Commit b6801099 authored by Yasset Perez-Riverol's avatar Yasset Perez-Riverol
Browse files

minor changes -- docs and about updated in Navs

parent c640fb70
......@@ -46,7 +46,7 @@
<Dropdown>
<a href="javascript:void(0)" @click="gotoLandingpage">
<i class="fas fa-home"></i>
<span class='sub-nav-title'>Home</span>
<span class='sub-nav-title'>Home</span>
</a>
</Dropdown>
</li>
......@@ -54,7 +54,7 @@
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<i class="fas fa-search"></i>
<span class='sub-nav-title'>Resources</span>
<span class='sub-nav-title'>Resources</span>
<Icon type="chevron-down"></Icon>
</a>
<DropdownMenu slot="list">
......@@ -68,11 +68,12 @@
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<i class="fas fa-cogs"></i>
<span class='sub-nav-title'>Tools</span>
<span class='sub-nav-title'>Tools</span>
<Icon type="chevron-down"></Icon>
</a>
<DropdownMenu slot="list">
<DropdownItem name="goToSpectraClustering">Spectra Clustering Toolsuite</DropdownItem>
<!--<DropdownItem name="goToSpectraClustering">Spectra Clustering Toolsuite</DropdownItem>-->
<DropdownItem name="goToPrideSubmission">PRIDE Submission Tool</DropdownItem>
<DropdownItem name="goToPrideInspector">PRIDE Inspector Toolsuite</DropdownItem>
<DropdownItem name="goToPrideUtilities">PRIDE Utilities Libraries</DropdownItem>
</DropdownMenu>
......@@ -80,34 +81,33 @@
</li>
<li class="sub-nav-list">
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<a href="javascript:void(0)" @click="gotoDocs">
<i class="fas fa-graduation-cap"></i>
<span class='sub-nav-title'>Docs</span>
<Icon type="chevron-down"></Icon>
<span class='sub-nav-title'>Docs</span>
</a>
<DropdownMenu slot="list">
<!--
<Dropdown placement="right-start">
<DropdownItem>
User Guide
<Icon type="ios-arrow-right"></Icon>
</DropdownItem>
<DropdownMenu slot="list">
<DropdownItem>PRIDE Archive</DropdownItem>
<DropdownItem>PRIDE Peptidome</DropdownItem>
</DropdownMenu>
</Dropdown>
-->
<DropdownItem name="goToPrideArchiveWS">PRIDE Archive WS</DropdownItem>
<DropdownItem name="goToPridePeptidomeWS">PRIDE Peptidome WS</DropdownItem>
</DropdownMenu>
<!--<DropdownMenu slot="list">-->
<!--&lt;!&ndash;-->
<!--<Dropdown placement="right-start">-->
<!--<DropdownItem>-->
<!--User Guide-->
<!--<Icon type="ios-arrow-right"></Icon>-->
<!--</DropdownItem>-->
<!--<DropdownMenu slot="list">-->
<!--<DropdownItem>PRIDE Archive</DropdownItem>-->
<!--<DropdownItem>PRIDE Peptidome</DropdownItem>-->
<!--</DropdownMenu>-->
<!--</Dropdown>-->
<!--&ndash;&gt;-->
<!--<DropdownItem name="goToPrideArchiveWS">PRIDE Archive WS</DropdownItem>-->
<!--<DropdownItem name="goToPridePeptidomeWS">PRIDE Peptidome WS</DropdownItem>-->
<!--</DropdownMenu>-->
</Dropdown>
</li>
<li class="sub-nav-list">
<Dropdown>
<a href="javascript:void(0)" @click="gotoAbout">
<i class="fas fa-info-circle"></i>
<span class='sub-nav-title'>About</span>
<span class='sub-nav-title'>About</span>
</a>
</Dropdown>
</li>
......@@ -140,7 +140,7 @@
this.successSearch();
},function(err){
this.failSearch();
});
});
},
successSearch(){
this.$Message.success({content:'success search', duration:3});
......@@ -164,6 +164,9 @@
else if(name=='goToSpectraClustering'){
this.$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'});
}
......@@ -178,10 +181,13 @@
}
},
gotoAbout(){
this.$router.push({path:'/markdownpage/about'});
this.$router.push({path:'/markdownpage/citationpage'});
},
gotoDocs(){
this.$router.push({path:'/markdownpage/documentationpage'});
}
},
}
</script>
<style scoped>
......@@ -241,7 +247,7 @@
}
.row{
margin:0 auto;
max-width: 150rem !important;
}
#local-nav{
......
