Lilly Clinical Open Innovation REST API Reference 62

This is a reference guide for the Lilly Clinical Open Innovation API (LCOI-API). It is divided into these sections: Getting Started Trial Resource API Requests Topic Catalog API Requests Appendix

Getting Started

Resource Overview

  • All resources are accessed using HTTP
  • Our server is located at http://api.lillycoi.com
  • This document is for Version 1 of the api, which is read-only: http://api.lillycoi.com/v1/
  • All responses are formatted as JSON
  • Some resources support JSON that is specially formatted for use by the MIT Exhibit application. ClinicalCollections.org is an example Django and JS app that consumes the exhibit format.
  • Status codes that any resource may return are listed here: Common Status Codes. Codes that are specific to a resource are listed in the documentation for that resource.
  • When making requests to the API server, values that you supply are shown in italics.

Clinical Trial Resources

  • The information returned by this resource is sourced from NIH clinicaltrials.gov registry. The data is refreshed daily.
  • The responses are augmented with additional data such as geo-spacial location data, and ranges for dates and ages.
  • Trials resources can be requested via search, list, or by trial id.
  • Each resource has a description, URL, HTTP methods, parameters, formats, authentication, limits, examples, and specific status codes.
  • See appendix for details on augmented data added to responses by Lilly COI.

/trials



Description

  • This endpoint will return all trials.

Resource URL

http://api.lillycoi.com/v1/trials.{format}

HTTP Methods

  • GET

Parameters

limit: (optional, number, default: 10 )

  • limits the number of results returned
  • example: limit=20

offset: (optional, number, default: 0 )

  • determines where to begin getting data
  • example: offset=23

fields: (optional, string of comma separated fields names, defaults to all fields)

  • the response will be constrained to only the fields listed in this parameter. NOTE: only top-level fields will be targeted.
  • see the appendix for a list of fields that can be supplied in this parameter
  • example for .json request: fields=id,location

Formats

  • .json
  • .exhibit

Authentication Required: No

Rate Limit: No Limit

Example Usage


/trials/{id}



Description

  • This endpoint will return a single trial
  • {id} is an NCT identifier from clinicaltrials.gov

Resource URL

http://api.lillycoi.com/v1/trials/{id}.{format}

HTTP Methods

  • GET

Parameters

fields: (optional, string of comma separated fields names, defaults to all fields)

  • the response will be constrained to only the fields listed in this parameter. NOTE: only top-level fields will be targeted.
  • example for .json request: fields=id,location

Formats

  • .json
  • .exhibit

Authentication Required: No

Rate Limit: No Limit

Example Usage


/trials/search



Description

  • This endpoint performs a search against trial data. If the provider parameter is passed (i.e.: provider=ctgov), the search is performed on that provider’s servers and returns IDs to get from our database.
  • See appendix for details on the clinicaltrials.gov search engine.

Resource URL

http://api.lillycoi.com/v1/trials/search.{format}

HTTP Methods

  • GET

Parameters

query: (required, a string query )

  • the query to execute on a search provider
  • the query syntax is provided in the provider’s query language (See appendix for details on the clinicaltrials.gov search engine.)
  • for clinicaltrials.gov, by default only the first 20 results are returned; to get more, include ‘count’ in the query, which represents the maximum number of trials to return from the query
  • example: query=cond:spondylitis,recr:open,count:500

provider: (optional, one of: ‘ctgov’, default: ctgov )

  • determines which search provider to use
  • for this version of the API the clinicaltrials.gov search engine is the only one available
  • example: provider=ctgov

fields: (optional, string of comma separated fields names, defaults to all fields)

  • the response will be constrained to only the fields listed in this parameter. NOTE: only top-level fields will be targeted.
  • example for .json request: fields=id,location

limit: (optionalnumberdefault: 20 )

  • limits the number of results returned
  • example: limit=30

offset: (optionalnumberdefault: 0 )

