Commit eb6a9d12 authored by Yasset Perez-Riverol's avatar Yasset Perez-Riverol
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minor changes - submission tool page done

parent 6589d32c
......@@ -81,7 +81,7 @@ Result files are standard file formats developed by HUPO-PSI Consortium to excha
- mzIdentML (version 1.1 and 1.2 http://www.psidev.info/mzidentml): mzIdentML is one of the standards developed by the Proteomics Informatics working group of the PSI. The extension of the file .mzid is used by the submission tool to recognize the file format. The mzIdentML only contains the peptide/protein identification information of a proteomics experiment not the Quantitation.
- mzTabb (version 1.0 http://www.psidev.info/mztab): mzTab is one of the standards developed by members of the Proteomics Informatics working group of the PSI to represent Quantification data. For PRIDE Archive the mzTab file MUST contains the Protein and PSM tables and is optional the Peptide section. **We recommended this file format to report the Quantification Results**
- mzTab (version 1.0 http://www.psidev.info/mztab): mzTab is one of the standards developed by members of the Proteomics Informatics working group of the PSI to represent Quantification data. For PRIDE Archive the mzTab file MUST contains the Protein and PSM tables and is optional the Peptide section. **We recommended this file format to report the Quantification Results**
| Software | Standard File format supported|
|----------|-------------------------------|
......
## PRIDE Submission Tool
The PRIDE Submission Tool is the main tool used to submit the proteomics experiment to [PRIDE Archive](wwwwebi.ac.uk/pride/archive/). This tool has been implemented as a Wizard, guiding the submitter trougth a set of simple steps to build the final submission.
The PRIDE Submission Tool is the main tool used to submit the proteomics experiment to [PRIDE Archive](wwww.ebi.ac.uk/pride/archive/). This tool has been implemented as a Wizard, guiding the submitter trougth a set of simple steps to build the final submission.
## Species chart
## Login Panel
The original spectrum comes from PRIDE Archive, which is a submission based data repository.
The first step to submit a dataset to PRIDE Archive is to log into PRIDE using an existing account as shown:
Due the diversity of PRIDE Archive submissions, we have spectrum from a large number of species and also covers many post translational modifications.
</br>
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.
![Login panel](/static/markdown/pridesubmissiontool/files/login-page.png)
## Submission Details
The user is asked to provide some basic details about the uploaded dataset such as the title, a list of keywords (in a comma separated format),
and a brief description of the data (similar to the abstract of the corresponding publication) a sample processing and a data processing protocol.
The user also picks a mass spectrometry experiment type from a drop-down menu.
## Modification chart
</br>
The current release of the PRIDE Cluster API is version 1. To find out more about this version, please refer to its documentaiton.
![Project description](/static/markdown/pridesubmissiontool/files/project-description.png)
## Web browsable API
## Add Files and assign file types
The PRIDE Cluster RESTful API is web browsable, which means that:
In this stage, you should choose the files you would like submit. You can add files by clicking on the highlighted button.
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.
![Add files](/static/markdown/pridesubmissiontool/files/add-files.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.
> Depending on the [files provided](/markdownpage/pridefileformats) and the type of submission, the tool will try to link the relation between files and also the file
type.
## Versioning
### Complete Submissions based on mzIdentML
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:
When a Complete submission is performed based on mzIdentMLs files. The dataset should contains at least one PEAK list associated with the mzIdentML
(identification file).
![Add files](/static/markdown/pridesubmissiontool/files/file-relations-1.png)
changing urls
deleting or renaming data fields
changing data field types
The following non-disruptive changes may be implemented to a public API:
The Submission tool will automatically detect the _Type_ of the File (e.g. RAW, PEAK, RESULT, SEARCH). In the case of ‘PEAK’ files, the tool will
check and validate that all the required file(s) that were referenced in the mzIdentML file’s <SpectraData> element are present.
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.
> Note: If your peak list files had an extension recognized by the tool (.mgf , .dta, .ms2, .pkl) then the tool will automatically annotate the
type as ‘PEAK’ but in other cases you have to assign the file type yourself.
For instance, .mzXML files, are recognized by the tool as them as ‘PEAK’ files by default but.
## API version 1 documentation
If you are adding a spectral library file, then please assign the file type manually as these files might come in many different flavors,
for instance as .msp, .splib or .nist files.
## Implementation
> Note: You can provide in Complete submissions the corresponding SEARCH files from the search engines in addition to the result files (e.g. the Mascot .dat files)
### Complete Submissions based on mzTab
Complete Submissions based on mzIdentML only contains the identified peptides/proteins and the corresponding spectra used to identified them. However, most of the
shotgun proteomics experiments are _Quantitative_ experiments.
For Quantitative Complete experiments the user should provide using [mzTab files](/markdownpage/pridefileformats#result_files)
## Assign relationships between the submitted files
This mapping step consist of assigning the relations between the ‘RESULT’ files and the other types of files included in the submission,
for example, which ‘RAW’ (mandatory), ‘PEAK’ (mandatory for mzIdentML and mztab), ‘SEARCH’, ‘QUANT’, ‘FASTA’, ‘SPECTRUM_LIBRARY’,
‘GEL’ or ‘OTHER’ files can be linked to a given ‘RESULT’ file or are associated with it.
