IDP ontology
IDP ontology formalizes terms and relationships describing intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) to enable interoperable, ontology-based annotations and integration with resources such as DisProt.
Key Features:
- Comprehensive Annotations: Contains over 800 manually curated entries of IDPs and IDRs with annotations derived from scientific literature and supported by experimental evidence such as X-ray crystallography, nuclear magnetic resonance (NMR), and other validated techniques.
- Intrinsically Disordered Proteins Ontology (IDPO) in OWL: The ontology is refined and formalized in OWL to improve structure, term definitions, and interoperability with other bioinformatics resources.
- Enhanced Curation Process: Curation employs a reviewing system and curator training, and curation activity is tracked and attributed via APICURON.
- Interoperability and Standards Compliance: Adoption of the Minimum Information About Disorder (MIADE) standard and links to Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) support cross-database interoperability.
- Research Support: Curated data are used to train and validate computational predictors of protein disorder and to study the 'dark' proteome not well characterized by traditional structural biology.
- Content Growth and Quality Assurance: The resource has grown by approximately 30% in recent updates, with efforts focused on improving annotation quality and consistency.
Scientific Applications:
- Disorder predictor development: Provides validated, literature-derived annotations for training and benchmarking computational predictors of intrinsic disorder.
- Proteome characterization: Enables study of the 'dark' proteome and investigation of function in proteins and regions lacking fixed tertiary structure.
- Cross-resource analyses: Supports integration with ontology-driven resources (GO, ECO) and MIADE-compliant datasets for combined analyses across databases.
Methodology:
The ontology is formalized in OWL and linked to standards such as MIADE, Gene Ontology (GO), and Evidence and Conclusion Ontology (ECO), with curation activity tracked via APICURON.
Topics
Details
- License:
- CC-BY-4.0
- Maturity:
- Mature
- Tool Type:
- database
- Added:
- 2/10/2022
- Last Updated:
- 11/24/2024
Operations
Publications
Piovesan D, Tabaro F, Mičetić I, Necci M, Quaglia F, Oldfield CJ, Aspromonte MC, Davey NE, Davidović R, Dosztányi Z, Elofsson A, Gasparini A, Hatos A, Kajava AV, Kalmar L, Leonardi E, Lazar T, Macedo-Ribeiro S, Macossay-Castillo M, Meszaros A, Minervini G, Murvai N, Pujols J, Roche DB, Salladini E, Schad E, Schramm A, Szabo B, Tantos A, Tonello F, Tsirigos KD, Veljković N, Ventura S, Vranken W, Warholm P, Uversky VN, Dunker AK, Longhi S, Tompa P, Tosatto SC. DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Research. 2016;45(D1):D219-D227. doi:10.1093/nar/gkw1056. PMID:27899601. PMCID:PMC5210544.
Quaglia F, Mészáros B, Salladini E, Hatos A, Pancsa R, Chemes LB, Pajkos M, Lazar T, Peña-Díaz S, Santos J, Ács V, Farahi N, Fichó E, Aspromonte MC, Bassot C, Chasapi A, Davey NE, Davidović R, Dobson L, Elofsson A, Erdős G, Gaudet P, Giglio M, Glavina J, Iserte J, Iglesias V, Kálmán Z, Lambrughi M, Leonardi E, Longhi S, Macedo-Ribeiro S, Maiani E, Marchetti J, Marino-Buslje C, Mészáros A, Monzon AM, Minervini G, Nadendla S, Nilsson JF, Novotný M, Ouzounis CA, Palopoli N, Papaleo E, Pereira PJB, Pozzati G, Promponas VJ, Pujols J, Rocha ACS, Salas M, Sawicki LR, Schad E, Shenoy A, Szaniszló T, Tsirigos KD, Veljkovic N, Parisi G, Ventura S, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Research. 2021;50(D1):D480-D487. doi:10.1093/nar/gkab1082. PMID:34850135. PMCID:PMC8728214.
Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A, Chemes L, Davey NE, Davidović R, Dunker AK, Elofsson A, Gobeill J, Foutel NSG, Sudha G, Guharoy M, Horvath T, Iglesias V, Kajava AV, Kovacs OP, Lamb J, Lambrughi M, Lazar T, Leclercq JY, Leonardi E, Macedo-Ribeiro S, Macossay-Castillo M, Maiani E, Manso JA, Marino-Buslje C, Martínez-Pérez E, Mészáros B, Mičetić I, Minervini G, Murvai N, Necci M, Ouzounis CA, Pajkos M, Paladin L, Pancsa R, Papaleo E, Parisi G, Pasche E, Barbosa Pereira PJ, Promponas VJ, Pujols J, Quaglia F, Ruch P, Salvatore M, Schad E, Szabo B, Szaniszló T, Tamana S, Tantos A, Veljkovic N, Ventura S, Vranken W, Dosztányi Z, Tompa P, Tosatto SCE, Piovesan D. DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Research. 2019. doi:10.1093/nar/gkz975. PMID:31713636. PMCID:PMC7145575.