  • determines where to begin getting data
  • example: offset=12

Formats

  • .json
  • .exhibit

Authentication Required: No

Rate Limit: No Limit

Example Usage


Topic Resources


/studytopics/categories



Description

  • This endpoint will return the root categories

Resource URL

http://api.lillycoi.com/v1/studytopics/categories.{format}

HTTP Methods

  • GET

Parameters

  • none

Formats

  • .json

Authentication Required: No Rate Limit: No Limit Example Usage


/studytopics/categories/{parent_id}



Description

  • This endpoint will return the sub categories of the passed parent category

Resource URL

http://api.lillycoi.com/v1/studytopics/categories/{parent_id}.{format}

HTTP Methods

  • GET

Parameters

  • none

Formats

  • .json

Authentication Required: No Rate Limit: No Limit Example Usage


Appendix

Common Status Codes

Status Code Description
200 Request succeeded with no error
404 url is not found
500 Request failed with an error

Augmented Data

  • We copy data from clinicaltrials.gov into the LCOI repository. We do not modify the values in this data for the .json responses.
  • Some data in the .exhibit responses are formatted with html to support layout.
  • We augment clinicaltrials.gov data with the following geographic data:
Lilly COI Data Format Derived from Type Description
.location.geodata.latitude .json ct.gov facility address float Latitude (city level)
.location.geodata.longitude .json ct.gov facility address float Longitude (city level)
.location.geodata.original .json N/A string Data sent to the geo-encoding service
.location.geodata.formatted .json N/A string formatted version of the “original” field
location_latlong .exhibit ct.gov facility address array of strings latitude/longitude coordinate (city level)

When we inject CT.gov data into the LCOI repository, the following fields are added or enhanced by LCOI in support of Exhibit facets and views:

.exhibit field comments
primary_outcomes formatted w/ HTML by LCOI
pubmed_links formatted w/ HTML by LCOI
results_links formatted w/ HTML by LCOI
secondary_outcomes formatted w/ HTML by LCOI
study_design CT.gov string converted by LCOI to json array
completion_date_iso8601 added by LCOI when injected to LCOI repository
completion_date_range added by LCOI when injected to LCOI repository
ctgov_results_link added by LCOI when injected to LCOI repository
duration_months added by LCOI when injected to LCOI repository
eligibility_maximum_age_range added by LCOI when injected to LCOI repository
eligibility_minimum_age_range added by LCOI when injected to LCOI repository
enrollment_range added by LCOI when injected to LCOI repository
has_results added by LCOI when injected to LCOI repository
last_changed_iso8601 added by LCOI when injected to LCOI repository
last_injected added by LCOI when injected to LCOI repository
location_latlong added by LCOI when injected to LCOI repository
primary_completion_date_iso8601 added by LCOI when injected to LCOI repository
primary_completion_date_range added by LCOI when injected to LCOI repository
start_date_iso8601 added by LCOI when injected to LCOI repository
start_date_range added by LCOI when injected to LCOI repository
type_name added by LCOI when injected to LCOI repository
start_date_range added by LCOI at http request time
completion_date_range added by LCOI at http request time
primary_completion_date_range added by LCOI at http request time

clinicaltrials.gov Search Engine

Top Level Fields

  • NIH has a page with definitions for data that we have sourced from their clinicaltrials.gov registry.
  • The data returned in trial responses can be constrained to specific top-level fields in .json and .exhibit Trial responses.
  • The LCOI .json format mimics the CT.gov XML schema

Here are the top-level fields for the .json format responses:

.json Top-level Fields Type Source
acronym string CT.gov
arm_group array CT.gov
attributes array CT.gov
biospec_descr object CT.gov
biospec_retention string CT.gov
brief_summary object CT.gov
brief_title string CT.gov
clinical_results object CT.gov
completion_date string CT.gov
condition array CT.gov
condition_browse object CT.gov
detailed_description object CT.gov
eligibility object CT.gov
end_date string CT.gov
enrollment object CT.gov
firstreceived_date object CT.gov
firstreceived_results_date string CT.gov
has_expanded_access string CT.gov
id string CT.gov
id_info object CT.gov
intervention array CT.gov
intervention_browse object CT.gov
is_fda_regulated string CT.gov
is_section_801 string CT.gov
keyword array CT.gov
last_injected string LCOI
lastchanged_date object CT.gov
link array CT.gov
location array CT.gov
location_countries object CT.gov
number_of_arms string CT.gov
number_of_groups string CT.gov
official_title string CT.gov
overall_contact object CT.gov
overall_contact_backup object CT.gov
overall_official array CT.gov
overall_status string CT.gov
oversight_info object CT.gov
phase string CT.gov
primary_completion_date object CT.gov
primary_outcome array CT.gov
reference array CT.gov
removed_countries object CT.gov
required_header object CT.gov
responsible_party object CT.gov
results_reference array CT.gov
secondary_outcome array CT.gov
source string CT.gov
sponsors object CT.gov
start_date object CT.gov
study_design string CT.gov
study_type string CT.gov
verification_date object CT.gov
why_stopped string CT.gov

