Creating Templates for Proteomics

FAIRDOM is establishing a support and service network for European Systems Biology. FAIRDOM is a joint action of ERA-Net ERASysAPP and European Research Infrastructure ISBE to establish a data and model management service facility for Systems Biology. Our prime mission is to support researchers, students, trainers, funders and publishers by enabling Systems Biology projects to make their Data, Operating procedures and Models, Findable, Accessible, Interoperable and Reusable (FAIR).

SysMO is a European transnational funding and research initiative on "Systems Biology of Microorganisms".

The goal pursued by SysMO was to record and describe the dynamic molecular processes going on in unicellular microorganisms in a comprehensive way and to present these processes in the form of computerized mathematical models.

Systems biology will raise biomedical and biotechnological research to a new quality level and contribute markedly to progress in understanding. Pooling European research ...

FAIRDOM will establish a support and service network for European Systems Biology. We will serve projects in standardising, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable.

Good data and model management improves the longevity and impact of your interdisciplinary research. FAIRDOM offers software and expertise to support you in better managing your interdisciplinary life-science projects, particularly in systems and synthetic biology. If you have never heard of data and model management, or are curious about it, or you are an expert keen to exchange ideas, our user meeting is the place for you!

At our users meeting you can:

• Learn why data and model management is ...

The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:

• facilitates and maximises the potential for data exchange between SysMO research groups;
• maximises the ‘shelf life’ and ...

Data integration is an essential part of Systems Biology. Scientists need to combine different sources of information in order to model biological systems, and relate those models to available experimental data for validation. Currently, only a small fraction of the data and models produced during Systems Biology investigations are deposited for reuse by the community, and only a smaller fraction of that data is standards compliant, semantic content. By embedding semantic technologies into familiar ...

Some examples of proteomics templates for Mass Spectrometry data that conform to the MIAPE specification

Examples of proteomics templates for gele electrophoresis data that conform to the MIAPE-GE specification

An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.

The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies

MIAPE based Gel Electrophoresis Data Entry Worksheet

This is an Excel template for Mass Spec data that contains all the necessary MIAPE metadata fields. It was derived from examples on the PRIDE website (PRoteomics IDEntifications database http://www.ebi.ac.uk/pride/)

An example of a completed data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of a MIAPE compliant data format taken from the PRIDE website (http://www.ebi.ac.uk/pride).

This template is a JERM compliant spreadsheet for use with gel electrophoresis data. It is in the style of the JERM MASTER template with worksheets for metadata, organism_sample, instrument and data. To conform to MIAPE-GE all worksheets are mandatory. A detailed description of MIAPE-GE is available from http://www.psidev.info/miape/MIAPE_GE_1_4.pdf

MIAPE (Minimum Information About a Proteomics Experiment) is the recommended format for proteomics data in SysMO-SEEK. The document attached provides more information and links to tools and resources.