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List of works by Henning Hermjakob

2016 update of the PRIDE database and its related tools

scientific article

2016 update of the PRIDE database and its related tools.

scientific article published on 28 September 2016

6th HUPO Annual World Congress - Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea

scientific article published in April 2008

A Data Citation Roadmap for Scholarly Data Repositories ⬇️

journal article from 'bioRxiv' published in 2016

A Reagent Resource to Identify Proteins and Peptides of Interest for the Cancer Community: Table I

article by Brian B. Haab et al published 24 July 2006 in Molecular & Cellular Proteomics

A common open representation of mass spectrometry data and its application to proteomics research

scientific article

A community standard format for the representation of protein affinity reagents

scientific article

A comparison of signal sequence prediction methods using a test set of signal peptides

scientific article

A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis

scientific article published on 17 July 2012

A data citation roadmap for scholarly data repositories

scientific article published on 10 April 2019

A domain level interaction network of amyloid precursor protein and Abeta of Alzheimer's disease

scientific article published on June 2010

A guide to the Proteomics Identifications Database proteomics data repository

scientific article (publication date: September 2009)

A new reference implementation of the PSICQUIC web service

scientific article published on 13 May 2013

A public repository for mass spectrometry imaging data

scientific article

A reference set of curated biomedical data and metadata from clinical case reports

scientific article published on 20 November 2018

A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology

scientific article

AAgAtlas 1.0: a human autoantigen database

scientific article published on 19 October 2016

Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences

scientific article published on 14 November 2015

Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>

Advances in the development of common interchange standards for proteomic data

scientific article

An informatic pipeline for the data capture and submission of quantitative proteomic data using iTRAQ

scientific article (publication date: February 2007)

An open invitation to the Understudied Proteins Initiative

scientific article published on 9 May 2022

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

article

Analyzing large-scale proteomics projects with latent semantic indexing

scientific article

Analyzing protein-protein interaction networks

scientific article published on 02 March 2012

Annotating cancer variants and anti-cancer therapeutics in reactome

scientific article

Annotating the human proteome

scientific article

Annual spring meeting of the Proteomics Standards Initiative

scientific article published in October 2009

Annual spring meeting of the Proteomics Standards Initiative 23-25 April 2008, Toledo, Spain

scientific article published in October 2008

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Author response: Wikidata as a knowledge graph for the life sciences

scholarly article, peer review and author response published on 24 January 2020

Autumn 2005 Workshop of the Human Proteome Organisation Proteomics Standards Initiative (HUPO-PSI) Geneva, September, 4–6, 2005

article

BioJS: an open source standard for biological visualisation - its status in 2014

scientific article

BioModels Parameters: a treasure trove of parameter values from published systems biology models

scientific article published on 23 June 2020

BioModels linked dataset

scientific article

BioModels-15 years of sharing computational models in life science

scientific article published on 01 January 2020

BioModels: Content, Features, Functionality, and Use

scientific article

BioModels: expanding horizons to include more modelling approaches and formats

scientific article published on 2 November 2017

BioModels: ten-year anniversary

scientific article

Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine

scientific article published in April 2018

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

scientific article

COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms ⬇️

journal article from 'Molecular Systems Biology' published in 2021

Calling on a million minds for community annotation in WikiProteins

scientific article

Capturing cooperative interactions with the PSI-MI format

scientific article (publication date: 2013)

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

scientific article published in Nature Communications

Capturing variation impact on molecular interactions: the IMEx Consortium mutations data set

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

scientific article published on 01 October 2019

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

scientific article published on 6 August 2018

Characterization, design, and function of the mitochondrial proteome: from organs to organisms

scientific article

Charting online OMICS resources: A navigational chart for clinical researchers.

scientific article published on 20 November 2008

Clinical proteomics: A need to define the field and to begin to set adequate standards

scientific article published on 22 January 2007

Common interchange standards for proteomics data: Public availability of tools and schema

scientific article

Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

scientific article published on 01 January 2019

Complex Portal 2022: new curation frontiers

scientific article

ComplexViewer: visualization of curated macromolecular complexes

scientific article published on 3 August 2017

Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 workshop report.

scientific article

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

scientific article published on 17 October 2011

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

scientific article

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations

scientific article

Current status of proteomic standards development

scientific article

DAS writeback: a collaborative annotation system ⬇️

scientific article

Dasty and UniProt DAS: a perfect pair for protein feature visualization

scientific article published on 19 May 2005

Dasty2, an Ajax protein DAS client

scientific article published on 11 August 2008

Dasty3, a WEB framework for DAS.

