This guide describes the various feature of EMERSE and how they can be used. The guide is directed towards regular EMERSE users. For technical details about implementing and running the system from an administrative perspective, please see our other guides.

What is EMERSE?

EMERSE is a search engine, sometimes referred to as an information retrieval system, for identifying terms and concepts in free text clinical notes from electronic health records. It is similar to a natural language processing (NLP) system, but EMERSE was designed mostly to be a simple, quick system to help people find the information they need, and to require minimal training to get up and running.

EMERSE was not designed to automatically "code" information. That it, it was not designed to find a concept, assign it a code, and then build up a spreadsheet of the concepts. Rather, it will help you find the information but it will still be up to you to decide if the context is correct, and how the concept should be coded.

EMERSE is a mature, feature rich application that has been in development since 2005. EMERSE should be considered to be a 'tool' in a toolbox of multiple software applications to support the data needs of users. It can work well in environments with other existing and commonly used tools. For example, EMERSE (which focuses on free text) complements systems such as i2b2 Workbench (which focuses on the coded, structure data). It also works well in environments that have tools such as REDCap, which is commonly used for electronic data capture. Of course, EMERSE can be used standalone as well, without other software tools.

An example of a typical workflow might include identifying an initial cohort based on structured data within i2b2 (ICD-10 codes, lab values, etc) and then searching that cohort within EMERSE. Data abstracted from EMERSE would then be stored within REDCap. However, many other software tools can be used in conjunction with EMERSE, depending on local needs and workflows.

EHR systems that work with EMERSE

EMERSE was designed to be vendor "agnostic" with respect to electronic health record (EHR) systems. That is, it is not directly coupled to any specific EHR. If there is a way to get data our of your EHR it should be possible to get it into EMERSE.

How can EMERSE be obtained?

EMERSE is available free of charge with open source licensing. However, it does require a technical team to install it, move data into it, and then manage the system including ensuring security, provisioning accounts, etc. Our other guides provide substantial detail on the processes requires to install and operate EMERSE.

Who should use EMERSE?

Anyone who has a need to find data "buried" within clinical notes could benefit from using EMERSE. EMERSE can be used for a wide variety of clinical and translational research tasks, as well as non-research tasks. A few examples are described below. Further examples of research supported by EMERSE are provided in a list of peer-reviewed publications.

Research Use Case Examples

  • Reviews preparatory to research: EMERSE is great for a review preparatory to research, where you want to estimate the number of patients available for a study in order to determine whether a study is feasible or not.

  • Rare diseases: EMERSE can quickly find mentions of rare disease in the notes, which is especially helpful when billing codes are too broad or used incorrectly. For example, there is only once ICD-10 code to represent all 13 types of Ehlers-Danlos syndrome. To find the specific type of interest, you would need to search the free text.

  • Eligibility determination: For studies in which eligibility determination is complex and may rely on data only captured within the free text portion of documents, EMERSE can be a rapid way to check for mentions of inclusion/exclusion criteria.

  • Data abstraction: For patients already on a study, EMERSE can be used to identify data for abstraction. These could include treatment courses, side effects, adverse events, or anything about the patient that requires a chart review.

Operational Use Case Examples

  • Quality Improvement (QI): EMERSE can be used for QI activities such as infection control monitoring. For example: Informatics and the American College of Surgeons National Surgical Quality Improvement Program: automated processes could replace manual record review.

  • Risk Management: Such tasks could include identifying falls or finding patients with device/implant recalls.

  • Health Information Management (HIM): HIM teams can use EMERSE for a wide variety of tasks including support for outside records, identifying unapproved abbreviations, contact moves, historical inpatients/outpatient volume searching, and even consents.

  • Billing/Coding: The billing/coding teams can use EMERSE to help identify supporting information, or verify that necessary details are actually mentioned in the notes. Using EMERSE can help save an institution hundreds of thousands of dollars each year!

  • Cancer Registries: Cancer Registrars can use EMERSE for a wide variety of data abstraction tasks including difficult-to-find information such as genetic and biomarker testing.

