Frequently Asked Questions
Table of Contents:
ClinicalCollections Frequently Asked Questions
Using the Clinical Collections Application
- What sorts of things can I do in the Clinical Collections application?
- How do I build a Clinical Collection?
- What views are available for me to explore?
- How do I refine the data displayed in the Collection Views?
- Can I sort the data?
- How can I get a new view of the data?
- Can I export the data in my collection?
- Can I save my collection?
- Can I share my collection with others?
- How can I learn more about the collection that someone has sent me?
Data
- What is the source of the data?
- How often is the data refreshed and kept current?
- Are you looking at other data types or sources?
- How big can a collection be?
- What is MeSH?
- Some ct.gov fields are not displayed, such as inclusion/exclusion criteria. Where are they?
- I do not see trial results. How can I see the results?
- The data is a bit messy, is it possible to have it cleaned up such as typos or upper/lower case?
Technical
- Why can't I use Internet Explorer?
- What export formats are available?
- What technologies did you use to create Clinical Collections?
Support
- What type of support do you offer?
- Is there someone I can talk to about the Clinical Collections application?
AnswersForum Frequently Asked Questions (FAQ)
- How is a Question/Answer community different from a typical forum?
- What kinds of questions can I ask here?
- What kinds of questions should be avoided?
- Why are email notifications so important?
- Who moderates this community?
- How does the karma (reputation) system work?
- What is a gravatar?
- To participate in this community, do I need to create an account?
- When I sign up, do I need to create a new username and password?
- Why can other people can edit my questions/answers?
Using the Clinical Collections Application
What sorts of things can I do in the Clinical Collections application?
Build a collection. The Clinical Collections app makes it easy to build and customize your own collection of clinical information using data housed in TB Commons. Today, the more than 100,000 clinical trials cataloged in the NIH clinicaltrials.gov registry have been imported into TB Commons for use in your collections.
Explore your collection. Once you have built a collection, you can easily explore it to find answers and gain insights. Filtering a Collection is simple and the resulting set of trials can be visualized in maps, timelines, and tables. You can bookmark your customized collections for later use.
Share your collection. Lastly, we have made it simple for you to share your customized collection with colleagues and community members. You can even send your collection to our TB Commons question and answers forum to ask community members a question about your collection.
How do I build a clinical collection?
Building a collection is easy. Simply search for trials. You can do a Google style term search or browse the topic index. The data for each trial will be assembled into a dataset that you can explore with the Collection Viewer. This viewer will allow you to explore, refine, and share a variety of interactive visualizations, including maps, timelines, listings, and tables.
What views are available for me to explore?
The main panel in the Collection Viewer has 5 views that you can select: Listing, Summary, Outcomes Table, Timeline by Phases, and Map by Phase. The views are interactive, so we encourage you to play around with the features in each one.
How do I refine the data displayed in the Collection Views?
The simplest way is with Keyword Search. This narrows the data displayed in the views by matching text across all the data in your collection. You also can filter with precision. To do this, open filters in the left column of the Collection Viewer and select the particular data you want. All of the views will automatically update to reflect your selected refinements. As you set filters, notice that the number of matching items changes in the views.
Can I sort the data?
Yes. The Listing, Summary, and Outcome Table Views allow sorting.
How can I get a new view of the data?
We will be continuously improving the tool. Please send us your ideas, thoughts, and needs by pressing the Comment button.
Can I export the data in my collection?
Yes. Click the orange scissors icon to export. This icon appears when you move your mouse into any of the Collection Views. It also appears in the filters used to refine data. This feature is really handy for getting your hands on individual lists such as trial ids, locations, interventions or sponsors. When exporting, select Tab Separated Values if you want to import into a spreadsheet.
Can I save my collection?
Yes. Simply bookmark the page with your web browser. The bookmark will open the collection with the same filter settings and view. Please note that our trial data is refreshed nightly. As a result, over time the data in your views will automatically change to reflect additions or updates to data in TB Commons.
Can I share my collection with others?
Yes. You can share the URL via email or send it to your favorite networks including Twitter, Facebook, and Linkedin. You can also post your collection to the TB Commons questions and answers forum (AnswersForum).
How can I learn more about the collection that someone has sent me?
Click the "About Collection" link.
Data
What is the source of the data?
Trial data is sourced from the clinicaltrial.gov public trial registry.
How often is the data refreshed and kept current?
We refresh the clinical collections every day, matching the refresh frequency of the clinicaltrials.gov data.
Are you looking at other data types or sources?
Yes. We intend to grow the data in TB Commons, eventually allowing you to build, explore, and share Clinical Collections with drug information, site/lab information, and regulatory actions. Our prioritization will come largely through your feedback and community needs.
How big can a collection be?
The Clinical Collections software is designed to handle collections of up to 1,500 items. When opening a collection that is too big you will be ask to filter the collection to a smaller set of items.
