ReviewBiochimica et biophysica acta2014
Controlled vocabularies and ontologies in proteomics: overview, principles and practice.
Review in Biochimica et biophysica acta, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- What Have Data Standards Ever Done for Us?Molecular & cellular proteomics : MCP · 2025Review
- The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study.Database : the journal of biological databases and curation · 2023Article
- MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.Bioinformatics (Oxford, England) · 2023Article
- 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
- Metadata integrity in bioinformatics: Bridging the gap between data and knowledge.Computational and structural biotechnology journal · 2023Review
- A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics.Metabolites · 2022Review
- Proteomics Standards Initiative's ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.Journal of proteome research · 2022Article
- CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator.Database : the journal of biological databases and curation · 2021Article
- Renal-Tubule Epithelial Cell Nomenclature for Single-Cell RNA-Sequencing Studies.Journal of the American Society of Nephrology : JASN · 2019Review
- Proteomics Standards Initiative Extended FASTA Format.Journal of proteome research · 2019Article
- psims - A Declarative Writer for mzML and mzIdentML for Python.Molecular & cellular proteomics : MCP · 2019Article
- iProX: an integrated proteome resource.Nucleic acids research · 2019Article
- JAMI: a Java library for molecular interactions and data interoperability.BMC bioinformatics · 2018Article
- Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.Journal of proteome research · 2017Article
- The arc of Mass Spectrometry Exchange Formats is long, but it bends toward HDF5.Mass spectrometry reviews · 2017Review
- PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.Molecular & cellular proteomics : MCP · 2016Article
- Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein-RNA Interactions.Molecular & cellular proteomics : MCP · 2015Article
- Data integration in biological research: an overview.Journal of biological research (Thessalonike, Greece) · 2015Review
- Development of data representation standards by the human proteome organization proteomics standards initiative.Journal of the American Medical Informatics Association : JAMIA · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.