Clinical Use Case Examples

  • Clinical Chart Review: EMERSE can be used to help find details about a patient rapidly, even during a clinical visit. For example, if a patient mentions that a certain medication helped their migraine 3 years ago but can’t remember the name, just search the chart for 'migraine' and find that note within seconds.

  • Prior authorizations: Often an insurance company won’t approve a specific drug unless documentation can be provided that cheaper alternatives were used without success. EMERSE can be used to find mentions of those ineffective alternatives very quickly.

EMERSE was designed to work with patient data. Therefore, access will be almost certainly be limited, and each site will have policies in place about who can or cannot have access to the system, and under what circumstances that access can be granted or revoked. In general, institutional review board (IRB) approval will always be required for EMERSE access when research is being conducted, whereas other types of requirements/approvals will need to be in place for other access types such as clinical care, operations, quality improvement, education, etc.

Guide Conventions

There are a few conventions used throughout the guide to ensure consistency and ease of understanding of the concepts discussed.

Italicized phrase
Most of the time an italicized phrase will refer to a specific component of EMERSE that a user can access or utilize.

Tab name
EMERSE uses multiple tabs within the user interface to separate out and organize various components of the system. When specific tabs are referenced, they will be in bold and have a top, left, and right border around it, but no bottom border.

Button name
Buttons names will also be bolded and will be surrounded by a rounded border on all sides.

Terms, sometimes called Search Terms or Keywords, will usually be shown in a monospace font to help them stand out from the rest of the text in this guide. They will also sometimes be shown with a colored background to show how they might be highlighted by the system.

The Navigation Panel is the area at the top of EMERSE that contains most of the navigation elements (buttons) of the system, as well as other information that can be useful to users such as the currently select patients and search terms.

When "Documents" are mentioned, this means clinical documents generated by a clinician about a patient. These documents are also commonly referred to as "Notes" or even "Reports" and often these terms are used interchangeably.

How to Get Help

There are various ways to get help or learn more about EMERSE. This guide is a good place to start. Also consider asking a colleague. Another place to look are the online videos. If you need more help, please ask your local EMERSE site administrator, especially if it deals with account and access information. If all else fails, you can contact the EMERSE team at the University of Michigan, which is where EMERSE was originally developed.

Moving Around Within EMERSE

EMERSE was designed as a "single-page application". This means that new screens within EMERSE are actually loaded within the same web page. You should avoid using the browser’s back button to go to previous pages. Rather, use only the buttons presented within the EMERSE application to navigate around.

Many things are clickable in EMERSE, even if they are not highlighted as such. It is safe to click around and try things out. You can’t ruin anything or change the original documents.

Most of the tables can be sorted. To sort a specific column in a table, click on the column header of interest. Columns that are sortable should have small black arrows next to the header name. To sort in the opposite direction, just click on the column header again.

EMERSE supports roles/privileges which are configured locally at each site. Depending on your specific role, some parts of EMERSE may not be accessible to you. If you think this is a problem, contact your local EMERSE administrator.

Getting Started and Logging In

To get started with EMERSE you will need an account. Because EMERSE contains protected health information, access will be limited. Access will be provided by your local institution, and requirements for access may vary. You will need institutional review board (IRB) approval for research. Additional training may also be required, especially as it related to human subjects research. You will likely need other reviews and approvals for non-research use (quality improvement work, operational work, etc.), which will be determined based on local policies.

Attestation Page

The Attestation Page is the first page you will land on after logging in to EMERSE. It is the page on which you define your specific reason for using EMERSE for that particular login session. This information is stored in the logs (audit trails) to capture specific use cases when looking up patient information.

The entries/selections on this page get recorded in the official audit trails which may be reviewed periodically to ensure that reasons for access are valid.

There are three separate sections on the Attestation Page that may or may not be available to you, depending on how EMERSE has been configured at your institution, described below.

Free Text Box

This is a box where you can type in your reason for using EMERSE. You can type in anything, but it should ideally be brief and should sufficiently describe why you are using the system. This free text box should really only be used as a last resort, in cases where you are unable to find any other options that match your reason for using EMERSE. Once you submit your response, it will be listed in the Table as a non-research entry during future logins, described below.

