MIAPE Extractor - ProteoRed Java MIAPE API - Webservices


MIAPE Extractor Tool

Link to download  latest version

Source code now available at gitHub: [ source code]

Tutorial (updated to v3.8.1 - 30-Dec-2015): [ pdf]

See some screenshots ScreenShots.

The MIAPE extractor tool is a Java standalone tool that allows:

  • to help to fulfil the HUPO-PSI MIAPE guidelines in the Proteomics datasets;
  • to integrate large amount of data;
  • to organize and store the data in the ProteoRed MIAPE repository ( pubmed) or in the local system (both workflows are available);
  • to filter the datasets by different and multiple criteria;
  • to visually and dynamically inspect numerous proteomics features of the datasets in different levels of aggregation (from single analysis of an MS run to the integration of multiple replicates of a complex sample analysis);
  • to allow the visual comparison of multiple proteomics datasets;
  • and to help to prepare a  ProteomeXchange dataset submission.


Quick guide to load the  PME6 example data (available by default in the package)

1- Download it from [ http://proteo.cnb.csic.es/miape-api/MIAPE_Extractor/v3.8.1/MIAPE_Extractor_v3.8.1.zip]
2- Unzip it to your computer.
3- Run it by executing any of the START_win_3Gb.bat (for windows) or START_linux_3Gb.sh (for Mac or linux). (This will use 3Gb of your RAM memory).
4- Click on “Offline mode”.
5- Go to “Data inspection” menu and click on “Data inspection project”.
6- Select “PME6_Reanalysis” value in the “Saved projects” dropdown control at the top left, and click on “Load”.
7- Click on “Next” and then click on “ok”.
8- The tool will load the dataset and you will be able to inspect all the data by selecting any “Chart type” and options at the left panels.


See latest changes and new features: here (last update:30-Dec-2015)

charts


Batch MIAPE extraction Tutorial: [ pdf]

PDF presentation (AOHUPO - JP Albar - May 2012):  pdf

Plenary lecture on 5th Congress of the Spanish Proteomics Society (Salvador Martínez-Bartolomé - Feb 2013):  pdf


Java MIAPE API

Updates and new features: here (last update:29-Dec-2015)

Getting Java MIAPE API: here

Java MIAPE API documentation: here

About MIAPE


Web Services

MIAPE API Webservices

This webservice provides the basic functionality to interact remotely with the MIAPE repository.
It allows retrieving, storing and deleting MIAPE documents and projects.
Authentication of the user is always performed previous to any action, so privacy is preserved in the API.

Link to WSDL file:  MiapeAPIWebservice.wsdl

List of functions provided by the webservice here.

Webservice documentation and examples here.

MIAPE Extractor Webservices

This webservice provides a set of functions related to the extraction of MIAPE information from standard XML files and related to the creation of standard XML files from MIAPE documents in the MIAPE repository.
At the moment the standard XML files that supports are:  mzML,  mzIdentML,  PRIDE XML and  XTandem output XML.
Authentication of the user is always performed previous to any action, so privacy is preserved in the API.

Link to WSDL file:  MiapeExtractor.wsdl

List of functions provided by the service here.

Webservice documentation and examples here.


The ProteoRed MIAPE repository

[ ProteoRed MIAPE repository]


Team

The Bionformatics group members are:

  • Salvador Martínez-Bartolomé (smartinez at proteored.org) [ Publications]
  • Miguel Angel López García (malgarcia at proteored.org) [Publications]
  • Alberto Medina Auñón (jamedina at proteord.org) [ Publications]


Group Coordinator:


Group publications (not updated): here

Attachments