scientific article published on 28 July 2011

Data Standardization by the HUPO-PSI: How has the Community Benefitted? ⬇️

scientific article published on January 1, 2011

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

scientific article

Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome Project

Data standardization and the HUPO proteomics standards initiative

Data standards and controlled vocabularies for proteomics

scientific article

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL

scientific article published in January 1998

Delivering 'Cool URIs' That Do Not Change ⬇️

Development of data representation standards by the human proteome organization proteomics standards initiative

scientific article

Discovering and linking public omics data sets using the Omics Discovery Index.

scientific article

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia

scientific article

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories

scientific article

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories

EBI Proteomics Services

ENFIN - An Integrative Structure for Systems Biology

article

ENFIN--A European network for integrative systems biology

scientific article

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany

scientific article

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

scientific article published on 11 April 2018

Entering the Implementation Era A report on the HUPO-PSI Fall workshop 25–27 September 2006, Washington DC, USA

scholarly article by Sandra Orchard published in February 2007

Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome

scientific article

Erratum: Corrigendum: Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

article

Expression data analysis with Reactome

scientific article

Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Supérieure (ENS), Lyon, France

scientific article

From Peptidome to PRIDE: public proteomics data migration at a large scale

scientific article

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland

scientific article published on February 2012

Further advances in the development of a data interchange standard for proteomics data

scientific article published in October 2003

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).

scientific article published in September 2005

Further steps towards data standardisation: the Proteomic Standards Initiative HUPO 3(rd) annual congress, Beijing 25-27(th) October, 2004.

scientific article published in February 2005

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

scientific article

HENA, heterogeneous network-based data set for Alzheimer's disease

scientific article published on 14 August 2019

HI-bone: a scoring system for identifying phenylisothiocyanate-derivatized peptides based on precursor mass and high intensity fragment ions

scientific article published on 20 March 2013

HUPO 2011: The new Cardiovascular Initiative - integrating proteomics and cardiovascular biology in health and disease

scientific article published on March 2012

Harnessing the heart of big data

scientific article

How to submit MS proteomics data to ProteomeXchange via the PRIDE database

scientific article

Human Proteome Organisation Proteomics Standards Initiative Pre-Congress Initiative

article

Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy

scientific article

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

scientific article

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

scientific article

ISPIDER Central: an integrated database web-server for proteomics

scientific article published on 25 April 2008

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article (publication date: 20 March 2017)

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

scientific article

Identifiers.org - Compact Identifier Services in the Cloud

scientific article published on 08 October 2020

Identifying novel biomarkers through data mining-a realistic scenario?

scientific article

Implementing data standards: a report on the HUPOPSI workshop September 2009, Toronto, Canada

scientific article published in May 2010

Improvements in the Protein Identifier Cross-Reference service

scientific article

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

scientific article published on 4 August 2016

Infrastructure for distributed protein annotation

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

IntAct--open source resource for molecular interaction data

scientific article (publication date: 2007)

IntAct: an open source molecular interaction database

scientific article

Integr8: enhanced inter-operability of European molecular biology databases

scientific article

Integrated omics dissection of proteome dynamics during cardiac remodeling

scientific article published on 9 January 2018

Integrating biological data--the Distributed Annotation System

scientific article

Integration of cardiac proteome biology and medicine by a specialized knowledgebase

scientific article

InterPro--an integrated documentation resource for protein families, domains and functional sites

scientific article (publication date: December 2000)

InterPro: an integrated documentation resource for protein families, domains and functional sites

scientific article

Interleukins and their signaling pathways in the Reactome biological pathway database

scientific article published on 25 January 2018

InteroPORC: an automated tool to predict highly conserved protein interaction networks

InteroPORC: automated inference of highly conserved protein interaction networks

scientific article published on 28 May 2008

Introducing the PRIDE Archive RESTful web services

scientific article

LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics

scientific article published on 7 May 2013

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

scientific article

Making proteomics data accessible and reusable: current state of proteomics databases and repositories

scientific article

Mapping plant interactomes using literature curated and predicted protein-protein interaction data sets

scientific article

Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

scientific article (publication date: 25 December 2010)

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany

scientific article published on 9 October 2014

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

scientific article

Minimum information about a bioactive entity (MIABE).

scientific article

Minimum information about a protein affinity reagent (MIAPAR)

scientific article published on 01 July 2010

MyDas, an extensible Java DAS server

scientific article

New open drug activity data at EBI

Omics Discovery Index - Discovering and Linking Public Omics Datasets

On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database

scientific journal article

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology

scientific article

Open Targets: a platform for therapeutic target identification and validation

scientific article

Open source libraries and frameworks for biological data visualisation: a guide for developers

scientific article

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

scientific article (publication date: 2014)

