ArticleBMC bioinformatics2018
Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future.Proteomics · 2023Article
- Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.Journal of proteome research · 2023Review
- TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species.Database : the journal of biological databases and curation · 2022Article
- HumanMine: advanced data searching, analysis and cross-species comparison.Database : the journal of biological databases and curation · 2022Article
- The IntAct database: efficient access to fine-grained molecular interaction data.Nucleic acids research · 2022Article
- Complex Portal 2022: new curation frontiers.Nucleic acids research · 2022Article
- Using FlyBase: A Database of Drosophila Genes and Genetics.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The protein-protein interaction ontology: for better representing and capturing the biological context of protein interaction.BMC genomics · 2021Article
- Computational resources for identifying and describing proteins driving liquid-liquid phase separation.Briefings in bioinformatics · 2021Article
- Ten simple rules for creating reusable pathway models for computational analysis and visualization.PLoS computational biology · 2021Article
- Analysing the yeast complexome-the Complex Portal rising to the challenge.Nucleic acids research · 2021Article
- The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).Bioinformatics (Oxford, England) · 2021Article
- A Network Biology Approach to Understanding the Tissue-Specific Roles of Non-Coding RNAs in Arthritis.Frontiers in endocrinology · 2021Review
- Towards a unified open access dataset of molecular interactions.Nature communications · 2020Review
- PhaSePro: the database of proteins driving liquid-liquid phase separation.Nucleic acids research · 2020Article
- CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.Bioinformatics (Oxford, England) · 2019Article
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30 authors.
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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.
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