IntAct—open source resource for molecular interaction data

By Samuel Kerrien, Y. Alam-Faruque, Bruno Aranda, I. Bancarz, Alan J. Bridge, C. Derow, E. Dimmer, Marc Feuermann, A. Friedrichsen, Rachael P. Huntley and 14 more. Nucleic Acids Res., 2006

621 citations recorded by the source corpus.

IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data. The data available in the database originates entirely from published literature and is manually annotated by expert biologists to a high level of detail, including experimental methods, conditions and interacting domains. The database features over 126 000 binary interactions extracted from over 2100 scientific publications and makes extensive use of controlled vocabularies. The web site provides tools allowing users to search, visualize and download data from the repository. IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from .

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9f6431be822a8a9df69ffab74bf84282def06787

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

In Molecular Biology

Citations in the corpus

Data Mining Techniques for the Life Sciences (2010, neutral): “0, based on the 1.73 release of SCOP, will eventually be extended to the whole PDB, omitting the nonprotein components.”
Extending CATH: increasing coverage of the protein structure universe and linking structure with function (2010, neutral): “These include protein–protein interaction (PPI) data (12), GO functional assignments (13), KEGG pathways (14) and FunCAT functional descriptions (15).”
Walking the interactome for prioritization of candidate disease genes. (2008, positive): “Additional interactions were extracted from IntACT, 23 and DIP.”
STRING 8—a global view on proteins and their functional interactions in 630 organisms (2008, neutral): “Apart form the resources already included in the previous release [MINT (10), HPRD (9), BIND (12), DIP (11), BioGRID (8), KEGG (13) and Reactome (14)], a number of resources have been newly included [IntAct (7), EcoCyc (15), NCI-Nature Pathway Interaction Database and Gene Ontology (GO) protein comp”
Bridging semantics and syntax with graph algorithms - state-of-the-art of extracting biomedical relations (2017, neutral): “Shared resources for biomedical relation extraction Utility category Data sources Terminology/Ontology/Knowledge Base GO [161], UMLS [58], MeSH [162], Wordnet [118], Verbnet [163], Biothesaurus [122], PDB [101], Uniprot [121], SIDER [164], DrugBank [165], HIVDB [166], RegaDB [167], Entrez Gene [153]”
ConsensusPathDB—a database for integrating human functional interaction networks (2008, neutral): “com), NetPath (http://www.netpath.org), IntAct ( 15 ) (data from small-scale experiments only), DIP (16), MINT (17), HPRD (18), BioGRID (19) and SPIKE (20).”
ATTED-II provides coexpressed gene networks for Arabidopsis (2008, positive): “Therefore, in the new ATTED-II we added PPI information from TAIR (7) and IntAct (20) databases (Table 2).”
Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins (2009, positive): “sents the union of experimentally verified PIs derived from low-throughput experiments extracted from the Database of Interacting Proteins (DIP) [35], the Biomolecular Interaction Network Database (BIND) [36], and the IntAct database [37].”
Network-based methods for human disease gene prediction. (2011, neutral): “…by small-scale experiments, as was done in a large number of databases such as Human Protein Reference Database (HPRD), Molecular Interaction database (MINT), Biological General Repository for Interaction data sets (BioGRID), Biomolecular Interaction Network Database (BIND) and IntAct [18–22].”
Protein interface conservation across structure space (2010, neutral): “1 and 2 for a review), and the results have been deposited into numerous databases (3, 4).”
LINNAEUS: A species name identification system for biomedical literature (2010, positive): “Evaluation is performed against a set of 621 full text documents where species mentions have been automatically generated from corresponding protein-protein interaction entries in the IntAct database [34], with a reported recall of 73.8% and precision of 74.2%.”
Overview of the protein-protein interaction annotation extraction task of BioCreative II (2008, positive): “The interaction databases MINT (Molecular Interactions Database) [6] and IntAct [7] contain the largest number of nonredundant direct human protein-protein interactions, exceeded in number only by HPRD.”
iRefIndex: A consolidated protein interaction database with provenance (2008, neutral): “Our construction of a protein interaction index involved parsing PSI-MI files provided by nine interaction databases including BIND [22,23], BioGRID [24], DIP [25], HPRD [26,27], IntAct [28,29], MINT [30], MPact [31], MPPI [32] and OPHID [33].”
Functional organization of the transcriptome in human brain (2008, neutral): “We obtained a set of 17,540 experimentally validated interacting human protein pairs from EBI (European Bioinformatics Institute)/IntAc”