Organelle proteomics experimental designs and analysis

scientific article

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

scientific article published in August 2005

PRIDE Cluster: building a consensus of proteomics data

scientific article

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets

scientific article

PRIDE Inspector: a tool to visualize and validate MS proteomics data

scientific article (publication date: 8 February 2012)

PRIDE: a public repository of protein and peptide identifications for the proteomics community

scientific article published in January 2006

PRIDE: new developments and new datasets

scientific article (publication date: 2008)

PRIDE: quality control in a proteomics data repository

scientific article (publication date: 2012)

PRIDE: the proteomics identifications database

scientific article

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

scientific article (publication date: 29 June 2011)

Path2Models: large-scale generation of computational models from biochemical pathway maps

scientific article

PathwayMatcher: proteoform-centric network construction enables fine-granularity multiomics pathway mapping

scientific article published on 01 August 2019

Perspectives on tracking data reuse across biodata resources

PhaSepDB: a database of liquid-liquid phase separation related proteins

scientific article published on 01 January 2020

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

scientific article published on 15 June 2015

Preparing molecular interaction data for publication

scientific article

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

scientific article published in October 2013

Present and future of proteomics data curation at the PRIDE database

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative

scientific article

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

scientific article (publication date: August 2008)

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

scientific article

Protein-protein interactions: analysis and prediction

scientific article (publication date: 2008)

ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome

article

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

scientific article (publication date: March 2014)

Proteomic Data Standardization, Deposition and Exchange

article published in 2006

Proteomic data exchange and storage: the need for common standards and public repositories

scientific article

Proteomics Data Visualisation

scientific article published on 01 April 2015

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

scientific article published on August 2006

Proteomics and data standardisation

Proteomics data validation: why all must provide data

scientific article

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data

scientific article (publication date: September 2011)

Publisher Correction: Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

scientific article published on 04 March 2019

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Quantifying the impact of public omics data

Quantifying the impact of public omics data

scientific article published on 05 August 2019

R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases

scientific article

RIFLE: rapid identification of microorganisms by fragment length evaluation.

scientific article published in January 1997

Reactome and ORCID-fine-grained credit attribution for community curation

scientific article published on 01 January 2019

Reactome diagram viewer: Data structures and strategies to boost performance.

scientific article published on 23 November 2017

Reactome enhanced pathway visualization.

scientific article published in November 2017

Reactome graph database: Efficient access to complex pathway data.

scientific article

Reactome knowledgebase of human biological pathways and processes

scientific article (publication date: 2009)

Reactome pathway analysis to enrich biological discovery in proteomics data sets

scientific article

Reactome pathway analysis: a high-performance in-memory approach

scientific article

Reactome: a database of reactions, pathways and biological processes

scientific article

ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis

scientific article published on 09 September 2020

ReactomeGSA: new features to simplify public data reuse

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

scientific article

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles)

scientific article

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

scientific article published on 3 November 2011

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

scientific article published on 14 December 2011

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

scientific article published in December 2011

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

scientific article (publication date: July 2009)

Recurated protein interaction datasets

article

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

scientific article

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

SPARQL-enabled identifier conversion with Identifiers.org

scientific article

Second Joint HUPO publication and Proteomics Standards Initiative workshop

scientific article published on October 2009

Second Proteomics Standards Initiative Spring Workshop

article

Shared resources, shared costs--leveraging biocuration resources

scientific article

Shouldn't enantiomeric purity be included in the 'minimum information about a bioactive entity? Response from the MIABE group

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition

scientific article

Swissknife - 'lazy parsing' of SWISS-PROT entries

article

TEMBLOR - Perspectives of EBI Database Services

scientific article

Tackling quantitation: a report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea

scientific article published in September 2010

Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop: April 12-14th, 2012, San Diego, USA

scientific article (publication date: September 2012)

Testing and Validation of Computational Methods for Mass Spectrometry

scientific article published on 9 November 2015

The EBI enzyme portal

scientific article

The ESF Programme on Functional Genomics Workshop on 'Data Integration in Functional Genomics: Application to Biological Pathways'.

scientific article

The European Bioinformatics Institute (EMBL-EBI) in 2021

scientific article published on 25 November 2021

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

The HUPO Brain Proteome Project jamboree: centralised summary of the pilot studies

scientific article published in March 2006

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

scientific article (publication date: February 2004)

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

scientific article

The HUPO initiative on Model Organism Proteomes, iMOP.

scientific article published in February 2012

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

scientific article (publication date: 2013)

