Introduction
This is the PRIDE Archive REST API service documentation. This provides information required to query about projects, files and stats in PRIDE.
If you want to explore by yourself our api, please visit this link PRIDE Archive API
Resources
Projects
Retrieve All Projects
GET request to obtain list of PRIDE Archive Projects. The following method do not allows to perform search,
for search functionality you will need to use the search/projects. The result list is Paginated using the pageSize and page.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-all-projects/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-all-projects/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-all-projects/response-body.adoc[]
Project With Accession ID
GET request to obtain a project associated with an accession in PRIDE database.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project/path-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project/response-body.adoc[]
Project Specific Files
GET request to obtain all files tagged to a particular project.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-files/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-files/path-parameters.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-files/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-files/response-body.adoc[]
Similar Projects
GET request to obtain projects similar to the provided project.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-similar-project/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-similar-project/path-parameters.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-similar-project/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-similar-project/response-body.adoc[]
Project Search Results
GET request to obtain list of PRIDE Archive Projects matching the search criteria. The result list is Paginated using the pageSize and page.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-search/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-search/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-search/response-body.adoc[]
Project Facet Results
GET Faceted results of information across projects in Pride Archive database.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-facet/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-facet/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-project-facet/response-body.adoc[]
Files
Retrieve File
GET request to obtain a file associated with a file accession in PRIDE database.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-file/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-file/path-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-file/response-body.adoc[]
Retrieve All Files
GET request to obtain all Files in PRIDE Archive.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-all-files/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-all-files/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-all-files/response-body.adoc[]
MSRun Metadata
Retrieve MSRun info by Project
GET request to obtain all the file information including MSRun data for the given project accession.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-msrun-by-project/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-msrun-by-project/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-msrun-by-project/response-body.adoc[]
Retrieve MSRun info by File
GET request to obtain all the file information including MSRun data for the given file accession.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-msrun-by-file/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-msrun-by-file/path-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-msrun-by-file/response-body.adoc[]
Update MSRun info of a File
PUT request to update the MSRun information of a given file.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-into-file/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-into-file/path-parameters.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-into-file/request-headers.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-into-file/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-into-file/response-body.adoc[]
Update Parts of MSRun info in a File
PUT request to update the parts of MSRun information of a given file.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-parts-into-file/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-parts-into-file/path-parameters.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-parts-into-file/request-headers.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-parts-into-file/request-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/put-msrun-parts-into-file/response-body.adoc[]
Stats
Retrieve Stats Names
GET request to obtain all the names of available statistic measures.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-stats-names/curl-request.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-stats-names/response-body.adoc[]
Retrieve Particular Statistic
GET request to obtain details of a particular statistic measure.
Example request
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-stat/curl-request.adoc[] Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-stat/path-parameters.adoc[]
Example response
Unresolved directive in api-guide.adoc - include::/app/target/generated-snippets/get-stat/response-body.adoc[]
Filtering Help
Some of the API endpoints support filtering to narrow the search results. There are two types of filters available - 'filter' and 'advanced filter'. The below examples help in understanding the different options supported by these filters and how they can be chained together to perform queries.
Filter
This type of filter supports conditions in the following format:
field==value
It also allows to chain the conditions to form queries as shown below:
field1==value,field2==value
If field is of date type value should be in format yyyy-MM-dd
Example 1
A simple query can be submited in this format.
countries==GermanyMultiple values can be sent and an OR condition applies on these words
countries==Germany ChinaExample 2
A date field can be queried by sending two parameters. A date in the format of yyyy-MM-dd and a value to the dateGap in following formats:
+1DAY,+1MONTH,+1YEAR
submission_date==2013-10-20Example 3
Multiple conditions can be chained together, delimited by comma
submission_date==2013-10-20,countries==Germany ChinaAdvance Filter
This type of filter supports different options like using a regular expression for matching, providing a date range and using in condition to supply multiple values.
Example 1
A simple query is of the form field==value
accession==PXF00000491725Example 2
The filter can be supplied with fields nested inside the json structure as well. The files API response has a fileCategory object and a value field within it.
This can be used as a query field to fetch values as shown below.
fileCategory.value==RESULTExample 3
A regex can be used for pattern matching and supplying complex queries. The below example filters for files which contain the word mzid in the name.
fileName=regex=mzidExample 4
A date range can be supplied while querying date fields in the below format.
publicationDate=range=[2006-01-01 TO 2015-12-31]Example 5
An in predicate can be used to supply multiple values to a field and it works like an OR condition.
accession=in=PXF00000491725|PXF00000000014Example 6
Multiple conditions can be supplied by seperating with comma.
fileCategory.value==RESULT,publicationDate=range=[2006-01-01 TO 2015-12-31]Appendix
HTTP verbs
RESTful notes tries to adhere as closely as possible to standard HTTP and REST conventions in its use of HTTP verbs.
| Verb | Usage |
|---|---|
|
Used to retrieve a resource |
|
Used to create a new resource |
|
Used to update an existing resource, including partial updates |
|
Used to delete an existing resource |
RESTful notes tries to adhere as closely as possible to standard HTTP and REST conventions in its use of HTTP status codes.
| Status code | Usage |
|---|---|
|
The request completed successfully |
|
A new resource has been created successfully. The resource’s URI is available from the response’s
|
|
An update to an existing resource has been applied successfully |
|
The request was malformed. The response body will include an error providing further information |
|
The requested resource did not exist |
Hypermedia
RESTful Notes uses hypermedia and resources include links to other resources in their
responses. Responses are in Hypertext Application
from resource to resource.
Language (HAL) format. Links can be found beneath the _links key. Users of the API should
not create URIs themselves, instead they should use the above-described links to navigate