Quick Buttons

Quick Buttons are buttons that are named for common EMERSE use-cases (e.g., "Quality Improvement", "Clinical Care", etc). The options for the buttons are programmed by your local site’s system administrators, and your system administrators can add or remove options to best fit the most common use cases at your site. To select one of the options, simply click on the button. Clicking the button will record that reason in the log files.

Table (Research and Non-Research)

The Table on the Attestation Page displays two types of entries. Non-research entries are prior reasons for using EMERSE that have been typed into the Free Text Box (see above). These can be removed from the table at any time by clicking on the Remove button. Note that this does not remove them from the logs for prior EMERSE logins. Research entries should include valid IRB-approved studies for which you are listed. How these studies get populated from their source systems (such as an electronic IRB tracking system) will differ for each EMERSE installation, but note that sometimes there can be delays between the time a study is approved and the time that it shows up in this table.

There is currently no way to change your Attestation selection once you have logged into EMERSE for a specific user-session. If you need to change it, log out of EMERSE and then log back in again.


There are two overall approaches for searching with EMERSE, based on whether a list of patients are provided or whether you conduct a search across All Patients without pre-defining a list. The Patient Lists are themselves divided into two categories: Temporary and Saved. Each is described below.

An important distinction to understand is that the way EMERSE searches differs depending on whether it is an All Patient search or a search across a pre-defined Patient List. These differences are described in detail in the section discussing the Terms.

When first logging into EMERSE, after completing the Attestion Page you will always land on a page where All Patients are selected. This is to ensure that you will be able to complete a search even if you do not know the patients you want to search. If you want to search a known set of patients instead, this can be changed with just a few button clicks.

All Patients

All Patients is the default setting after logging into EMERSE. As the name implies, this setting will search across all of the patients in the system. To select All Patients any other time, simply click on PatientsAll Patients and then click on the single row in the table to choose all patients. When this is selected, the system will show the word "All" next to the Patients button in the upper-left of the Navigation Panel, as well as the total patient count in parentheses. After choosing All Patients, navigate to the Terms to enter your search terms, then click on the Find Patients button to identify the patient set.

When searching across All Patients you will be able to see an overall patient count that matches the search criteria, a subset of up to 100 text snippets (Summaries) to quickly review the context of what was found, as well as a summary of the demographic characteristics of the patients that were found.

A Summary in EMERSE is a small snippet of text that shows the keyword or phrase of interest (the search term) highlighted with additional text (about 20-30 characters or 5-6 words) on either side to show the term in its original context. This is to enable rapidly skimming the results.

To review patients found through an All Patient search in more detail, the patients first have to be moved to a Patient List, described below.

Patient Lists

Patient lists are based on medical record numbers (MRNs). Each patient list can contain anywhere from a single patient up to 100,000 patients per list. Patient lists can be created through an All Patient search (using Find Patients ), or by entering a set of medical record numbers.

Depending on your local configuration, it may also be possible to have a patient list automatically submitted to EMERSE from another system (such as i2b2), which would then appear as a Saved Patient List, described below.

There are two basic types of patient lists: Temporary and Saved and there are difference between the two types regarding what you can do with them and when you should use them. The following table provides a high level overview of these differences, with additional details following.

Table 1. Feature Comparison between the Temporary Patient List and the Saved Patient List


Temporary Patient List

Saved Patient List

Maximum number of patients per list



Maximum number of lists per user



Ideal for "Reviews Preparatory To Research"



Ideal for teams working together from the same list



Supports sharing with other users



Saved between sessions



Supports Tags



Supports Comments



Supports Exporting/Saving to Excel



Can be used with the Merge Lists feature



Temporary Patient List

A Temporary Patient List is a list that a user can make that, by its nature, cannot be saved. That is, it can be used for a single session but is erased when the user logs out. Such a list is useful in cases where a patient, or set of patients, needs to be reviewed but there is no need to save the list of patients for another time. A "review preparatory to research" should utilize this Temporary Patient List since such a list should not be saved during this type of research review phase.

A Temporary Patient List is meant to be fast and simple, and has a limited set of features. By contrast, a Saved Patient List (see next section) provides more features. For example, with a Temporary Patient List it is not possible to share the list with other users, nor is it possible to annotate the list with Comments or Tags, both of which are only possible with a Saved Patient List.

Converting to a Saved Patient List

A Temporary Patient List can be converted to a Saved Patient List by clicking on the Convert to Saved Patient List button, which can be found on the View Patients tab.

Removing Patients from a Temporary Patient List

To remove a single patient from a Temporary Patient List simply click on the View Patients tab and then the Remove button next to that patient’s name. Or, to remove all of them from the list at once, choose the Clear tab for the Temporary Patient List and then click on the button Clear All Patients From List.

Saved Patient Lists

A Saved Patient List is a list that a user can make and save between sessions. There is no limit to the number of Saved Patient Lists that a user can have, and each list can contain between 1 and 100,000 patients. Because these lists are saved, each list should be given a name and a description, available under the Name/Description Tab. A Saved Patient List is very similar to a Temporary Patient List but there are several notable advantages when using the Saved Patient List.

Sharing Saved Patient Lists

These Saved Patient Lists can be shared with other EMERSE users. To share them, click on the Sharing tab and enter the user names of those who should have access to the list. These other users will be able to view the list, but because they are not the "owner" of the list they will not be able to add new patients or remove existing patients. However, these users will be able to add/edit the Comments and Tags, both of which are described below. These Comments and Tags belong to the list and are shared and available to all users who have access to the list. Thus, among teams sharing a Saved Patient List, it is important to establish a protocol for changing these Comments and Tags since one user could modify (or delete) a Comment or Tag entered by another user. Further details about Comments and Tags can be found below.


A Comment is a short bit of text that can be entered by users who are reviewing patients in a Saved Patient List. These Comments can be used for any purpose but could be useful for recording notes about the patients as the reviews are occurring. For example, if a study coordinator/data abstractor has a question about a patient that needs additional review by the study team, the Comment section would be a good place to enter that. It could be also used for some simple/basic data abstraction. Comments (and Tags) can be exported to an Excel file. Exporting Saved Patient Lists is described in a separate section. Comments are saved immediately when a user clicks out of, or removes focus from, a Comment field.

EMERSE is not intended to be a full-fledged electronic data capture system. For storing data as you are reviewing records in EMERSE you may need an additional system running in tandem with EMERSE, such as REDCap.

A Tag is a simple checkbox that can be used when reviewing patients in a Saved Patient List. Similar to Comments, it is up to each user (or team sharing the list) to determine how this Tag should be used, but a common use would be to mark certain patient as being of interest/eligible for a study. The Tags belong to the list and all users who have access to the Saved Patient List will see the Tag and be able to change it. Tags are saved immediately upon clicking on the checkbox (either checked or unchecked).

Removing Patients from a Saved Patient List

It is possible to individually remove patients from a Saved Patient List by simply clicking on the View Patients tab and then the Remove button next to each patient’s name. Or, to remove all of them from the list at once, choose the Clear/Delete tab for that list and then click on the button Clear All Patients From List. Clearing (but not deleting) the list could be advantageous in cases where you want to preserve the sharing preferences for a group of users but want to work with a new set of patients in the list.

Deleting A Saved Patient List

It is also possible to delete the entire list by pressing the Delete Patient List button under the Clear/Delete tab. Be careful because once it is deleted there is no undo option.

Exporting a Saved Patient List

Saved Patient Lists can be exported/saved as an Excel spreadsheet. The file requires a password which you will have to enter at the time of saving it. The exported spreadsheet will contain each patient’s name, medical record number, date of birth, current age, and any Comments or Tags that were added. This can be useful for a variety of reasons. One thing you can do with such an Excel file is use it to further select/filter for patients of interest. For example, if certain patients were tagged within EMERSE, you can sort the Excel sheet by the Tag column, delete those without a tag, and then copy just the MRNs of those with a tag and paste them back into EMERSE to create a new list with just the subset of tagged patients, or move that reduced list to another research system.

