Commit f5e2bb11 authored by Yasset Perez-Riverol's avatar Yasset Perez-Riverol
Browse files

minor changes in the documentation

parent bcd1df92
......@@ -73,7 +73,7 @@
</a>
<DropdownMenu slot="list">
<!--<DropdownItem name="goToSpectraClustering">Spectra Clustering Toolsuite</DropdownItem>-->
<DropdownItem name="goToPrideInspector">PRIDE Submission Tool</DropdownItem>
<DropdownItem name="goToPrideSubmission">PRIDE Submission Tool</DropdownItem>
<DropdownItem name="goToPrideInspector">PRIDE Inspector Toolsuite</DropdownItem>
<DropdownItem name="goToPrideUtilities">PRIDE Utilities Libraries</DropdownItem>
</DropdownMenu>
......@@ -164,6 +164,9 @@
else if(name=='goToSpectraClustering'){
this.$router.push({path:'/markdownpage/spectraclustering'});
}
else if(name=='goToPrideSubmission'){
this.$router.push({path:'/markdownpage/pridesubmissiontool'});
}
else if(name=='goToPrideInspector'){
this.$router.push({path:'/markdownpage/prideinspector'});
}
......
## PRIDE Submission Tool
For each cluster, we offer a detailed summary page where you can view the key statistics and quliaty metrics of a cluster. 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.
## Species chart
The original spectrum comes from PRIDE Archive, which is a submission based data repository.
Due the diversity of PRIDE Archive submissions, we have spectrum from a large number of species and also covers many post translational modifications.
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.
## Modification chart
The current release of the PRIDE Cluster API is version 1. To find out more about this version, please refer to its documentaiton.
## Web browsable API
The PRIDE Cluster RESTful API is web browsable, which means that:
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.
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.
## Versioning
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.
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:
changing urls
deleting or renaming data fields
changing data field types
The following non-disruptive changes may be implemented to a public API:
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.
## API version 1 documentation
## Implementation
......@@ -11,32 +11,31 @@ Before submitting to PRIDE database the user need to be sure that it has an acco
## Prepare submission
The first step to prepare your submission for PRIDE Archive is to know which files are **Mandatory**, which are **Optionals**; and the benefit of providing each file type. Each submitted dataset to PRIDE Archive **MUST** contain the following information (following ProteomeXchange guidelines):
The first step to prepare your submission for PRIDE Archive is to know which files are **Mandatory**, which are **Recommended**; and the benefit of providing each file type. Each submitted dataset to PRIDE Archive **MUST** contain the following information (following ProteomeXchange guidelines):
- Mass spectrometer output files (called ‘RAW’): The RAW files are the native machine data files - Thermo .RAW, ABSCIEX .wiff, .scan, Agilent .d, Waters .raw, Bruker .yep, Bruker .baf - [check the full list here](/markdownpage/pridefileformats#search_files)
- Mass spectrometer output files (called ‘RAW’) (**Mandatory**): The RAW files are the native machine data files - Thermo .RAW, ABSCIEX .wiff, .scan, Agilent .d, Waters .raw, Bruker .yep, Bruker .baf - [check the full list here](/markdownpage/pridefileformats#search_files). Each RAW file needs to be realted with at least one SEARCH file.
- Peptide/protein identification files (called ‘SEARCH’): These are the files provided by the software used to perform the data analysis - Mascot .dat, ProteomeDiscover .msf - [check the full list here](/markdownpage/pridefileformats#peak_files)
- Peptide/protein identification files (called ‘SEARCH’) (**Mandatory**): These are the files provided by the software used to perform the data analysis - Mascot .dat, ProteomeDiscover .msf - [check the full list here](/markdownpage/pridefileformats#peak_files). Each SEARCH file needs to be related with at least one RAW file.
- mzTab or mzIdentML result files (called 'RESULT') (**Recommended**): The mzTab and mzIdentML are standard file formats provided by most of the analysis software tools [check the full list here](/markdownpage/pridefileformats#result_files)
- mzTab or mzIdentML result files (called 'RESULT') (**Recommended**): The mzTab and mzIdentML are standard file formats provided by most of the analysis software tools [check the full list here](/markdownpage/pridefileformats#result_files). The mzIdentML contains only identification information, were the mzTab can contains Quantitation/Idnetification results. These files needs to be related with at least one PEAK file.
- PEAK List files (called 'PEAK') (**Recommended**): If the mzTab or mzIdentML is provided the corresponding peak list files should be provided in order to ba able to check the MS/MS evidences that support the peptide/protein identifications.
- PEAK List files (called 'PEAK') (**Recommended**): If the mzTab or mzIdentML is provided the corresponding peak list files should be provided in order to be able to check the MS/MS spectrum evidences that support the peptide/protein identifications ([check the full list here](/markdownpage/pridefileformats#peak_files)).
> The submissions that provides the 'RESULT' and corresponding 'PEAK' files are classify in PRIDE Archive as **Complete Submissions** following the ProteomeXchange guidelines. Those submimssions are
> The submissions that provides the 'RESULT' and corresponding 'PEAK' files are classify in PRIDE Archive as **Complete Submissions** following the ProteomeXchange guidelines. Please, read here the [benefits of Complete Submissions](/markdownpage/whycompletesubmissions#whycompletesubmissions).
Optionally other files can be included in your submission to facilitate the reproduce of the original results and better understanding of the dataset:
Optionally other files can be included in your submission to facilitate the review process or reproduce of the original results and better understanding of the dataset:
- Images of gels generated in the experiment (‘GEL’), sequence database files (FASTA), spectral libraries
(SPECTRUM_LIBRARY) and any other, relevant file types (‘OTHER’).
- Images of gels generated in the experiment (‘GEL’), sequence database files (FASTA), spectral libraries (SPECTRUM_LIBRARY) and any other, relevant file types (‘OTHER’).
## Submit dataset
When have check that you can provide all the files in previous section, the next step is to Download the [Submission Tool](/submissiontool). The Submission Tool guide the users throught the submission process generating the [submission.px file] (/static/markdown/submitData/PAge/files/Submission_Summary_File.pdf). The submission.px file contains 2 types crucial information:
If you have check that you can provide all the files in previous section, the next step is to Download the [Submission Tool](/submissiontool). The Submission Tool guide the users throught the submission process generating the [submission.px file](/static/markdown/submitdatapage/files/Submission_Summary_File.pdf). The submission.px file contains 2 types crucial information:
**Metadata**: experimental metadata like experiment description, sample taxonomy information, instruments and modifications used.
**Metadata**: Minimun experimental metadata like experiment description, sample taxonomy information, instruments and modifications used.
**Mapping between the uploaded files**: for instance between the raw files and the corresponding result or search engine output files.
>If you are using the PX submission tool, the file will be created automatically for you. If you are using the Aspera command line submission mode, you will need to create one. You can do it using with the PX submission tool (without actually uploading the data and saving the submission.px independently) or with scripting.
>If you are using the PX submission tool, the file will be created automatically for you.
Finally the user can submit the dataset using the Aspera or FTP protocols.
......@@ -45,14 +44,16 @@ Finally the user can submit the dataset using the Aspera or FTP protocols.
Submitted datasets are 'private' by default, which means you need to be [logged-in](https://www.ebi.ac.uk/pride/archive/login) to view your data. During the submission process we create a PX reviewer account for your submission which you can include in your letter to the editor or manuscript to be used during the review process. The PX reviewer account will give you access to all of the files belonging to your submission. You can access the private dataset files in two ways:
- PRIDE Archive web page
#### PRIDE Archive web page
PRIDE Archive web site is available at http://www.ebi.ac.uk/pride/archive. Registered submitters can use their personal accounts or the reviewer accounts to access and download the individual PX datasets. For every submission there is a separate reviewer account generated. Once logged in with your registered User (the e-mail account you used to register in PRIDE) or an issued Reviewer Account you are going to see the private dataset/s listed.
</br>
![Private Submission List](/static/markdown/submitDataPage/files/private-submission.png)
- PRIDE Inspector
#### PRIDE Inspector
[PRIDE Inspector](/prideinspector) is a Java Standalone Desktop tool that can be used in to query and retrieve the information from PRIDE Archive data:
......@@ -68,7 +69,7 @@ In case of Complete Submissions you can alternatively launch PRIDE Inspector wit
## Post-submission
The particular post-submission steps include the following: modifying the original dataset, referencing the dataset in your manuscript, and making the dataset public (/pridepostprocessing).
The particular post-submission steps include the following:
- Modifying the original dataset: In case you need to add to a small number of additional "other files" (like csv, plain text files, spreadhseets, scripts) we can provide you with FTP details to upload and can add these to the original dataset without you resubmitting the whole dataset. In case you have used the PX Submission Tool and you need to add additional raw files and accompanying result or search files, you need to resubmit the whole dataset again. Please follow the procedure here. In case of an Aspera bulk submission you have to upload the modified and missing files into a new subdirectory within your target directory and regenerate the submission summary file including all the old and modified and new files again.
......@@ -76,11 +77,13 @@ The particular post-submission steps include the following: modifying the origin
- Releasing the dataset: By default, your data will be made publicly available after your manuscript has been accepted, or when we have your instructions to do so. While we may also receive acceptance notifications from some journals, we would like to ask all submitters to kindly notify us separately. Otherwise, it can happen that we don’t now that your manuscript is already published. You can notify us two ways:
- Via the PRIDE Archive web site (http://www.ebi.ac.uk/pride/archive). Once you have logged in with your user account at http://www.ebi.ac.uk/pride/archive/login you can click the green “Publish” buttons located next to your unpublished datasets. Here you can provide details for your dataset and submit a web form, please see Figure 5.
- Via the PRIDE Archive web site (http://www.ebi.ac.uk/pride/archive). Once you have logged in with your user account at http://www.ebi.ac.uk/pride/archive/login you can click the green “Publish” buttons located next to your unpublished datasets. Here you can provide details for your dataset and submit a web form.
**Public Release**
### Public Release
- Contacting pride-support@ebi.ac.uk.
Upon making the project public, a project page will be released over at ProteomeCentral (http://proteomecentral.proteomexchange.org) and from a particular dataset page an FTP location will be available.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment