-567 1347448 16381933
36. Wu CH Huang H Nikolskaya A Hu Z Barker WC The iProClass integrated database for protein functional analysis Comput Biol Chem 2004 28 87-96 15022647
37. Kretzschmar M Liu F Hata A Doody J Massague J The TGF-beta family mediator Smad1 is phosphorylated directly and activated functionally by the BMP receptor kinase Genes Dev 1997 11 984-995 9136927
38. Abdollah S Macias-Silva M Tsukazaki T Hayashi H Attisano L Wrana JL TbetaRI phosphorylation of Smad2 on Ser465 and Ser467 is required for Smad2-Smad4 complex formation and signaling J Biol Chem 1997 272 27678-27685 9346908
39. Funaba M Zimmerman CM Mathews LS Modulation of Smad2-mediated signaling by extracellular signal-regulated kinase J Biol Chem 2002 277 41361-41368 12193595
40. Yagi K Goto D Hamamoto T Takenoshita S Kato M Miyazono K Alternatively spliced variant of Smad2 lacking exon 3. Comparison with wild-type Smad2 and Smad3 J Biol Chem 1999 274 703-709 9873005
41. Matsuzaki K Smad3 phosphoisoform-mediated signaling during sporadic human colorectal carcinogenesis Histol Histopathol 2006 21 645-662 16528675
42. Mi H Vandergriff J Campbell M Narechania A Majoros W Lewis S Thomas PD Ashburner M Assessment of genome-wide protein function classification for Drosophila melanogaster Genome Res 2003 13 2118-2128 403707 12952880
43. Massague J Seoane J Wotton D Smad transcription factors Genes Dev 2005 19 2783-2810 16322555
44. Weinstein M Yang X Deng C Functions of mammalian Smad genes as revealed by targeted gene disruption in mice Cytokine Growth Factor Rev 2000 11 49-58 10708952
45. Dunn NR Koonce CH Anderson DC Islam A Bikoff EK Robertson EJ Mice exclusively expressing the short isoform of Smad2 develop normally and are viable and fertile Genes Dev 2005 19 152-163 540233 15630024