Moving Patients to a Patient List

Patients identified through an All Patient search can be moved to a Temporary Patient List for more detailed searching and viewing of their notes. Once an All Patient search is completed, simply click on the button called Move patients to Temporary Patient List. This will transfer the set of patients identified from an All Patient search to a Temporary Patient List, which is not saved between sessions. Once that move occurs, the list of patients will be shown. To then change that Temporary Patient List to a Saved Patient List, simply click on the button called Convert to Saved Patient List.

Adding Patients to a Patient List

In addition to moving patients to a list from an All Patient search, patients can also be added to a list (either an existing list or a new list). This process is the same regardless of whether you are using a Temporary Patient List or a Saved Patient List. Entering patients is done via the Add/Upload Patients tab for the patient lists. To enter new patients, you can type each MRN one-by-one into the MRN text entry box, or you can paste an entire set of MRNs at once. For example, it is possible to copy and paste an entire column of MRNs from an Excel spreadsheet and paste them into the MRN text entry box to create a patient list. You can also upload a set of MRNs from a plain text file, with one MRN on each line. If there are already patients in a patient list, adding new MRNs will append them to the existing list, up to the maximum number allowed.

Any time an MRN is entered, that MRN is checked against the complete set of patients within EMERSE. If an MRN is not found, a warning to the user will be provided. Similarly, if a duplicate MRN is entered for a list, the duplicates will be removed automatically and the user will be alerted.

Merge Patient Lists

The Merge Patients feature allows for two Saved Patient Lists to be compared to each other with respect to the patients contained within each list. This feature can be accessed via the Merge Patient Lists button which can be found above the table displaying the Saved Patient Lists.

Merge Patients allows for two lists to be merged together but also provides additional functionality that can be useful for separating out only those patients of interest that may be found among two lists. This feature essentially builds a Venn diagram showing the overlap of patients between any two Saved Patient Lists. You can then select any part of the diagram you are interested in simply by clicking on the appropriate section of the diagram. Once your selection is finalized, click on the Save New List button and you will then have a new Saved Patient List based on your selection. Note that when lists are merged, duplicates will be removed automatically.

Table 2. Operations that can be performed with Saved Patient Lists using the Merge Patient Lists feature
             (List 1 is represented by the left circle, List 2 is represented by the right circle)

All patients in List 1 that are not in List 2

user guide Venn1.png

Only those patients from List 1 and List 2 that are not already in both lists

user guide Venn3.png

All patients from Lists 1 and 2 (an actual merge)

user guide Venn4.png

All patients in List 2 that are not in List 1

user guide Venn6.png

Only those patients that were originally in both List 1 and List 2

user guide Venn7.png

It may be useful to use Merge Patient Lists when you want to compare patients found through two different mechanisms or searches. For example, suppose you find a set of patients who had "back pain" and a separate set of patients who had "acupuncture". Using the Merge feature you can find the set of all patients who had both concepts mentioned in their notes at least once, even if the mentions were in completely separate notes or sections of the EHR.

Or, suppose you have a set of patients with a diagnosis of "amyotrophic lateral sclerosis" (List 1) and now you want to exclude any patients with a mention of "packs per year" (List 2). You can make two separate lists, one based on each search. Then using the Merge feature, you can select out the list of patients from List 1 that did not also appear in List 2.


Terms are the words and phrases you specify in your searches. EMERSE provides a lot of flexibility in what you can do with the Terms. There are three general ways to enter Terms (Quick Terms, Term Bundle, and Advanced Terms), each of which is described in detail below.

Before getting into the details, there are several aspects about EMERSE that are worth pointing out:

  • All searches are, by default, case-insensitive. This means that you will get the same result whether you search for HELLP syndrome or hellp syndrome (though it is possible to enable a case-sensitive search when necessary).

  • "Stemming" is not turned on with the default configuration of EMERSE. This means that if you search for echo you will only find that exact word. You will not automatically find variations such as echoing, echoed, etc. and thus if you want those variations you will need to add them yourself. This was intentional to allow users maximum control over the terms found. For example, if you are looking for echocardigram, which is often abbreviated echo, you would not want to find terms such as echoing. EMERSE does provide various options, described elsewhere, for expanding your search to capture these kinds of variations, including the use of Wildcards and Synonyms.

