Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions

Abstract

BackgroundSystems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes.ResultsThe Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal.ConclusionsPSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2118-1) contains supplementary material, which is available to authorized users.

Non-coding RNA regulatory networks

“…Indeed, most of the collected interactions derive from large-scale experiments or text mining import, result in an urgent need for sets of gold standard interactions, manually curated from the literature. Appropriate standards and data formats to enable this are supplied by the HUPO PSI-MI data exchange formats and associated controlled vocabulary [81].…”

“…IntAct has in fact expanded its remit to molecular entities other than proteins, including both genes and non-coding RNAs, and now features over 42,000 interactions involving some form of nucleic acid. The well-established PSI-MI-XML 2.5 data format enables the capture of molecular features relevant to the binding, such as post-transcriptional and translational modifications, mutations, regions involved in the interaction and so on, that are not captured in other ncRNA databases [80][81][82]. Although only experimental evidences of physical associations are annotated in IntAct and indirect causal relations are not included in this repository, annotated regulatory networks are automatically integrated with the huge amount of protein interaction data already collected.…”

Using the MINT Database to Search Protein Interactions

“…MINT, together with IntAct (Orchard et al, 2014) and the Database of Interacting Proteins (DIP; Salwinski et al, 2004), is a founder and active member of the IMEx consortium, whose purpose is to coordinate curation efforts between its members in order to make available a unified, non-redundant, and standardized molecular interaction dataset. The IMEx Consortium adopts the PSI-MI standard formats (Sivade Dumousseau et al, 2018) to export molecular interaction data. In 2013, MINT and IntAct merged their efforts in order to create a unified resource, optimize reduced developer resources, and increase curation productivity.…”

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

“…In response to the "reproducibility crisis" in science [21], novel projects focus on setting up formal structures for data management with collaborations between domain experts [22][23][24]. For instance, the description of molecular interactions has been formalized by the Human Proteome Organization (HUPO) PSI-MI community [25], leading to standard guidelines (MIMIx [26]), exchange formats (PSI-MI TAB [7], PSI-MI XML [27]), and CVs (PSI-MI CV [28]). These standards are adopted by biological databases (e.g., IntAct [14], the IMEx Consortium [29], SIGNOR [4,15], Reactome [30]), and researchers are called upon to describe their data following these standards.…”