Here are the top-level fields for the .exhibit format responses:

.exhibit Top-level Fields Type Source
acronym string CT.gov
alt_link string CT.gov
arm_groups array CT.gov
biospec_description string CT.gov
biospec_retention string CT.gov
brief_summary string CT.gov
cities array CT.gov
collaborators array CT.gov
completion_date string CT.gov
completion_date_iso8601 string LCOI
completion_date_range string LCOI
completion_date_type string CT.gov
condition_mesh_terms array CT.gov
conditions array CT.gov
countries array CT.gov
ctgov_results_link string LCOI
detailed_description string CT.gov
duration_months num LCOI
eligibility_criteria string CT.gov
eligibility_gender string CT.gov
eligibility_healthy_volunteers string CT.gov
eligibility_maximum_age_range string LCOI
eligibility_maximum_age_years num CT.gov
eligibility_minimum_age_range string LCOI
eligibility_minimum_age_years num CT.gov
eligibility_sampling_method string CT.gov
eligibility_study_population string CT.gov
enrollment num CT.gov
enrollment_range string LCOI
enrollment_type string CT.gov
funded_by string CT.gov
has_expanded_access string CT.gov
has_results string CT.gov
has_results string LCOI
health_authorities array CT.gov
id string CT.gov
intervention_mesh_terms array CT.gov
intervention_types array CT.gov
interventions array CT.gov
is_fda_regulated string CT.gov
is_section_801 string CT.gov
keywords array CT.gov
label string CT.gov
last_changed string CT.gov
last_changed_iso8601 string LCOI
last_injected string LCOI
lead_sponsor string CT.gov
lead_sponsor string CT.gov
location_latlong array LCOI
locations array CT.gov
nct_id string CT.gov
number_of_arms num CT.gov
official_title string CT.gov
org_study_id string CT.gov
overall_contact_backup_email string CT.gov
overall_contact_backup_last_name string CT.gov
overall_contact_backup_phone string CT.gov
overall_contact_backup_phone_extension string CT.gov
overall_contact_email string CT.gov
overall_contact_last_name string CT.gov
overall_contact_phone string CT.gov
overall_contact_phone_extension string CT.gov
overall_officials array CT.gov
overall_status string CT.gov
primary_completion_date string CT.gov
primary_completion_date_iso8601 string LCOI
primary_completion_date_range string LCOI
primary_completion_date_type string CT.gov
primary_measures array CT.gov
primary_outcomes array CT.gov formatted w/ LCOI HTML
pubmed_links array CT.gov formatted w/ LCOI HTML
responsible_party_name_title string CT.gov
responsible_party_organization string CT.gov
results_links array CT.gov formatted w/ LCOI HTML
secondary_id array CT.gov
secondary_measures array CT.gov
secondary_outcomes array CT.gov formatted w/ LCOI HTML
start_date string CT.gov
start_date_iso8601 string LCOI
start_date_range string LCOI
states array CT.gov
study_design array CT.gov string converted by LCOI to array
study_phase string CT.gov
study_type string CT.gov
type_name string LCOI
url string CT.gov
why_stopped string CT.gov

62 comments

  1. Pingback: LCOI-API Series: Introducing the Lilly Clinical Open Innovation API « lillycoi

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  4. Hello, My name is GOPINATH and I work for Merck & CO. I am trying out the API’s, it works great, however I always get null for clinical_results. I know this trial has data in clinicaltrial.gov and I am not sure whether I am using the API wrong or the clinical_results does not work. Please let me know either way how can I access clinical_results using this API. I checked with few other trials as well for which I know clinicalrials.gov has results.
    Regards
    GOPI

    http://api.lillycoi.com/v1/trials/search.json?query=id:NCT00092677,count:20&fields=id,clinical_results

    • Gopi, thank you for your interest in our API. The clinical_results element in the clinicaltrials.gov XML schema is very new (see http://clinicaltrials.gov/ct2/html/images/info/public.xsd). At this time it appears that while the clinical_results element is present in the schema, the data is not being provided in the XML view of the trial (which is how we get the data). I have reached out to my contact at clinicaltrials.gov to see if we can get an update on this and will relay any pertinent info I get.

      Regards,
      Dave

  5. Hello David, Thanks for your response. I am using ClinicalTrials.gov and I can consistently see the data in clinical_results for the trials which says “has results” in the XML. We have developed an application using Clinical Trials.gov data directly, and so far I have not encountered any situation where the trial says “has results” and there is no data in clinial_results.

    We wanted to switch over and start using lilly api due to the the additional attributes to add to the dataset. I am trying a small POC to see what it would take to switch over and thatz how I noticed it.

    I am attaching 3 example trials, they all have clinical results in the xml.

    http://clinicaltrials.gov/show/NCT00462748?resultsxml=true

    http://clinicaltrials.gov/show/NCT00654628?resultsxml=true

    http://clinicaltrials.gov/show/NCT00783263?resultsxml=true

    Regards
    GOPI

    • Yes, you are right. I have checked and we are currently pulling data from clinicaltrials.gov without the results. We will look into seeing what it will take to include the results data. Thank you for bringing this to our attention.

      Regards,
      Dave

    • Gopi, we have just pushed an update to our API that now includes the clinical results data. Can you please take a look and see if it is working as you expect? Thank you.

    • Hi GOPI – any chance you might be working with or know of Greg T. at Merck? Just curious. He and I chatted a bit at the DPharm conference in Boston and I was curious whether your effort might be connected to Greg in any way. If so, please pass along greetings. Thanks for taking an interest in the API and please do feel free to let us know of ways it might be improved.

      • Hello Jerry, Yes I know him well. Gregg is aware of this work and he is helping me to stand in a framework for this development
        Regards
        GOPI

  6. Thanks much GOPI – please do pass on my best wishes. I’d welcome a reconnection with Gregg at some point, as he was just getting started when we chatted. And, if there’s anything we might collaborate on we’re certainly open to that.

    • Hello Jerry and Dave, Using your API I have developed an IPAD app and I wanted to share and collect your feedback, I also wanted to discuss further on Clinical Collections, Can you please send your official email through which I can contact you ?
      REgards
      GOPI

      • HI GOPI! We’re very excited to learn more about the IPAD app and to have the discussion on Clinical Collections. If you could send a quick e-mail to coi@Lilly.com I’ll send along a response from my official Lilly e-mail that we can use to coordinate the discussions. Thanks for sharing!

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  9. Ah yes, you are right. So WE had the malformed URL. I have updated the document accordingly, and also used a real example trial that better shows how the filtering works. Thanks for bringing this to our attention!

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  13. Do you have any plans to support searches which would compare to CT.gov’s RSS feed? Currently, I can create an RSS feed out of an arbitrary search scoped to condition “Show studies that were added or modified in the last 14 days”.

    This is useful for keeping my local data in sync with CT; ideally, I just want to poll for all studies which were changed in the n hours since the last sync.

    Thanks for the great work!

  14. Thanks for your interest in our API. At this time we do not have any plans to support searches against the clinicaltrials.gov RSS feed. We have found that there are some changes made to trials that are not reflected in the RSS feed (although few), so we are doing a full compare on a daily basis (note the clinicaltrials.gov site updates its data once a day). But your question is helpful to know there is interest in such information. Our team will discuss this for future possibilities.

    You may also be interested in our Follow Clinical application that allows you to subscribe to changes to a particular search against clinicaltrials.gov. It is not designed to subscribe to all trial changes, but for particular conditions or interventions. You can also subscribe to your “follows” via RSS.

    Thanks again!

  15. Hello, My name is Kate Lau and I am working for my challenge on the Patient Engagement Project.

    I am trying out the API’s (get a list of clinical trials, get clinical detail by ID), it works great. However, I am trying to query an impact explanation of a specific clinical trial and a detail description of the treatment, However I can not find out any relevant information on the clinical detail.