  • Terms can be highlighted in one of 18 colors. In fact, the reason that that EMERSE interface is so gray and drab is to help those colored terms stand out.

  • The way EMERSE uses the Terms for searching depends on the searching context, and this context differs whether you are searching through All Patients in the system or whether you are searching through a pre-defined list of patients (either a Temporary Patient List or a Saved Patient List). This distinction is important, and it is described in more detail in the section about Searching.

  • Many non-alphanumeric characters are ignored by EMERSE, so there is no advantage to including them in your search terms. Alphanumeric characters include the the letters A-Z and the numbers 0-10. Examples of non-alphanumeric characters normally ignored by EMERSE include, but are not limited to:
    ! ? . > < + - #
    This is important because there may be some things you will not be able to definitively find using EMERSE. For example, if you are looking for HIV+ patients, the + is ignored and thus from the perspective of a search you would be able to find HIV but EMERSE cannot distinguish between HIV+ and HIV- (you could find phrases like HIV positive and HIV pos, however).
    Some of these non-alphanumeric characters can play a role in searching with the Advanced Search feature, described elsewhere.

  • EMERSE indexes words based on what are known as "tokens". A token is usually a term separated by white space (such as a space), or by some of the non-alphanumeric characters that are ignored (e.g., ! ? . - etc). Thus, if you are looking for echocardiogram you will not find echo-cardiogram (since the latter is considered two separate words when it is tokenized) unless you specifically search for that kind of variation as well, with or without the hypen which is ignored by the system. Note that many of these variations can still be found by leveraging the Synonyms that EMERSE offers.

There are three basic types of Terms you can work with: Quick Terms, Term Bundles and Advanced Terms. Each of these are described in detail below. Additionally, the following table provides a high level overview of the differences:

Table 3. Feature Comparison between the Quick Terms, the Term Bundles, and the Advanced Terms


Quick Terms

Term Bundles

Advanced Terms

Maximum number of terms per list

no limit*

no limit*

no limit*

Supports 18 colors for terms




Full control over the choice of colors for terms




Ideal for teams working together




Supports sharing with other users




Saved between sessions




Supports Term History




Has a Term Upload feature




Can take advantage of Synonym suggestions




Spell Checking of Terms




Supports the ability to search for terms in a case-sensitive manner




Supports advanced search features including customizable proximity searches, fuzzy searches, Boolean searches (AND, OR NOT), and regular expressions




*While there is no limit on the number of terms, a large number > 100-200 will cause the system to run quite slow.
**The most recent 40 to 50 queries are saved and accessible as part of the Term History

Quick Terms

Quick Terms is the fastest and easiest way to get started with a search. A simple text box is provided where you can type in the terms you are looking, with each term or concept separate by a space. With Quick Terms EMERSE assigns the colors to the search terms, and you have no control over the colors assigned. There are, however, several Search Options available to you to make the search more powerful and effective:

Search Option: Double quotes

To search for a multi-word phrase that contains one or more spaces, simply put that phrase in double quotes. This will force EMERSE to search for those words together, in that specific order, as opposed to separately, in any order, and in any place in the document. For example, if you search for motor vehicle accident without the quotes, you will end up finiding the terms motor, vehicle, and accident separately. However, if you put the phrase in double quotes ("motor vehicle accident") you will find only the specific phrase motor vehicle accident.

Search Option: Case sensitive searches

Some medical acronyms are identical to common English words, including NO (nitric oxide), ALL (acute lymphblasic leukemia) and RICE (rest, ice, compression, elevation). Because EMERSE, by default, searches for all terms in a case-insensitive manner, you can end up with a lot of false positives for these otherwise commons words. To help reduce the number of false positives, you can specify a term to be case-sensitive by adding a carat (^) symbol in front of the term. For example, to search for a case-sensitive capitalized ALL, enter ^ALL as the search term, with the carat symbol (^) directly in front of the term. This well help reduce false positives by not returning the common word all as a hit.

