Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Minimum Information Standards - all for one and one for all

27.08.2007
Three papers published by EMBL scientists and their collaborators will make it much easier to share and compare information from large-scale proteomics data. The papers are published in Nature Biotechnology on 8th and 26th August.

As the quantity of available biological information and the use of public data repositories increases, consistency in the information held in these databases is vital to allow full integration, exchange and comparison of their contents. As Europe’s main provider of biological data, the EMBL-European Bioinformatics Institute (EBI) is involved in setting the precedent for reporting standards by applying these to its own data repositories such as ArrayExpress (microarray and gene expression data), IntAct (molecular interaction data) and PRIDE (protein identification linked to experimental evidence and publications).

The Minimum Information About a Proteomics Experiment (MIAPE) and the Minimum Information required for reporting a Molecular Interaction Experiment (MIMIx) guidelines propose the range of information to be recorded to document proteomics and molecular interaction data, respectively. The standards aim to reduce ambiguity and capture all the necessary information from an experiment to set the experimental results in both a biological and a methodological context, thereby providing a deeper level of understanding to others exploring the data. Henning Hermjakob from the EMBL-EBI, a co-author on both Perspectives papers published on 8th August, said “Through the community-wide uptake of agreed minimum reporting standards, we can all benefit from easier identification and use of information that is most relevant to our own areas of work. This is the next step in providing freely accessible data repositories of the highest possible quality.”

The Nature Biotechnology Perspectives papers, published as open-source articles, outline the proposed reporting requirements for proteomics and molecular interaction experiments and discuss their implementation, impact and benefits. The later research paper, published in the same journal on 26th August, shows how implementation of these standards benefits not only the reporting researchers, but also the wider community through the development of more detailed and comprehensive information resources.

Setting the standards

Both sets of reporting requirements, MIAPE and MIMIx, have been shaped by input from the scientific community and developed to minimise the burden on individual researchers. The MIAPE reporting guidelines are being developed as a range of individual modules, which can be combined as necessary to cover an entire experimental workflow – from study design to statistical data analysis. As the first finalised module, the MIMIx guidelines implement the general MIAPE principles for describing molecular interactions and also present recommendations on data deposition prior to publication.

Standards in action

Both sets of reporting requirements were put into practice by Bantscheff et al. in the reporting of a large-scale approach to profile the interaction of protein kinases with small inhibitory molecules. The Cellzome researchers used this method to validate the action of three drugs sharing a particular kinase target and also to identify novel drug targets. The binding information shed light on the drug binding specificities and downstream effects on signalling pathways. The MIAPE and MIMIx-compliant mass spectrometry and interaction data were entered into the EBI-hosted PRIDE, IntAct, and ChEBI databases, and accession numbers are included in the research publication to provide direct access to the proteomic information, mass spectra and molecular interaction data. The interconnected EBI data resources serve not only to hold the direct experimental results, but also set them within a wider biological context, for example, by linking the identified kinases to known functions in the UniProt database.

The quantitative profiling method used has potential application in drug discovery and in gaining a greater understanding of drug action in patients. The systematic recording of such information in public repositories and adherence to reporting standards ensures that maximum use can be made of this progression in knowledge, offering benefits to the scientific community, and in the case of drug discovery, development and healthcare, there are clearly benefits to be had for society too.

Anna-Lynn Wegener | alfa
Further information:
http://www.embl.org/downloads/

Further reports about: Kinase MIAPE Minimum Repositories Standards benefit experimental proteomic

More articles from Life Sciences:

nachricht Cryo-electron microscopy achieves unprecedented resolution using new computational methods
24.03.2017 | DOE/Lawrence Berkeley National Laboratory

nachricht How cheetahs stay fit and healthy
24.03.2017 | Forschungsverbund Berlin e.V.

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

Im Focus: Researchers Imitate Molecular Crowding in Cells

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to simulate these confined natural conditions in artificial vesicles for the first time. As reported in the academic journal Small, the results are offering better insight into the development of nanoreactors and artificial organelles.

Enzymes behave differently in a test tube compared with the molecular scrum of a living cell. Chemists from the University of Basel have now been able to...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

Argon is not the 'dope' for metallic hydrogen

24.03.2017 | Materials Sciences

Astronomers find unexpected, dust-obscured star formation in distant galaxy

24.03.2017 | Physics and Astronomy

Gravitational wave kicks monster black hole out of galactic core

24.03.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>