    I am not sure whether I am using the API wrong or the impact and detail description of the treatment does not store on clinical.gov. Please let me know either way how can I access to any information relevant to impact and detail description of the treatment/ trial by using this API.

    Regards
    Kate.

    • Hi Kate. It is quite possible that the impact and detail description of the treatment is not available in Clinicaltrials.gov. A suggestion would be to query using the same NCTID (the unique ClinicalTrials.gov identifier) for the trial you are interested in directly from Clinicaltrials.gov web-site, and then compare the results with what is returned from the API. If you find the data you need from the ClinicalTrials.gov directly but can’t find it in the API then we know there’s an issue with the API. Please give this a try, and let us know what you find. It there is an API issue I’ll pass the issue on to our technical team when they return in the New Year.

  16. Hi Jerry,

    Thank for your suggestion. I have made a search clinical trial detail by Lilly API and ClinicalTrial.gov. The search results is really different . The Detail Description, Eligibility, Location are available on ClinicalTrial.gov, but not available on the Lilly API’s result.
    Please refer to http://api.lillycoi.com/v1/trials/NCT00843700.json
    and http://clinicaltrials.gov/ct2/show/NCT00843700?term=Effectiveness+of+IPT+Adapted+for+Depressed+Women+With+Trauma+Histories+in+a+Community+Mental+Health+Center&rank=1
    Thank for any advice. and Happy New Year !

  17. Hi Jerry,

    Thank you so much , now I got the same data in Detail Description, Eligibility, Location. Your suggested links are really helpful. Again, thank you very much.

  18. Hello,
    One quick question, do you support the API to update/retrieve schedule with health provider/ researcher? Thank in advance

  19. Hello Kate. No, our API does not manage schedules for the investigator sites. At this time we only reflect the information that was provided to clinicaltrials.gov. For investigator sites this includes facility and contact information.

  20. Hi Roger. The terms used for filtering by country and state are a little tricky. We are using the same terms that clinicaltrials.gov uses in their advanced search — http://clinicaltrials.gov/ct2/search/advanced, but applying them to the format of our API.

    For example, to limit your example to studies in Germany, it would be http://api.lillycoi.com/v1/trials/search.json?query=cond:fabry,recr:open,cntry1=EU%3ADE. If you wanted to filter by a US state, say California, it would be http://api.lillycoi.com/v1/trials/search.json?query=cond:fabry,recr:open,state1=NA%3AUS%3ACA. You can get the values for the various countries and states by viewing the source of the clinicaltrials.gov advanced search page. Look for the select elements with ID “Country1″, “State1″, “Country2″, “State2″, etc. and see the values of the options elements within each.

    Note the %3A is a URL encoded colon, which is necessary because a colon is a reserved character in our API.

    I hope this helps. Let us know if you need any additional assistance. Thanks for using our API!

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  23. Hi,

    Thanks for all of your work.

    Under the .exhibit query, in the “primary_outcomes” field, there is a key named “SI”. What does this acronym mean? Is there any standard field that indicates if the outcome of a study was positive or negligible?

  24. Thanks for your question. “SI” stands for safety issue. This is a field provided by clinicaltrials.gov. Here is the help text they provide on this field — http://clinicaltrials.gov/ct2/help/safety_issue.

    To our knowledge, there is no specific field indicating study results such as “positive or negligible”. There are, however, two fields in the data available through our API that may be helpful:

    1. A Lilly COI derived field indicating whether or not results have been posted (“has_results”)
    2. The associated clinicaltrials.gov link for viewing results (“ctgov_results_link”)

    Here is an example using our ClinicalCollections application that makes use of these two fields for filtering on results and providing links to the results:

    http://www.clinicalcollections.org/trials/viewer?phase=1&cond=ALS&title=Advanced%20Search%20%3E%20ALS%20Phase%20II#has_results=Yes&view=view_outcomestable

    Let us know if you have any other questions. Thanks for using our API!

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  28. Thanks so much for this wonderful resource! We’ve been using your API, and had a few questions about how often it’s updated, and which studies were included in the results from ClinicalTrials.gov and which are not.