You can mix case-insensitive terms and case sensitive terms as long as they are separate terms. For example, the query terms…​

chemotherapy    "diagnosed on"    ^ALL

…​will find documents with chemotherapy (case-insensitive), diagnosed on (case-insensitive), and ALL (case- sensitive)

However, if you have a multi-word phrase in double quotes, you cannot have just a single word in that phrase be case-sensitive. The case-sensitive symbol must go in front of the entire phrase, and the entire phrase would be case sensitive. For example, the query term…​

^"diagnosed with ALL"

…​would match: diagnosed with ALL but would not match Diagnosed with ALL or the phrase diagnosed with all since the case does not exactly match the query which specifies that diagnosed and with should be lower-case and ALL should be all upper-case.

And, as described above, the following query is not permitted since a single word in a multi-word phrase can’t be case-sensitive. It is essentially an all or nothing choice where the entire phrase is case-sensitive, or the entire phrase is case-insensitive. The following query is not allowed and will not work:

"diagnosed with ^ALL"

Thus, for searches that require terms to be case-sensitive, in general it is best to just have a single term be case-sensitive and not an entire phrase.

Case-sensitive searches can be done within the Advanced Terms feature. However, the process for conducting a case-sensitive search with Advanced Terms feature differs from the Quick Terms and Term Bundles features. Details about how this is done can be found in the section on Case Sensitive Searches in Advanced Terms.

Search Option: Wildcards

Wildcards help with finding concepts where you may not be able to specify the exact details/phrasing/spelling of the terms.

For example, sometimes you may want to look for a term where the ending of the word may be variable. Suppose you want to look for terms related to hypertension. If you just search for hypertension you may miss other variations. Using the wildcard symbol, the asterisk (*), you can overcome this problem. Simply type in something like hyperten* and you will be able to match terms such as hypertension, hypertensive, hypertensives, etc. This would also match potential misspellings such as hypertenion.

In addition to adding a wildcard to the end of a word, you can also add it to the middle of a word. If you search for hyper*ia you will match terms such as hypercapnia, hypernatremia, and others. In this example, the search term with the embedded wildcard will look for words that start with hyper and end with ia.

Finally, you can place the wildcard (*) in between two words, in which case EMERSE will look for those two words within 5 words of each other, in any order. For example, "pain * leg" will match pain shooting down her right leg as well as leg with severe pain.

There are few caveats with using wildcards:

  • You cannot use a wildcard at the beginning of a term. In other words, *oma is not allowed.

  • You must have at least three characters in a word before using the wildcard. Thus, hyp* is allowed, but hy* is not allowed.

  • If your wildcard search ends up matching > 1024 distinct terms, the search will likely fail.

  • If you are using the wildcard within a quoted phrase, it cannot be combined with a word, but must be between two words. For example "pain * leg" is allowed, but "pain shoot*" is not allowed.

Exclude Terms

EMERSE supports a concept of excluding terms with a search. This is similar to the idea of "negation" but works a bit differently. Essentially, this is a way of ignoring certain phrases so that you can find the terms of interest in the appropriate context, and remove potentially positives.

For example, if you are searching for complication or complications in the context of a surgical complication, you may want to simply look through operative notes for the terms complication or complications. However, you don’t want to find negated forms of this such as no complications or without complications (this would be traditional "negation"). Additionally, you may not want to find the terms in other contexts that are not necessarily negated but are still the wrong context (e.g., complications from diabetes).

To ignore/exclude these phrases using Quick Terms, simply include a minus sign in front of the quoted phrase to exclude. For example:

complications -"no complications" -"without complications" -"complications from diabetes"

When the terms are displayed to the user in the Navigation Panel, the excluded terms will be shown with strikethrough text, to emphasize that they are being excluded from the search. For example:

complications     "no complications"     "without complications"     "complications from diabetes"

It is worth pointing out that an Exclude Terms phrase will only be effective if the excluded phrase contains a term that you are interested in looking for. This feature does not exclude documents that contain the term, it only excludes that phrase when highlighting the term of interest in other contexts found within the document. (You can exclude documents with certain words and phrases using the Boolean NOT operator with an Advanced Terms search).

