(Q34594396)

3 August 2017

1 reference

25 November 2020

Controlled vocabularies and ontologies in proteomics: overview, principles and practice (English)

1 reference

3 August 2017

0 references

1 reference

25 November 2020

Juan Antonio Vizcaíno

7

1 reference

3 August 2017

8

1 reference

3 August 2017

Luisa Montecchi-Palazzi

6

Luisa Montecchi-Palazzi

0 references

Gerhard Mayer

Gerhard Mayer

1

0 references

Pierre-Alain Binz

Pierre-Alain Binz

3

0 references

Andrew Jones

Andrew R Jones

2

0 references

Sandra Orchard

Sandra Orchard

5

0 references

Eric W Deutsch

4

Eric W Deutsch

1 reference

3 August 2017

13

Martin Eisenacher

1 reference

3 August 2017

author name string

Luisa Montecchi-Palazzi

6

1 reference

3 August 2017

David Oveillero

9

1 reference

3 August 2017

Randall Julian

10

1 reference

3 August 2017

Christian Stephan

11

1 reference

3 August 2017

Helmut E Meyer

12

1 reference

3 August 2017

language of work or name

English

0 references

publication date

19 February 2013

1 reference

Biochimica et Biophysica Acta

3 August 2017

1 January 2014

1 reference

25 November 2020

2 references

3 August 2017

25 November 2020

1844

1 reference

3 August 2017

issue

1 Pt A

1 reference

3 August 2017

page(s)

98-107

1 reference

Creative Commons Attribution 3.0 Unported

3 August 2017

copyright license

1 reference

The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

25 November 2020

0 references

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The Units Ontology: a tool for integrating units of measurement in science

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

File formats commonly used in mass spectrometry proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

OLSVis: an animated, interactive visual browser for bio-ontologies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Molecular interaction databases

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Semantic Web meets Integrative Biology: a survey

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The mzIdentML data standard for mass spectrometry-based proteomics results

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

TraML--a standard format for exchange of selected reaction monitoring transition lists

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Controlled vocabularies and semantics in systems biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The ProteoRed MIAPE web toolkit: a user-friendly framework to connect and share proteomics standards

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

mz5: space- and time-efficient storage of mass spectrometry data sets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Selected reaction monitoring applied to proteomics.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Mapping between the OBO and OWL ontology languages

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Software pipeline and data analysis for MS/MS proteomics: the trans-proteomic pipeline

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

mzIdentML: an open community-built standard format for the results of proteomics spectrum identification algorithms

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The BRENDA Tissue Ontology (BTO): the first all-integrating ontology of all organisms for enzyme sources

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The Protein Ontology: a structured representation of protein forms and complexes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Relations as patterns: bridging the gap between OBO and OWL

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

mzML--a community standard for mass spectrometry data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

An efficient data format for mass spectrometry-based proteomics

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Modeling biomedical experimental processes with OBI

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The Ontology Lookup Service: bigger and better

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

jmzML, an open-source Java API for mzML, the PSI standard for MS data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

OLS dialog: an open-source front end to the ontology lookup service

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Mass spectrometer output file format mzML

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Molecular interactions and data standardisation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The Proteomics Identifications database: 2010 update

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

A community standard format for the representation of protein affinity reagents

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

BioPortal: ontologies and integrated data resources at the click of a mouse

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

mzAPI: a new strategy for efficiently sharing mass spectrometry data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

OBO Explorer: an editor for Open Biomedical Ontologies in OWL.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

ChEBI: a database and ontology for chemical entities of biological interest

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The minimum information about a proteomics experiment (MIAPE)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

OBO-Edit--an ontology editor for biologists

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Relations in biomedical ontologies

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Medical Subject Headings (MeSH).

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Gene ontology: tool for the unification of biology

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Probability-based protein identification by searching sequence databases using mass spectrometry data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Flexible sequence similarity searching with the FASTA3 program package

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

The PSI-MOD community standard for representation of protein modification data.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Guidelines for reporting the use of mass spectrometry informatics in proteomics.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Reporting protein identification data: the next generation of guidelines.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Guidelines for reporting the use of gel image informatics in proteomics

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Guidelines for reporting the use of column chromatography in proteomics

9 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3898906

Creation of a clinical classification. International statistical classification of diseases and related health problems--10th revision, Australian modification (ICD-10-AM)

9 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23429179

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

https://opencitations.net/index/coci/api/v1/citations/10.1038/SCIENTIFICAMERICAN0501-34

25 July 2022

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1016/J.BBAPAP.2013.02.017

The evolution of Protégé: an environment for knowledge-based systems development

1 reference

5 May 2024

https://opencitations.net/index/api/v1/references/10.1016/J.BBAPAP.2013.02.017

Identifiers

DOI

10.1016/J.BBAPAP.2013.02.017

1 reference

3 August 2017

1 reference

3 August 2017

1 reference