......@@ -81,27 +81,26 @@
</li>
<li class="sub-nav-list">
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<a href="javascript:void(0)" @click="gotoDocs">
<i class="fas fa-graduation-cap"></i>
<span class='sub-nav-title'>Docs</span>
<Icon type="chevron-down"></Icon>
</a>
<DropdownMenu slot="list">
<!--
<Dropdown placement="right-start">
<DropdownItem>
User Guide
<Icon type="ios-arrow-right"></Icon>
</DropdownItem>
<DropdownMenu slot="list">
<DropdownItem>PRIDE Archive</DropdownItem>
<DropdownItem>PRIDE Peptidome</DropdownItem>
</DropdownMenu>
</Dropdown>
-->
<DropdownItem name="goToPrideArchiveWS">PRIDE Archive WS</DropdownItem>
<DropdownItem name="goToPridePeptidomeWS">PRIDE Peptidome WS</DropdownItem>
</DropdownMenu>
<!--<DropdownMenu slot="list">-->
<!--&lt;!&ndash;-->
<!--<Dropdown placement="right-start">-->
<!--<DropdownItem>-->
<!--User Guide-->
<!--<Icon type="ios-arrow-right"></Icon>-->
<!--</DropdownItem>-->
<!--<DropdownMenu slot="list">-->
<!--<DropdownItem>PRIDE Archive</DropdownItem>-->
<!--<DropdownItem>PRIDE Peptidome</DropdownItem>-->
<!--</DropdownMenu>-->
<!--</Dropdown>-->
<!--&ndash;&gt;-->
<!--<DropdownItem name="goToPrideArchiveWS">PRIDE Archive WS</DropdownItem>-->
<!--<DropdownItem name="goToPridePeptidomeWS">PRIDE Peptidome WS</DropdownItem>-->
<!--</DropdownMenu>-->
</Dropdown>
</li>
<li class="sub-nav-list">
......@@ -183,7 +182,10 @@
}
},
gotoAbout(){
this.$router.push({path:'/markdownpage/citationpage'});
this.$router.push({path:'/markdownpage/citationpage'});
},
gotoDocs(){
this.$router.push({path:'/markdownpage/documentationpage'});
}
},
......
......@@ -46,7 +46,7 @@
<Dropdown>
<a href="javascript:void(0)" @click="gotoLandingpage">
<i class="fas fa-home"></i>
<span class='sub-nav-title'>Home</span>
<span class='sub-nav-title'>Home</span>
</a>
</Dropdown>
</li>
......@@ -54,7 +54,7 @@
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<i class="fas fa-search"></i>
<span class='sub-nav-title'>Resources</span>
<span class='sub-nav-title'>Resources</span>
<Icon type="chevron-down"></Icon>
</a>
<DropdownMenu slot="list">
......@@ -68,11 +68,12 @@
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<i class="fas fa-cogs"></i>
<span class='sub-nav-title'>Tools</span>
<span class='sub-nav-title'>Tools</span>
<Icon type="chevron-down"></Icon>
</a>
<DropdownMenu slot="list">
<DropdownItem name="goToSpectraClustering">Spectra Clustering Toolsuite</DropdownItem>
<!--<DropdownItem name="goToSpectraClustering">Spectra Clustering Toolsuite</DropdownItem>-->
<DropdownItem name="goToPrideSubmission">PRIDE Submission Tool</DropdownItem>
<DropdownItem name="goToPrideInspector">PRIDE Inspector Toolsuite</DropdownItem>
<DropdownItem name="goToPrideUtilities">PRIDE Utilities Libraries</DropdownItem>
</DropdownMenu>
......@@ -80,34 +81,33 @@
</li>
<li class="sub-nav-list">
<Dropdown @on-click="resourcesClick">