What is MeSH?
Medical Subject Headings (MeSH) is the National Library of Medicine's controlled vocabulary thesaurus. MeSH terms are applied by clinicaltrials.gov to the condition and intervention data attributes. MeSH is a helpful categorization thesaurus to harmonize data, especially where the raw data is represented in many different ways. A good example is ACS, Acute Cardiac Syndrome, Acute Coronary Syndrome all are harmonized in MeSH as Acute Coronary Syndrome.
Learn more about MeSH.
Some ct.gov fields are not displayed, such as inclusion/exclusion criteria. Where are they?
We have chosen to keep collection data as lean as possible for performance reasons. You can click through to the source record in clinicaltrials.gov to see all the trial data.
I do not see trial results. How can I see the results?
We have not imported trial results into TB Commons at this time. We do provide links to results when they exist. Please note that you can use the "Results" filter to limit the data to only those with results posted in ClinicalTrials.gov.
The data is a bit messy, is it possible to have it cleaned up such as typos or upper/lower case?
Clinical Collections display data as it was entered at clinicaltrials.gov by the trial sponsor. In future releases, we will provide tools and workflows to support curation and annotation.
Technical
Why can't I use Internet Explorer?
We want your experience to be productive. Internet Explorer is not fast enough to support our Clinical Collections application. Chrome and Firefox are supported and Safari should work as well. If you must use IE, our application is designed to utilize the Google IE browser plug-in (ChromeFrame).
What export formats are available?
Data displayed in the Collection Views can be exported in Tab Separated Values (good for excel), Semantic wikitext, and Exhibit JSON. Data listed in filters can be copied to your clipboard and then pasted into any application including a spreadsheet.
What technologies did you use to create Clinical Collections?
Clinical Collections is built with open source software. The center piece is an open REST API for trial data in TB Commons. This API is used to supply JSON data to the ClinicalCollections web application which uses a customized version of Simile Exhibit software (Javascript) from MIT. The app is written Django Python. TB Commons data is managed in Amazon Relational Database Services (RDS) databases.
Support
What type of support do you offer?
The Clinical Open Innovation team is a small team. We have designed the Clinical Collections application to minimize support needs and maximize self-service. The servers are designed to autoscale on demand. We monitor the system for uptime and any system errors. If you have questions or problems, please use the comment button to send us a message.
Is there someone I can talk to about the Clinical Collections application?
If you have comments, questions or ideas please use the "Comments" button on the right side of any screen within the TB Commons site.
AnswersForum Frequently Asked Questions (FAQ)
How is a Question/Answer community different from a typical forum?
A Question/Answer community is different from a typical forum because it focuses on finding answers to the questions of its members. A typical forum, by contrast, operates more like a discussion group, where people are free to give their opinions and topics tend to be more subjective.
By keeping a laser focus on questions and answers, this community ensures that finding answers to existing questions - and getting answers to new questions - can be done without any distractions.
What kinds of questions can I ask here?
Most importantly, questions should be relevant to this community.
Before you ask, please make sure to search for a similar question. You can search for questions by their title, content, or tags.
What kinds of questions should be avoided?
Please avoid asking questions that are not relevant to this community, are too subjective, or are argumentative.
Why are email notifications so important?
Email notifications are the bedrock of a successful question and answer community. These notifications allow community members to be notified of important events, such as:
- when their questions have been answered
- when one of their posts is commented on by another member
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The success of the community relies upon community member involvement, and members are much more likely to become involved, active participants on the site when they're notified of interesting developments. That is why this community considers a valid email address as a requirement for participating in the community and using this site.
If you're already a member of this community and haven't validated your email address, you can do so here. If you aren't yet a member of this community, you can join by clicking the login link and following the steps to register.
Who moderates this community?
The short answer is: you. This website is moderated by the users. The community features a karma system that allows users to earn rights to perform a variety of moderation tasks.
How does the karma (reputation) system work?
When a question or answer is up-voted, the user who posted them will gain points, which are called "karma" or reputation points. These points serve as a rough measure of the community trust in him/her. Various moderation tasks are gradually assigned to the users based on those points.
For example, if you ask an interesting question or give a helpful answer, your input will be upvoted. On the other hand if the answer is misleading, it will be downvoted. Each vote in favor will generate 10 points, each vote against will subtract 2 points. There is a limit of 200 points that can be accumulated per question or answer.
What is a gravatar?
Gravatar means globally recognized avatar - your unique avatar image associated with your email address. It's simply a picture that shows next to your posts on the websites that support gravatar protocol. The default gravatar appears as a square filled with a snowflake-like figure. You can set your image at gravatar.com.
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Why can other people edit my questions/answers?
Allowing experienced members of this community to curate the questions and answers improves the overall quality of the knowledge base content.