H
Henning Hermjakob
Researcher at European Bioinformatics Institute
Publications - 334
Citations - 72741
Henning Hermjakob is an academic researcher from European Bioinformatics Institute. The author has contributed to research in topics: Proteomics Standards Initiative & UniProt. The author has an hindex of 80, co-authored 323 publications receiving 64702 citations. Previous affiliations of Henning Hermjakob include St. John's University & Birkbeck, University of London.
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Journal ArticleDOI
jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.
TL;DR: The jmzReader library is a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML‐based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mZXML, mzData, and mzML (based on the already existing API jmZML).
Proceedings ArticleDOI
The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.
TL;DR: This paper will discuss the development of ontologies by the user community and their current utilization in the fields of protein:proein interactions and mass spectrometry.
Journal ArticleDOI
Dasty and UniProt DAS: a perfect pair for protein feature visualization
Philip Jones,Nisha Vinod,Thomas A. Down,Andre Hackmann,Andreas Kähäri,Ernst Kretschmann,Antony F. Quinn,Daniela Wieser,Henning Hermjakob,Rolf Apweiler +9 more
TL;DR: A DAS reference server that provides up-to-date sequence and annotation from UniProt, with additional feature links and database cross-references from InterPro and a DAS client implemented using Java and Macromedia Flash that is optimized for the display of protein features are presented.
Journal ArticleDOI
A reference set of curated biomedical data and metadata from clinical case reports
J. Harry Caufield,Yijiang Zhou,Yijiang Zhou,Anders O. Garlid,Shaun P. Setty,David A. Liem,Quan Cao,Jessica M. Lee,Sanjana Murali,Sarah Spendlove,Wei Wang,Li Zhang,Yizhou Sun,Alex A. T. Bui,Henning Hermjakob,Henning Hermjakob,Karol E. Watson,Peipei Ping +17 more
TL;DR: A standardized metadata template and MACCR set are developed that render CCRs more findable, accessible, interoperable, and reusable while serving as valuable resources for key user groups, including researchers, physician investigators, clinicians, data scientists, and those shaping government policies for clinical trials.
Journal ArticleDOI
Dasty2, an Ajax protein DAS client
Rafael C. Jimenez,Antony F. Quinn,Alexander Garcia,Alberto Labarga,Kieran O'Neill,Fernando Martinez,Gustavo A. Salazar,Henning Hermjakob +7 more
TL;DR: Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS), freely available under the terms of the Apache License 2.0.