The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

Abstract

Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)–Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS–related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies.Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo

Proteomics in cancer research: Are we ready for clinical practice?

“…Currently however, the new guidelines and recommendations for proteomic biomarker discovery studies (including quality control) are more and more implemented, with a multitude of cancer biomarker candidates surviving verification stages and waiting for large-scale validation as a result. Initiatives, such as the Proteome Standardization Initiative (PSI) of the Human Proteome Organization (HUPO) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC) are well-known and of high importance to the field (Mayer et al, 2013;Edwards et al, 2015). With advances in MS-based targeted technologies for high-throughput validation, large cohorts of biomarker candidates are expected to be measured in a short amount of time which might speed up translation of scientific results to clinical settings.…”

ProCon — PROteomics CONversion tool

“…But these tools don't support the conversion of ProteomeDiscoverer ® and ProteinScape ® result at the moment and also the M2Lite converter [50] has still its weaknesses. ProCon makes the conversion of proteomics data of PD and PS into the standard formats mzIdentML [11] resp. PRIDE XML easy even for laboratories without access to specialized bioinformatics expertise.…”

“…Furthermore, the assessment of the performance of newly developed software algorithms analyzing the data is made easier by having access to the data in such data repositories. These XML-based formats defined by the HUPO-PSI working group [8,9] incorporate also semantic annotations of the data by the use of controlled vocabulary terms from a set of ontologies [10,11]. The use of these ontology terms ensures that standardized terms are used and thereby avoids problems resulting from the usage of synonyms, the use of capital and small initial letters and misspellings.…”

PPIM: A Protein-Protein Interaction Database for Maize

“…A pair of proteins were regarded to possibly interact if the proteins of interest cooccur in one abstract together with at least one interaction term described in controlled vocabularies of interaction types from the HUPO Proteomics Standards Initiative (http://www.psidev.info; Mayer et al, 2013) and the organism name maize or Zea mays occurs in the abstract. The resultant candidates were further manually curated to keep only those clearly described functional interactions.…”