IID


31583635	Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). [PMID: 31583635] Pastrello C, Kotlyar M, Jurisica I. Abstract Protein-protein interaction data is fundamental in molecular biology, and numerous online databases provide access to this data. However, the huge quantity, complexity, and variety of PPI data can be overwhelming, and rather than helping to address research problems, the data may add to their complexity and reduce interpretability. This protocol focuses on solutions for some of the main challenges of using PPI data, including accessing data, ensuring relevance by integrating useful annotations, and improving interpretability. While the issues are generic, we highlight how to perform such operations using Integrated Interactions Database (IID; http://ophid.utoronto.ca/iid ). Methods Mol Biol. 2020:2074() \| 8 Citations (from Europe PMC, 2025-03-29)
30407591	IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. [PMID: 30407591] Kotlyar M, Pastrello C, Malik Z, Jurisica I. Abstract Knowing the set of physical protein-protein interactions (PPIs) that occur in a particular context-a tissue, disease, or other condition-can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains limited, and for most non-human species context-specific networks are completely unavailable. The Integrated Interactions Database (IID) provides one of the most comprehensive sets of context-specific human PPI networks, including networks for 133 tissues, 91 disease conditions, and many other contexts. Importantly, it also provides context-specific networks for 17 non-human species including model organisms and domesticated animals. These species are vitally important for drug discovery and agriculture. IID integrates interactions from multiple databases and datasets. It comprises over 4.8 million PPIs annotated with several types of context: tissues, subcellular localizations, diseases, and druggability information (the latter three are new annotations not available in the previous version). This update increases the number of species from 6 to 18, the number of PPIs from ?1.5 million to ?4.8 million, and the number of tissues from 30 to 133. IID also now supports topology and enrichment analyses of returned networks. IID is available at http://ophid.utoronto.ca/iid. Nucleic Acids Res. 2019:47(D1) \| 103 Citations (from Europe PMC, 2025-03-29)
26516188	Integrated interactions database: tissue-specific view of the human and model organism interactomes. [PMID: 26516188] Kotlyar M, Pastrello C, Sheahan N, Jurisica I. Abstract IID (Integrated Interactions Database) is the first database providing tissue-specific protein-protein interactions (PPIs) for model organisms and human. IID covers six species (S. cerevisiae (yeast), C. elegans (worm), D. melonogaster (fly), R. norvegicus (rat), M. musculus (mouse) and H. sapiens (human)) and up to 30 tissues per species. Users query IID by providing a set of proteins or PPIs from any of these organisms, and specifying species and tissues where IID should search for interactions. If query proteins are not from the selected species, IID enables searches across species and tissues automatically by using their orthologs; for example, retrieving interactions in a given tissue, conserved in human and mouse. Interaction data in IID comprises three types of PPI networks: experimentally detected PPIs from major databases, orthologous PPIs and high-confidence computationally predicted PPIs. Interactions are assigned to tissues where their proteins pairs or encoding genes are expressed. IID is a major replacement of the I2D interaction database, with larger PPI networks (a total of 1,566,043 PPIs among 68,831 proteins), tissue annotations for interactions, and new query, analysis and data visualization capabilities. IID is available at http://ophid.utoronto.ca/iid. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. Nucleic Acids Res. 2016:44(D1) \| 112 Citations (from Europe PMC, 2025-03-29)

Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). [PMID: 31583635]

Pastrello C, Kotlyar M, Jurisica I.

Abstract

Protein-protein interaction data is fundamental in molecular biology, and numerous online databases provide access to this data. However, the huge quantity, complexity, and variety of PPI data can be overwhelming, and rather than helping to address research problems, the data may add to their complexity and reduce interpretability. This protocol focuses on solutions for some of the main challenges of using PPI data, including accessing data, ensuring relevance by integrating useful annotations, and improving interpretability. While the issues are generic, we highlight how to perform such operations using Integrated Interactions Database (IID; http://ophid.utoronto.ca/iid ).

Methods Mol Biol. 2020:2074() | 8 Citations (from Europe PMC, 2025-03-29)

IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. [PMID: 30407591]

Kotlyar M, Pastrello C, Malik Z, Jurisica I.

Abstract

Knowing the set of physical protein-protein interactions (PPIs) that occur in a particular context-a tissue, disease, or other condition-can provide valuable insights into key research questions. However, while the number of identified human PPIs is expanding rapidly, context information remains limited, and for most non-human species context-specific networks are completely unavailable. The Integrated Interactions Database (IID) provides one of the most comprehensive sets of context-specific human PPI networks, including networks for 133 tissues, 91 disease conditions, and many other contexts. Importantly, it also provides context-specific networks for 17 non-human species including model organisms and domesticated animals. These species are vitally important for drug discovery and agriculture. IID integrates interactions from multiple databases and datasets. It comprises over 4.8 million PPIs annotated with several types of context: tissues, subcellular localizations, diseases, and druggability information (the latter three are new annotations not available in the previous version). This update increases the number of species from 6 to 18, the number of PPIs from ?1.5 million to ?4.8 million, and the number of tissues from 30 to 133. IID also now supports topology and enrichment analyses of returned networks. IID is available at http://ophid.utoronto.ca/iid.

Nucleic Acids Res. 2019:47(D1) | 103 Citations (from Europe PMC, 2025-03-29)

Integrated interactions database: tissue-specific view of the human and model organism interactomes. [PMID: 26516188]

Kotlyar M, Pastrello C, Sheahan N, Jurisica I.

Abstract

IID (Integrated Interactions Database) is the first database providing tissue-specific protein-protein interactions (PPIs) for model organisms and human. IID covers six species (S. cerevisiae (yeast), C. elegans (worm), D. melonogaster (fly), R. norvegicus (rat), M. musculus (mouse) and H. sapiens (human)) and up to 30 tissues per species. Users query IID by providing a set of proteins or PPIs from any of these organisms, and specifying species and tissues where IID should search for interactions. If query proteins are not from the selected species, IID enables searches across species and tissues automatically by using their orthologs; for example, retrieving interactions in a given tissue, conserved in human and mouse. Interaction data in IID comprises three types of PPI networks: experimentally detected PPIs from major databases, orthologous PPIs and high-confidence computationally predicted PPIs. Interactions are assigned to tissues where their proteins pairs or encoding genes are expressed. IID is a major replacement of the I2D interaction database, with larger PPI networks (a total of 1,566,043 PPIs among 68,831 proteins), tissue annotations for interactions, and new query, analysis and data visualization capabilities. IID is available at http://ophid.utoronto.ca/iid. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Nucleic Acids Res. 2016:44(D1) | 112 Citations (from Europe PMC, 2025-03-29)

URL:	http://ophid.utoronto.ca/iid
Full name:	Integrated interactions database
Description:	IID (Integrated Interactions Database) is the first database providing tissue-specific protein-protein interactions (PPIs) for model organisms and human.
Year founded:	2016
Last update:	2015
Version:	v1.0
Accessibility:	Accessible
Country/Region:	Canada

Data type:	Protein
Data object:	Animal
Database category:	Interaction
Major species:	Homo sapiens
Keywords:	tissue-specific PPIs

University/Institution:	University Health Network
Address:	Princess Margaret Cancer Centre, Toronto, ON, M5G 1L7, Canada
City:	Toronto
Province/State:
Country/Region:	Canada
Contact name (PI/Team):	Igor Jurisica
Contact email (PI/Helpdesk):	juris@ai.utoronto.ca

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IID

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Database Commons
a catalog of worldwide biological databases