This will enable others users to understand how your data is connected and structured.
![Add files](/static/markdown/pridesubmissiontool/files/file-relations-2.png)
> By default, the tool makes an attempt to generate the mapping between the ‘RESULT’ and the other - most importantly ‘RAW’ - files.
For instance, if there has been only 1 ‘RESULT’ file found during the previous ‘Add Files’ step then all the other files will be mapped to this ‘RESULT’ file.
If there are multiple ‘RESULT’ files the tool maps the other files – ‘RAW’, ‘PEAK’, ‘SEARCH’, … - with the same file name prefix, but without the
file extension, to the corresponding ‘RESULT’ files. This mapping is done even if the suffix part of the ‘RAW’ files contains different numbers
(for instance indicating different replicates).
If the automatic mapping is partial only or does not apply, the submitter is asked to manually assign the relationships between the files.
## Additional submission metadata
Additional metadata need be provided for each ‘RESULT’ file in the case of a ‘Complete’ submission, and what is needed is the same for both subtypes
of submissions (mzTab and mzIdentML).
![Annotate Result Files](/static/markdown/pridesubmissiontool/files/annotate.png)
Previous figure shows the screen where the _‘Annotate’_ button can be clicked for each ‘RESULT’ file. This information is usually imported automatically
in the case of a mzTab file (if the recommended CVs/ontologies are used). For mzIdentML, the information needs to be manually annotated.
The following additional metadata is **Mandatory**:
- Species: The species, where the experiment was performed.
- Tissue: Tissue (not applicable should be used in case of cell line experiments).
- Instrument information.
![Annotate Result Files](/static/markdown/pridesubmissiontool/files/annotate-2.png)
Each of these information should be provided in Controlled Vocabulary (CV) terms from a drop-down menu. Optionally, providing information
about the _cell type_, _disease_ and _quantification method_ (if applicable) is recommended.
> Note: If you have more than one ‘RESULT’ file, as it is usually the case, then you can pick the ‘Apply to all’ box for species and tissue information
instead of doing this many times.
In the majority of the cases you will find the metadata annotation you are looking for in the drop-down menu since the elements of the drop-down
menus have been selected based on frequency. Sometimes the annotation you are looking for is not going to be available from the drop-down lists.
If that’s the case, you have to select to the OLS (Ontology Lookup Service) panel and search for the annotation you want to provide.
For the more extensive search you need to click on the “other” options on the bottom of the drop-down menu. For instance, if you have samples from
e.g. the fish Grayling (Thymallus thymallus) the species is not available from the drop-down list menu. You have to click on
_Other species_ and search for Thymallus thymallus in the OLS panel.
![OLS Client](/static/markdown/pridesubmissiontool/files/ols-client.png)
## Last steps
### Providing contact details for the Lab Head
![Add Lab Head](/static/markdown/pridesubmissiontool/files/la-head.png)
### Optional metadata annotation
In this panel, it is recommended to provide additional metadata in four cases:
- Your dataset is part of a bigger project/effort (for instance the Human Proteome Project or the EU project ‘PRIME-XS’). It is a way to tag your dataset to enable grouping of datasets this way.
- There is already a PubMed ID associated with it (the data has been already published).
- Your dataset represents a reanalysis of an earlier public PX dataset.
- There are other “omics” datasets (for instance transcriptomics, metabolomics data present in other repositories) that can be associated with it. In this case, please provide the accession number of the dataset in the corresponding repository.
![Additional Information](/static/markdown/pridesubmissiontool/files/additionals.png)
### Check before submission
This is the last step before the file upload actually starts. You should double-check that all the necessary files are included in the submission summary before continuing to the upload step, see an example of an mzIdentML based ‘complete’ submission.
![Check Before Submission](/static/markdown/pridesubmissiontool/files/check-final.png)
## File Submission
This is the actual step when all your files are uploaded to PRIDE and ProteomeXchange. Once the upload is finished, an e-mail will
be sent to you to confirm that all your files have been uploaded successfully and that are waiting to be validated. If for any reason the tool crashes
at this point, the PX Submission Tool can be restarted and the file upload will restart in the same point before it crashed.
By default, the PX submission Tool (since version 2.1) is using the fast Aspera upload transfer protocol with which terabytes can be potentially
transferred within a day. Aspera functionality usually provides much faster file transfer speeds than FTP (typically up to 50 times). Should there be
any issues with the Aspera upload (probably due to the Internet/ data transfer local settings), submitters can always switch to the slower FTP
file transfer protocol by changing the ‘px.upload.protocol = aspera’ line to ‘px.upload.protocol = ftp’ in the plain config.props text file
located in the ‘config’ subdirectory in the PX Submission Tool’s working directory. You will be also issued with a temporary submission reference,
to help us to quickly identify and track your submission should you have any questions. This is not the PX accession number.
......@@ -32,7 +32,7 @@ Optionally other files can be included in your submission to facilitate the revi
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**: Minimun experimental metadata like experiment description, sample taxonomy information, instruments and modifications used.
**Metadata**: Minimum 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.
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