Commit 4503cd78 authored by Yasset Perez-Riverol's avatar Yasset Perez-Riverol
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prin inspector updated

parent eb6a9d12
## prideinspector
## PRIDE Inspector: Reviewing public proteomics data
For each cluster, we offer a detailed summary page where you can view the key statistics and quliaty metrics of a cluster.
The GUI module of the PRIDE Inspector organizes itself in the form of several views, where each view focuses on a particular aspect of the data.
There are currently six views:
## prideinspector
1. ‘Overview’ view – shows experimental metadata.
A spectrum cluster is a group of Mass Spec spectra that share the same characteristics, namely the shapes of their peaks. The spectra that are similar are grouped together in the PRIDE Cluster pipeline.
2. Protein view – shows protein identifications
## Species chart
3. Peptide view – shows peptides used to generate the protein identifications
The original spectrum comes from PRIDE Archive, which is a submission based data repository.
4. Spectrum view – shows spectra and chromatograms
Due the diversity of PRIDE Archive submissions, we have spectrum from a large number of species and also covers many post translational modifications.
5. Quantification view – show quantitative data for both proteins and peptides
In order to keep the data submitted to us save and secure, we only take the public experiments into account for running the PRIDE Cluster production pipeline.
6. ‘Summary charts’ view – provides data chars for assessing data quality
To enable maximum reusability, each view is implemented as an independent component using [Java Swing](http://download.oracle.com/javase/tutorial/uiswing/).
This way, more views can be added easily in the future.
[Inspector-mzgraph-browser](https://github.com/PRIDE-Toolsuite/inspector-mzgraph-browser), the component responsible for visualizing spectra and chromatograms,
is released and available as self-contained Java library and distributed as part of the PRIDE Inspector. Both this component and the statistical charts in the
‘Summary Charts’ view, are implemented using the [JFreeChart](http://www.jfree.org/jfreechart/) API.
## Modification chart
Next to the previous six layers, a generic application management framework maintains the context and information shared by the whole environment.
It consists of features frequently required by medium or large Java Swing based applications, such as: lifecycle services for background tasks, in-memory caching,
event bus, user property management and error handling. The framework is independent from the PRIDE Inspector and therefore can be reused for other rich
client applications.
The current release of the PRIDE Cluster API is version 1. To find out more about this version, please refer to its documentaiton.
## Visualising Peptide/Protein Information
## Web browsable API
### PSMs
The PRIDE Cluster RESTful API is web browsable, which means that:
The ‘Peptide View’ tab includes the information at PSM level for every peptide. The Peptide Table panel shows for each peptide the list of PSMs with
the corresponding scores from the search engines, the list of modifications, Precursor charge and precursor mass. In the example ech PSM contains the
information of the OMSSA and XTandem Score, also the table provides the information of the peptide sequence length; start and end position in the protein
sequence.
The query results returned by the API are available in JSON format. This ensures that they can be viewed by human and accessed programmatically by computer.
![PSMs Information](/static/markdown/prideinspector/files/peptideTable2.png)
The main RESTful API page provides a simple web-based user interface, which allows developers can familiarise themselves with the API and get a better sense of the PRIDE Cluster data before writing single line of code.
### Peptide Information
## Versioning
The Peptide Table also provides the information about each protein identified in the file. It provides information about the peptide sequence,
Protein identifier, sequence length, isoelectric point, number of PSMs, and modification summary.
To ensure that changes in the PRIDE Cluster API don't break the applications relying on it, the API is versioned, and the version is included in the API's URL.
![Peptide Table](/static/markdown/prideinspector/files/peptideTable.png)
No backward-incompatible changes are made to each version after it's been made public. More specifically, it's guaranteed that within one version there will be no:
### Protein Information
changing urls
deleting or renaming data fields
changing data field types
The following non-disruptive changes may be implemented to a public API:
The protein panel shows all the information about identified proteins: protein level scores, protein sequences, protein identifier, number of
PSM for each protein, modifications and number of unique peptides. The first column is a three table structure when the protein inference
is provided (![](/static/markdown/prideinspector/files/plus.png)), if the use
click in the sign the group is collapsed.
adding new endpoints
adding new data fields
adding new filtering methods
An advance notice will be given before obsoleting an API version. To stay up to date, please consider signing up for the PRIDE Twitter account.
![Protein Table](/static/markdown/prideinspector/files/proteinTable.png)
## API version 1 documentation
Finally, the sequence coverage is shown in a column for each protein:
## Implementation
![Protein Sequence coverage](/static/markdown/prideinspector/files/coverage.png)
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