    For example, a “completed” trial from May 25 that appears on ClinicalTrials.gov (like this study: http://clinicaltrials.gov/ct2/show/NCT02152865) returns no results from your API (http://api.lillycoi.com/v1/trials/NCT02152865.json) whereas a different “completed” study from on the same day (http://clinicaltrials.gov/ct2/show/NCT02149979) returns perfect results from your API (http://api.lillycoi.com/v1/trials/NCT02149979.json)

    Do you have a certain selection criteria for which studies you include and which you don’t? Any information would be very helpful! Thanks and all the best.

    • Hi erin – thank you for using the API, and for your questions. We do include all studies from ClinicalTrials.gov, and update nightly any changes made to the source CT.gov data. However – you’ve helped us identify a problem we are having with our update process. Our technical team is on it, and we expect to have this problem addressed today. Thank you so much for bringing this problem to our attention! We’ll report back here when the problem is solved.

    • erin (and all!) – We have addressed the problem, and all should be well now. Please do let us know if we may be of assistance. Again, thank you for letting us know!

      • Fantastic! Thanks so much for your incredibly fast response. This really is a wonderful API, thanks for taking such good care of it!

      • Hi again Jerry! Just wondering – is your code open source? If so, where might it be available?

    • Hi erin (and all). The API code is not open source currently. We’re in process of working through our long term strategy, while continuing to forge ahead with some nearer term advances in the API. We’ll be sharing more as we evolve on these fronts.

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  30. 1. Is there a nomenclature (dictionary of conditions) that could be shown to users as a drop down (ajax) when searching for conditions such lung cancer.
    2. Same for location? That is when one enters the first few letters, choices show up.
    3. Also how to use distance from a zip code or location as a search/filtering criteria?

  31. Hello Autl. Thanks for your interest in our API. We do extract study topics from clinicaltrials.gov that may help. See the “studytopics” section on this reference page for more info. You can do a simple filter on the results by adding a “filter=” query parameter, e.g. http://api.lillycoi.com/v1/studytopics/links/conditions?filter=lung. Use the “callback=” parameter to wrap the result as a JSONP callback.

    As for your last two questions, we actually developed a sample app that demonstrates these features — http://trials4me.lillycoi.com. This app actually has its own API that includes these two features:

    1. Cities: http://trials4me.lillycoi.com/cities/us/ and http://trials4me.lillycoi.com/cities/ous/. It will return a maximum of 10 results that match the string. So the more characters you provide, the better the results will be of course. Note these results come from a cities database (http://download.geonames.org/export/dump/cities1000.zip) for the purpose of the Trials4Me app. They are not associated with the actual cities in the clinicaltrials.gov data.

    2. Proximity: http://trials4me.lillycoi.com/near?query=&lat=&lng=&mi=. It will return the trials that have locations within the radius of the location specified, arranged by location. You can use km instead of mi to specify kilometers for the radius. The query parameter uses the same format as the trials API described on this page (see /trials/search endpoint). For example, http://trials4me.lillycoi.com/near?query=cond:asthma,recr:open&lat=41.85&lng=-87.65&mi=50. Also, instead of providing lat/lng coordinates, you can provide an address, e.g. http://trials4me.lillycoi.com/near?query=cond:asthma,recr:open&addr=1600+Amphitheatre+Pkwy,+Mountain+View,+CA+94043&mi=200

    A couple notes:

    1. All of these API calls can be wrapped with JSONP by adding the “callback=” parameter.

    2. The API at trials4me.lillycoi.com is only a sample. While the data is updated daily, it is not supported and performance may vary depending on how it is called.

    I hope this helps. Let us know if you have any further questions.

  32. Atul, you are correct. The Trials4Me app provides limited trial information in its API. At this time there isn’t a single API to do what you want, but what you could do is mash up the two APIs, keyed on NCT ID. i.e. once you do the Trials4Me API call, you can use the resulting NCT IDs to call the main trials API to get the eligibility/etc info.

  33. Hello Dave, Greatly appreciate your feedback!

    1. How do we get around the problem of having to make multiple calls? For example for retrieving 10 records we end up making 11 calls. Which significantly degrades performance.

    2. Would one way be for you to club the additional information in your trials4me api or for you to allow /trials/{id} API to accept multiple NCT IDs?

    3. Furthermore, does triials4me API support offset and limit?

    Have a great weekend! Hopefully its as nice in Indiana as it is on Long Island. Cheers.

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