Explorer

Selection - select concepts to explore

From Selection you can begin exploring concepts in Coremine Medical. The process is like most search engines, but also includes some more nuanced features. The simplest example is to select one concept to explore. But you can also select several concepts to explore simultaneously. Another nuance is the ability to limit the selection of concepts to specific categories. In addition, there is the possibility that the concept you wish to explore is missing from Coremine Medical dictionaries, in which case you will be prompted to report the concept to Coremine Medical experts to be considered for possible inclusion in future dictionaries.

Finally, there is an option to select among the names of experts. To illustrate this idea, notice that an example concept, "Influenza," and an example expert "Edwards, RG" are shown in connection with Selection. Concepts and Experts are two fundamentally different approaches offered by Coremine Medical: you can either select concepts from biomedical dictionaries or authors of scientific papers (Biomedical experts).

• Select one concept to explore
• Select several concepts
• Select concepts from specific concept categories
• Report a missing concept
• Select an expert

Select one concept to explore

• Begin typing in the input field (where grayed text "Type one concept or expert" is visible);
• Choose from suggested concepts (these appear directly under the input field as a list with the heading "Choose one of the concepts below");
• Notice that the selected concept is now included in the selected concept box below the input field;
• Submit search (click "Explore" button).

Note that suggested concepts appear in a list below as you type. These concepts are drawn from the dictionaries used by Coremine Medical. Each suggested concept belongs to a category relevant to health and medicine (choosing concept categories will be discussed later).

Continue typing characters while inspecting the list to find the concept you wish to explore. The suggestions may also include names of biomedical experts recognized as authors of scientific articles.

Also, Coremine Medical dictionaries include synonym matching. Sometimes a commonly used concept differs from a more correct concept. For example, typing "cancer" will show "Neoplasms (alias Cancer)."

Once you have identified the concept that you wish to explore, use a mouse click or the enter key to include it to the selection box. Additional information shown with the selected concept is the category - that is, whether the selected concept represents a disease, drug, etc. - and the number of connections made by the concept. The "connections" number indicates how many other unique concepts co-occur with the selected concept. More about how Coremine Medical assigns and ranks connections between concepts will be discussed under the Extracted knowledge section.

When you click the Explore button, Coremine Medical will display a Network ("Concept Map") around the submitted concept as well as text and links relevant to that concept.

Select several concepts

• If Select panel is not visible, bring it back into view (Explorer "Click here to modify your search");
• Type and choose from suggested concepts;
• Additional concept will appear in selected concepts box;
• Include or remove concepts using check-boxes and controls;
• Submit to Explore (click "Explore" button).

Coremine Medical is designed to allow you to readily expand your search to include several concepts and explore the intersection of concepts.

If you already have the results of a search visible the Explorer window, you can bring the selection panel back into view using the "Click here to modify your search" tab near the top of the screen. The similar tab "Click here to cancel" will return you to search results will return the results view without initiating further action.

If the Selection input fields is visible, simply repeat the process just described to add more concepts to be explored together (type text into the input field and choose from among suggested concepts). concepts added will appear in the selected concepts box.

Notice that selected concepts include check-boxes that allow them to be deactivated or reactivated as part of the focus of an exploration. Also, there are controls "All|None|Delete select" at the bottom of the box that initiate the indicated action on the check-boxes and selections.

Select concepts from specific concept categories

As suggestions are shown while typing in the Selection input field, a text link ("Filter...") appears below the concept entry field (to the right of the text Choose one of the concepts to explore:). If you choose to open the filter you will see a list of concept categories. By default, concepts in all categories are used to provide a match to the text you type. If you wish to limit concepts to a specific set of categories you can do so by using the associated check boxes. concept suggestion categories include:

• Disease
• Drug
• Symptom
• Procedure
• Anatomy
• Food
• MeSH
• Chemical
• Cellular Component
• Biological Process
• Molecular Function
• Gene/Protein (with options for specific organisms)

Each category is a list of biomedically relevant concepts and associated synonyms. The source of each concept type is described below under the heading Categories.

Once having changed settings, click the "Update suggestions" link to apply the filter to the suggestions that appear in the concept entry field. The filter will remain in effect throughout your explorations session unless you choose to change it.

Report a missing concept

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There are times when a legitimate and useful concept does not appear among the suggestions offered while typing a concept into the input field. A dialog box will appear whenever Coremine Medical is unable to suggest a concept in response to the text you have typed. In this dialog are suggestions for how a match might be achieved, but also a text-link stating "please report the missing medical concept or biomedical expert to us here!"

The link will open a new dialog box that allows you to submit the suggested concept to Coremine Medical experts for review and possible inclusion in and updated dictionary. The dialog box includes fields that allow you to write the missing search phrase and a comment. There is also a menu that can be used to select a concept category that you believe is appropriate for the concept. In addition, you can enter an email address if you would like to be contacted regarding the review status of the concept you submitted.

Although Coremine Medical dictionaries are drawn from sources like the Medical Subject Headings (MeSH) thesaurus of concepts and other large dictionaries addressing biomedical concepts, some important concepts may not be included in these source materials. Sometimes even fairly common concepts are missing because these may differ from a stricter use applied by experts. Other times there are acronyms or other variants used by one group of specialists that are unknown to another group. We appreciate the input of our users any time a missing concept is brought to our attention.

Select an expert

If you know the name of a Biomedical expert, you can use Coremine Medical to search for that expert and colleagues.

Alternatively, if you wish to find an expert in a given field, use keywords to search within the field and then view the Biomedical experts list to be discussed in the section on the Focus panel under Extracted Knowledge.

To search for an expert from the selection menu, begin by typing the last name of the expert. A list of suggestions will appear. Add first name initials if you need to refine the search to fewer suggestions.

If the expert name does not appear you may choose to report the missing name to our experts for evaluation, as described above regarding missing concepts for concepts.

Categories - choose concept categories

The icons under the text "Categories (click to disable)" are "switches" that allow you to limit the scope of your search results to concepts within various concept categories.

To illustrate the function of these category filters, consider the question "how is breast cancer treated?" To explore possible answers to this question, and to avoid suggestions outside of its scope, you can choose to leave only the Drug and Procedure categories active (click all other categories to "gray out" their icons). Now you can type "breast cancer" in the Selection field and you will see the concept "Breast carcinoma" suggested as a match.

The concept map generated by this process would show one Disease concept (Breast Carcinoma) and five concepts each from Drugs and Procedure categories. The search concept will always be included, even if its category is "deselected" (in the case of this example, Breast Carcinoma, by virtue of it being the search concept, is included even though Disease category concepts are excluded from search results).

Note that these buttons affect the types of concepts that will be retrieved once you have clicked the Explore button and launched a search. The Categories buttons do NOT change the concept suggestions seen during concept selection (see Select concepts from specific concept categories for a description of that process).

The concepts used by Coremine Medical to identify concepts and other entities in scientific and popular literature make up dictionaries of recognized concepts compiled from trusted sources. Concepts can be assigned to higher-order groupings and Coremine Medical operates with twelve such categories that can be used to define your search.

Below is a list of the biomedical concept categories used by Coremine Medical and an indication of the sources used: