HUPO-PSI

[…] tabase knowledge include the BioPAX-ontology [], Systems Biology Markup Language (SBML) [], the Human Proteome Organization (HUPO) Proteomics Standards Initiative standard for Molecular Interactions (HUPO PSI-MI) [] and NDEx []. In combination with mapping services, for example BioMart [], these packages enable the integration and merging of prior knowledge for further analyses. Table  includes a […]

[…] distribution of the data. A prototype service will be built at EMBL-EBI for testing by other service providers before a final decision is made.All formats and CVs are available at https://github.com/HUPO-PSI and accompanying tools at https://github.com/MICommunity. The work of the PSI-MI is described at http://www.psidev.info/groups/molecular-interactions. […]

[…] tExporter tool to convert the idXML files into tabular text files (.csv) for further analysis in external tools. It is also possible to convert the idXML files from any stage of the pipeline into the HUPO PSI standard formats mzIdentML and mzTab using the TOPP tools IDFileConverter and MzTabExporter, respectively. […]

[…] ition considers indirect relationships and was recently merged into IntAct []. Data were returned and stored in the Human Proteome Organization Proteomics Standards Initiative—Molecular Interactions (HUPO PSI-MI) Tab 2.5 format. In this text format one binary interaction is stored per line. Supplementary data for each interaction is stored in 15 columns and contains, for example, information regar […]

[…] l. .The next milestone was the development of data‐sharing standards and associated software libraries, allowing ready access to otherwise proprietary data formats . This ongoing endeavor, led by the HUPO‐PSI (Human Proteome Organization−Proteomics Standards Initiative−http://www.psidev.info), has resulted in key data standards for the field, including mzML (for MS data), mzIdentML (for peptide/pr […]

[…] nsone et al. ) within the Metabolomics Standards Initiative (MSI) and work at the Wishart lab and earlier reporting requirements (Rubtsov et al. ). The format has also heavily borrowed ideas from the HUPO-PSI mzML standard (Martens et al. ), including an XML schema that defines the structure of an nmrML file and a supporting controlled vocabulary (nmrCV), which allows the reuse of nmrCV terms in o […]