Commit 29bef79f authored by Yasset Perez-Riverol's avatar Yasset Perez-Riverol
Browse files

new pages added

parent 9e57dcae
......@@ -82,14 +82,14 @@
{
"title":"How to review data",
"content":"How to review private and public experiments in PRIDE Archive",
"moreID":"xxx",
"markdownFolder":"xxxxx"
"moreID":"review_pride_data",
"markdownFolder":"reviewpridedata"
},
{
"title":"Searching public datasets",
"content":"Searching public datasets for reanalysis and reuse in PRIDE Archive",
"moreID":"searching_pride_data",
"markdownFolder":"searchingpridedata"
"markdownFolder":"searchpridearchive"
},
{
"title":"Retrieving PRIDE data programmatically",
......
## Reviewing PRIDE data
When a user submit the data to PRIDE Archive, the data is automacillaty **private** and a reviewer account is created for the user to share with the publication reviewers. Currently, PRIDE data can be reviewed in two different ways depending of the type of the dataset **Partial** or **Complete**.
## Finding and Download private data
The best way to download and review the PRIDE Archive data is using the [Pride Inspector Toolsuite](/markdownpage/prideinspector). Users and reviewers can use the provided account to log in to PRIDE:
![Reviewer login](/static/markdown/reviewpridedata/files/reviewer-login.png)
After login, a panel with the datasets that belowns to the user (private) or submitted by him, will be shown:
</br>
![Datasets Access](/static/markdown/reviewpridedata/files/private-datasets.png)
Finally, a panel with all the _files_ in the datasets are shown to be download:
![Dataset files](/static/markdown/reviewpridedata/files/private-files.png)
## Reviewing Partial Submissions
Private **PARTIAL** submissions only contains [RAW Files](/markdownpage/pridefileformats#search_files) and [SEARCH Files](/markdownpage/pridefileformats#search_files) which can bread only by propietary softwares such as Mascot, MaxQuant, etc. [Please Read](/markdownpage/pridefileformats)
## Reviewing Complete Submissions
For **COMPLETE** submissions the corresponding mzIdentML or mzTab, [RSULT Files](/markdownpage/pridefileformats#result_files)
## Dataset search in PRIDE Archive
## Basic term-based search
In order to perform a term-based search, a term or a set of terms have to be entered in the search box in the top-right part of the page. Each term will be treated as separate search term. That is, the search results will include projects that match any of the search terms.
The higher the number of terms matched, the more relevant the result of the search will be. If a set of terms should be considered as a single unit, double quotes must be used (for example: "label free" will only match projects where the whole experssion could be matched rather than matching projects with 'label' and/or 'free').
</br>
![Login panel](/static/markdown/searchpridearchive/files/search-terms.png)
The search accepts terms for dataset identifiers (PX datasets or PRIDE assay/experiment numbers), PubMed identifiers, sample details (e.g. organisms, organism part, diseases), instruments, post-translational modifications and any word/phrase included in the title or description of a dataset.
Dataset tags, for instance biomedical, cardiovascular, metaproteomics, are particular terms displayed in different colours on the particular released dataset page and in the search results. Their main aim is to help organise and connect datasets together thereby making targeted search more powerful. When searching for a tag name in the search box on the PRIDE Archive web page, the search engine will prioritise the tagged datasets and return them first. See our dedicated 'PRIDE dataset tags' page to learn how to interact with dataset tags in order to browse/search/interrogate PRIDE data.
## What happens
The search terms will be matched against the records in PRIDE Archive and a list of project summaries, if any records match, will be shown as a result. A project summary includes the following default information:
- Project accession (dataset identifier)
- Project Title
- Project description (shortened)
- Organism
- Project publication date
If the terms match a word that is not included in those properties, the user can see where they match by collapsing the _Matched Items_ option:
![Login panel](/static/markdown/searchpridearchive/files/matched-items.png)
## Highlighting
Highlighting provides search results feedback to the PRIDE Archive user. The pieces of information that matched the search will appear highlighted in the search results.
## Sorting criteria for search results
The default sorting is done by relevance. That is, by how relevant a project may be considering the search terms provided. At present, the relevance is affected by several fields, from more to less important:
- Project accession
- Title
- Relevance
- Submission Date
- Publication Date
Apart from the relevance, it is possible to sort search results by accession, title, and date. Clicking a sort criteria twice will invert the sort order.
## Browsing all PRIDE Archive projects
To browse all PRIDE Archive results is equivalent to performing a basic search with no search terms. It will return the whole list of public projects available in PRIDE Archive. The same filter and sorting mechanisms as for a basic search apply.
## Filtering
Through filtering we can ensure some information to be present in our search results. When a certain filter is active, all the search results shown will pass that filter. For example, if a filter is active specifying that the species has to be 'Homo Sapiens (Human)' all the resulting projects will carry this species annotation (although a project could have more than one species annotation). The available filters types are:
- Organism
- Organism Part
- Diseases
- Modification
- Instrument
- Experiment Type
When one of the filter types is selected, the second drop-down list will be populated with the available values for that filter type.
![Login panel](/static/markdown/searchpridearchive/files/filtering.png)
Multiple filters, of the same or differnt types, can be added. They are cumulative under an AND condition. That is, the search results must pass all the filters (and not just one of them). For example applying filters for 'Homo Sapiens (Human)' and 'Mus musculus (Mouse)' will only list results that have been annotated with both species. Filters can be removed in any order and the results are updated accordingly.
## Private data
**Only public data can be searched. Private data is only available for viewing onces logged in, but it is not available via the search.**
......@@ -16,7 +16,7 @@ The first step to prepare your submission for PRIDE Archive is to know which fil
- 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’) (**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.
- 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#search_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). 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.
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