<a href="javascript:void(0)">
<a href="javascript:void(0)" @click="gotoDocs">
<i class="fas fa-graduation-cap"></i>
<span class='sub-nav-title'>Docs</span>
<Icon type="chevron-down"></Icon>
<span class='sub-nav-title'>Docs</span>
</a>
<DropdownMenu slot="list">
<!--
<Dropdown placement="right-start">
<DropdownItem>
User Guide
<Icon type="ios-arrow-right"></Icon>
</DropdownItem>
<DropdownMenu slot="list">
<DropdownItem>PRIDE Archive</DropdownItem>
<DropdownItem>PRIDE Peptidome</DropdownItem>
</DropdownMenu>
</Dropdown>
-->
<DropdownItem name="goToPrideArchiveWS">PRIDE Archive WS</DropdownItem>
<DropdownItem name="goToPridePeptidomeWS">PRIDE Peptidome WS</DropdownItem>
</DropdownMenu>
<!--<DropdownMenu slot="list">-->
<!--&lt;!&ndash;-->
<!--<Dropdown placement="right-start">-->
<!--<DropdownItem>-->
<!--User Guide-->
<!--<Icon type="ios-arrow-right"></Icon>-->
<!--</DropdownItem>-->
<!--<DropdownMenu slot="list">-->
<!--<DropdownItem>PRIDE Archive</DropdownItem>-->
<!--<DropdownItem>PRIDE Peptidome</DropdownItem>-->
<!--</DropdownMenu>-->
<!--</Dropdown>-->
<!--&ndash;&gt;-->
<!--<DropdownItem name="goToPrideArchiveWS">PRIDE Archive WS</DropdownItem>-->
<!--<DropdownItem name="goToPridePeptidomeWS">PRIDE Peptidome WS</DropdownItem>-->
<!--</DropdownMenu>-->
</Dropdown>
</li>
<li class="sub-nav-list">
<Dropdown>
<a href="javascript:void(0)" @click="gotoAbout">
<i class="fas fa-info-circle"></i>
<span class='sub-nav-title'>About</span>
<span class='sub-nav-title'>About</span>
</a>
</Dropdown>
</li>
......@@ -141,7 +141,7 @@
this.successSearch();
},function(err){
this.failSearch();
});
});
},
successSearch(){
this.$Message.success({content:'success search', duration:3});
......@@ -165,6 +165,9 @@
else if(name=='goToSpectraClustering'){
this.$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'});
}
......@@ -179,10 +182,13 @@
}
},
gotoAbout(){
this.$router.push({path:'/markdownpage/about'});
this.$router.push({path:'/markdownpage/citationpage'});
},
gotoDocs(){
this.$router.push({path:'/markdownpage/documentationpage'});
}
},
}
</script>
<style scoped>
......@@ -242,7 +248,7 @@
}
.row{
margin:0 auto;
max-width: 150rem !important;
}
#local-nav{
......
## PRIDE Resources Documentation
## Docs one
## General Help Pages
## Docs two
- [How to submit data to PRIDE Archive](./submitdatapage)
## Docs three
- [PRIDE Archive supported file formats](./pridefileformats)
## Submitting your data to PRIDE:
- [How to review proteomics data in PRIDE Archive](./reviewpridedata)
- [Search PRIDE datasets in PRIDE Archive](./searchpridearchive)
PRIDE welcomes direct user submissions of protein and peptide identification/quantification data with the accompanying mass spectral evidence to be published in peer-reviewed publications. The main focus of PRIDE is to support the deposition of shotgun MS/MS proteomics datasets.
