CLUE API

The CLUE API offers programmatic access to annotations and perturbational signatures in the CMap L1000 dataset via a collection of HTTP-based RESTful web services. These services support complex queries via simple HTTP GET requests that can be executed in a web browser or any programming language. If you are using a web browser to display results, it is best to add your favorite JSON viewer add-on or plugin. The results are returned as standard JSON objects. Click on the links on the side for usage instructions and examples. API requests is based on the loopback framework syntax.

API Access

Registration is required to obtain a user-specific API key. If you already have a clue account and you are signed in, click on your name in the upper right corner, then click on "Account Settings" to find your API Key. The examples below use a limited demonstration key.

Instructions and examples

Cell service

The cell service returns cell line information.

Examples

Gene service

The gene service returns meta-information for measured and inferred genes in the CMap L1000 dataset.

Examples

Perts service

The pert service returns meta-information for perturbagens in the CMap L1000 dataset.

Examples

Pertubational Classes

ThePCL service returns meta-information for perturbational classes in the CLUE dataset.

Examples

Plate service

The plate service returns plate information.

Examples

Probeset conversion

Theprobeset_to_entrez_id service is used to convert affy ids to gene entrez ids.

Examples

This is an HTTP POST request, using the endpoint https://api.clue.io/api/probeset_to_entrez_id/convert. The data this method takes in is a list of affy ids in the form of an array of strings, and it will return a string representing associated gene entrez id.

Input:

["1007_s_at","121_at","1255_g_at","1438_at","1487_at"]

Output:

{"1007_s_at": "780","121_at": "7849","1255_g_at": "2978","1438_at": "2049","1487_at": "2101"}

The CURL of this example is as follows:

curl -X POST --header "Content-Type: application/json" --header "Accept: application/json" --header "user_key: XXX" -d "[\"1007_s_at\",\"121_at\",\"1255_g_at\",\"1438_at\",\"1487_at\"]" "https://api.clue.io/api/probeset_to_entrez_id/convert"

Profile service

Theprofile service returns meta-information for profiles in Clue. This includes data for the CMap L1000 datasets as well as the proteomic GCP and P100 datasets.

Examples

Query service

Using various API endpoints, users can submit queries and poll for their status. A full article describing how this is done can be found in the Query API tutorial in Connectopedia.

Repurposing Hub database

Therep_fda_exclusivity service returns information about the exclusivity period of a given drug. This information was obtained from the FDA Orange Book publication.

Examples

Therep_drug_moa service returns information about the mechanism of action of a drug.

Examples

Therep_fda_orange-book_term service returns information describing abbreviations used in the Orange Book.

Examples

Therep_fda_patent service returns information about the patent of a given drug extracted from the Orange Book.

Examples

Therep_sample service returns information about the purity, chemical structure, source, and various textual identifiers of the compound.

Examples

Therep_drug service returns information about drug synonyms, clinical status, corresponding FDA Orange Book ingredient(s), and external database identifiers.

Examples

Therep_drug_indication service returns information about the indications and disease areas for approved drugs.

Examples

Therep_fda_product service returns information about a product extracted from the FDA Orange Book publication.

Examples

Therep_drug_target service returns information about the gene target of a compound.

Examples

Signatures

Thesig service returns meta-information for signatures in the CMap L1000 dataset.

Examples

API Playground

The CLUE API playground allows end consumers to visualize and interact with the API's resources/services.

The CLUE API playground allows end consumers to visualize and interact with the API's resources/services.

After you have clicked on the link above, you will reach the CLUE API Explorer page. From here, you want to add your personal API Key. You can do so by clicking on the "Edit API Key" button.

You will notice that there is already an API key there. You want to replace that with your own. To find your personal API Key, head over to clue.io and log in to your account. Click on your username and copy and paste the string under the heading "API Key" and paste it in the CLUE API Explorer.

Now, you can interact with the API’s services. For instance, you can click on a field, such as "pert" and a drop down menu will display all of its API endpoints.

To view more, you can click on "GET/perts" for an expansion of additional operations.

This expansion allows you to search in the parameters. Let’s say that you want to query the compound sirolimus. You can do so by typing in this syntax:

{"where":{"pert_iname":"sirolimus"}}

Click "Try it out!" to submit this query request.

You will then get a Response Body that shows the information available for your query.