Robust advances in interactome analysis demand comprehensive, non-redundant , consistently annotated datasets. To enable efficient retrieval, annotation and exchange of protein-protein interaction data, proteomics community has been developing infrastructures under Proteomics Standards Initiative and IMEx consortium. However, there is presently no resource that would provide all features necessary to construct reference interaction networks in URLanisms. The recently developed iRefIndex databaseincludes interactions from most popular repositories with a standardized protein nomenclature . We have developed ppiTrim, a script that can process iRefIndex to produce a consolidated dataset of physical interactions for, in principle, every URLanism. For the current publication we processed only the three largest datasets: yeast, human and fruitfly. ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases. Our results indicate that ppiTrim is able to significantly reduce the complexity of interaction datasets. URL: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/ppiTrim/
Robust advances in interactome analysis demand comprehensive, non-redundant and consistently annotated datasets. By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent experimental support is counted exactly once, no more, no less. While many interactions are shared among public repositories, none of them contains the complete known interactome for any URLanism. In addition, the annotations of the same experimental result by different repositories often disagree. This brings up the issue of which annotation to keep while consolidating evidences that are the same. The iRefIndex database, including interactions from most popular repositories with a standardized protein nomenclature , represents a significant advance in all aspects, especially in comprehensiveness. However, iRefIndex aims to maintain all information/annotation from original sources and requires users to perform additional processing to fully achieve the aforementioned goals. To address issues with iRefIndex and to achieve our goals, we have developed ppiTrim, a script that processes iRefIndex to produce non-redundant, consistently annotated datasets of physical interactions . Our script proceeds in three stages: mapping all interactants to gene identifiers and removing all undesired raw interactions, deflating potentially expanded complexes, and reconciling for each interaction the annotation labels among different source databases. As an illustration, we have processed the three URLanismal datasets: yeast, human and fruitfly. While ppiTrim can resolve most apparent conflicts between different labelings, we also discovered some unresolvable disagreements mostly resulting from different annotation policies among repositories. URL: URL
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To enable efficient retrieval, annotation and exchange of protein-protein interaction data, proteomics community has been developing infrastructures under Proteomics Standards Initiative and IMEx consortium. However, there is presently no resource that would provide all features necessary to construct reference interaction networks in URLanisms. The recently developed iRefIndex databaseincludes
By non-redundant, we mean that the accounting of evidence for every interaction should be faithful: each independent experimental support is counted exactly once, no more, no less. While many interactions are shared among public repositories, none of them contains the complete known interactome for any URLanism. In addition, the annotations of the same experimental result by different repositories often disagree. This brings up the issue of which annotation to keep while consolidating evidences that are the same. The iRefIndex database, including
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, represents a significant advance in all aspects, especially in comprehensiveness. However, iRefIndex aims to maintain all information/annotation from original sources and requires users to perform additional processing to fully achieve the aforementioned goals. To address issues with iRefIndex and to achieve our goals, we
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non-redundant, consistently annotated datasets
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for, in principle, every URLanism. For the current publication we processed only the three largest
. Our script proceeds in three stages: mapping all interactants to gene identifiers and removing all undesired raw interactions, deflating potentially expanded complexes, and reconciling for each interaction the annotation labels among different source databases. As an illustration, we have processed the three URLanismal
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ppiTrim maps interactants to NCBI Gene IDs, deflates possibly spoke-expanded complexes and reconciles annotation labels between different source databases. Our results indicate that ppiTrim is able to significantly reduce the complexity of interaction datasets. URL: ftp://ftp.ncbi.nlm.nih.gov/pub/qmbpmn/ppiTrim/
While ppiTrim can resolve most apparent conflicts between different labelings, we also discovered some unresolvable disagreements mostly resulting from different annotation policies among repositories. URL: URL