## Tools Help Pages
The current way of submitting data to PRIDE is following the [ProteomeXchange (PX) consortium](http://www.proteomexchange.org/) guidelines. The current page contains summarized introduction to the 2 main PX Submission modes. If you need more information a detailed tutorial is [available](http://www.proteomexchange.org/sites/proteomexchange.org/files/documents/px_submission_tutorial2.pdf) at the ProteomeXchange web site. Alternatively please contact pride-support@ebi.ac.uk for assistance or advice.
- [PRIDE Inspector Toolsuite](./prideinspector)
The main tool to submit data is the PX Submission Tool than can be downloaded by clicking on the button below.
- [Submission Tool](./pridesubmissiontool)
- [PRIDE Archive API](http://pride-archive.github.io/PrideAPIDocs)
![Minion](../../static/markdown/submitDataPage/image/download.png)
The PX/ PRIDE submission process involves the following elements seen on the figure below.
![Minion](../../static/markdown/submitDataPage/image/Slide1.jpg)
Follow these steps to submit your data:
1. Lorem ipsum dolor sit amet
2. Consectetur adipiscing elit
3. Integer molestie lorem at massa
1. Register
If you do not already have a PRIDE account, create one here. Currently we don't send out automatic emails upon succesful registration. Please contact pride-support@ebi.ac.uk if your login information is not valid after 24 hours following registration.
2. Choose submission type
You can choose between 2 main submission types depending on the availability of mzIdentML or PRIDE XML files as "Result" files for Complete Submissions. The recommended submission subtype is a Complete Submission, but alternatively Partial Submissions are accepted as well.
## 2A. Complete Submission: mzIdentML- or PRIDE XML-based
The 2 subtypes of Complete Submissions are either mzIdentML- or PRIDE XML-based. Complete Submissions mixing the 2 types of ‘RESULT’ files are not allowed.
- Marker character change forces new list start:
- Result files: mzIdentML 1.1 files with identifications provided. In the submission tool they should be tagged as “RESULT”. It is also recommended to check your mzIdentML files before submission using the PRIDE Inspector tool (the mzIdentML supporting version will be out in early January, 2014). mzIdentML version 1.0 files are not supported.
- Peak list files: Since the mzIdentML files themselves do not contain the spectra information it is mandatory to provide the peak list files (eg. mgf files) that were used for the original search and are referenced in the mzIdentML file. These are different from the provided mandatory raw files. In the submission tool they should be tagged as “PEAK” and the submission tool will try to automatically map the peak files to the mzIdentML file where they are listed.
- Raw files: the MS instrument output files, for instance Thermo RAW files. As an alternative, lightly processed mzML, mzXML, mzData files are acceptable if MS1 level spectra information is available and the different peak processing steps are known. In the submission tool they should be tagged as “RAW”.
## PRIDE Submission Tool
##PRIDE Tools
## PRIDE Submission Tool
The [PRIDE Submission Tool](./pridesubmissiontool) 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 trough a set of simple steps to build the final submission.
## PRIDE Inspector Toolsuite
The [PRIDE Inspector Toolsuite](./prideinspector) is the main tool used to review and download the proteomics data from [PRIDE Archive](wwww.ebi.ac.uk/pride/archive/). The Java Desktop tool provides different panels or view focuses on a particular aspect of the data. There are currently six views:
- _Overview_ view – shows experimental metadata.
- _Protein_ view – shows protein identifications
- _Peptide_ view – shows peptides used to generate the protein identifications
- _Spectrum_ view – shows spectra and chromatograms
- _Quantification_ view – show quantitative data for both proteins and peptides
- _Summary charts_ view – provides data chars for assessing data quality
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.
## PRIDE Utilities
[Libraries and Algorithms](./prideutilities) supporting the PRIDE Database.
## PRIDE Archive API
The [PRIDE Archive API](www.ebi.ac.uk/pride/ws/archive) (Restful WS Service) provides a way to retrirve the data from PRIDE Archive programatically. The documentation pape for the tool can be [found here](http://pride-archive.github.io/PrideAPIDocs).
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