The HUPO proteomics standards initiative--easing communication and minimizing data loss in a changing world

scientific article

The HUPO proteomics standards initiative--overcoming the fragmentation of proteomics data

scientific article

The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions

scientific article published on 16 June 2020

The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions

scientific article published on 01 January 2020

The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.

scientific article published on 7 January 2017

The IntAct database: efficient access to fine-grained molecular interaction data

scientific article published on 21 October 2021

The IntAct molecular interaction database in 2010

scientific article (publication date: 2010)

The IntAct molecular interaction database in 2012

scientific article

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

scientific article (publication date: 2001)

The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases

scientific article (publication date: 2014)

The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)

scientific article published on 30 June 2020

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

scientific article published on 28 February 2006

The Ontology Lookup Service: bigger and better

scientific article (publication date: July 2010)

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries

scientific article

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

scientific article (publication date: December 2012)

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013

scientific article (publication date: 2013)

The PSI formal document process and its implementation on the PSI website

scientific article published on July 2007

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

scientific article

The Protein Feature Ontology: a tool for the unification of protein feature annotations

scientific article

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

scientific article (publication date: 18 October 2007)

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

scientific article

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics

scientific article published on 01 January 2020

The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible.

scientific article

The Proteomics Identifications database: 2010 update

scientific article (publication date: 2010)

The Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

scientific article

The Reactome BioMart

scientific article (publication date: 2011)

The Reactome Pathway Knowledgebase 2024

The Reactome Pathway Knowledgebase.

scientific article published on 14 November 2017

The Reactome pathway Knowledgebase

scientific article published on 9 December 2015

The Reactome pathway knowledgebase

scientific article from 2014

The Reactome pathway knowledgebase

scientific article published on 01 January 2020

The cardiovascular gene annotation initiative: Impact on data analysis

scientific article published in July 2015

The complex portal--an encyclopaedia of macromolecular complexes

scientific article

The effects of pathogenic and likely pathogenic variants for inherited hemostasis disorders in 140 214 UK Biobank participants

The evolution of standards and data management practices in systems biology

scientific article

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

scientific article published on 29 June 2020

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

scientific article (publication date: September 2010)

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study

scientific article published in January 2023

The minimum information about a genome sequence (MIGS) specification

scientific article

The minimum information required for reporting a molecular interaction experiment (MIMIx).

scientific article published on August 2007

The mzIdentML data standard for mass spectrometry-based proteomics results

scientific article (publication date: July 2012)

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

scientific article

The omics discovery REST interface

scientific article published on 06 May 2020

The proteomics standards initiative

scientific article

The publication and database deposition of molecular interaction data

scientific article

The reactome pathway knowledgebase 2022

scientific article published on 14 October 2021

The role SWISS-PROT and TrEMBL play in the genome research environment.

scientific article

The systematic annotation of the three main GPCR families in Reactome

scientific article

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

scientific article

The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI).

scientific article published on January 2006

Tools (Viewer, Library and Validator) that facilitate use of the peptide and protein identification standard format, termed mzIdentML

scientific article (publication date: November 2013)

Toward interoperable bioscience data

scientific article (publication date: 27 January 2012)

Towards a unified open access dataset of molecular interactions

scientific article published on 01 December 2020

Towards the collaborative curation of the registry underlying Identifiers.org

scientific article (publication date: 2013)

Understudied proteins: opportunities and challenges for functional proteomics

scientific article published on 9 May 2022

Uniform Resolution of Compact Identifiers for Biomedical Data

preprint

Uniform resolution of compact identifiers for biomedical data.

scientific article

Using Reactome to build an autophagy mechanism knowledgebase

scientific article published on 02 June 2020

VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL

article

Wikidata as a FAIR knowledge graph for the life sciences

scholarly article posted as a preprint in BioRxiv on 11 February 2020

Wikidata as a knowledge graph for the life sciences ⬇️

scientific article published on 17 March 2020

easyDAS: automatic creation of DAS servers

scientific article published on 18 January 2011

iAnn: an event sharing platform for the life sciences

scientific article published on 05 June 2013

iProX in 2021: connecting proteomics data sharing with big data

scientific article published in 2021

iProX: an integrated proteome resource.

scientific article published in January 2019

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

scientific article (publication date: March 2012)

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

scientific article

jmzTab: a java interface to the mzTab data standard

scientific article

ms-data-core-api: an open-source, metadata-oriented library for computational proteomics

scientific article

mzML--a community standard for mass spectrometry data

2011 scientific article

qcML: an exchange format for quality control metrics from mass spectrometry experiments

scientific article published on 23 April 2014

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