The Exclude Terms feature only works when conducting a search using the Highlight Documents mode, and not when in the Find Patients mode. In other words, if you are searching across All Patients this feature will be ignored, but it will work if you are using a Temporary Patient List or a Saved Patient List.

Spell checking

EMERSE will check the spelling of terms entered. With Quick Terms this checking occurs after pressing the search button (which is either Highlight Documents for a Patient List or Find Patients with an All Patient Search). After running the search, you can view any potentially misspelled words by going back to the Quick Terms entry page. If anything is found to be misspelled it will be shown under the Terms text entry box in bold, preceded by "Did you mean". For example, if you enter your terms as word misspeling you will see:

Did you mean word misspelling

To correct the spelling you can simply click on the spelling suggestion and the misspelled words will be replaced with the corrected version. Of course, sometimes you may want to search for misspellings, in which case just leave those spelling errors as-is.

Term history

The Quick Terms section keeps a short Term History, containing the last 40-50 searches conducted. This can be access by clicking on the Term History button and the clicking on the desired row in the table. Clicking on the row will fill the Quick Terms entry box with the prior set of search terms, but the search will not occur right way. This is so you can edit the terms further if desired.


Synonyms are a very powerful feature of EMERSE, and are described in detail in a separate section. To access the Synonyms within the Quick Terms section, simply click on any of the terms in the Navigation Panel. This will take you to a page within EMERSE that looks similar to how the Term Bundles are managed. Note that many of the Term Bundle features are not enabled with Quick Terms. Nevertheless, you can access Synonym suggestions from this page and add those Synonyms to your current set of search terms, and you can also remove terms from this page. While you can add Synonym suggestions from this page, you cannot add other new terms here (you can add new terms only in the main Quick Terms text entry box).

It is important to note that in keeping with the way Quick Terms works, all added Synonyms will be assigned a color by the system and they will not be the same color. For more control of these colors, use a Term Bundle. It is also important to consider this when conducting a search, since the colors of the terms can affect what is found, at least for an All Patient Search.

Upload Terms

You can add many terms at once by pasting them into the Upload Terms text entry box. This can be accessed in the same way that Synonyms are accessed. That is, by clicking on any of the terms in the Navigation Panel. Then click on the Add/Upload Terms tab, and then the Upload Terms button. Inside the box that appears simply type or paste in the list of terms or phrases, one term or phrase per line. Then press the Upload button.

Converting Quick Terms to a Term Bundle

A set of search terms within a Quick Terms search can be saved as a Term Bundle, which will allow you to keep and re-use the set of search terms permanently, have more control over the colors assigned to each term, and share it with other users. To perform this conversion, click on any of the terms in the Navigation Panel, and then click on the View Terms tab, and then the Convert to Term Bundle button. You will be asked to provide a Name and Description and then that list of terms will be saved as a Favorite within your list of Term Bundles, which are described in detail below.

Term Bundles

A Term Bundle is a collection of search terms that can provide a lot of power and flexibility with searching. Users can make their own Bundles and they can be shared with others users on the system. Using the same Term Bundle by a team helps ensure reproducibility between team members, and some research groups have even included their Bundles as an Appendix with their peer-reviewed publication. Another useful feature about Bundles is that you have control over the specific color for each term. This means that you can color-code concepts by color. For example you could make all pain medications in green, all side effects in orange, and all diagnoses of interest in blue. This can make it very efficient to identify concepts of interest when rapidly reviewing clinical notes.

Many of the same "rules" that apply to Quick Terms also apply to the Term Bundles. These include the bullet points listed in the beginning of the overall section on Terms (e.g., searches are case-insensitive by default). In addition, you can leverage most of the same features available within the Quick Terms section, including:

  • Double quotes for multi-word phrases

  • Case-sensitive terms

  • Wildcards

  • Exclude Terms (which are entered in a separate column from the Terms to Highlight)

  • Spell Checking

  • Synonyms

Term History is not available within the Term Bundles section.

Term Bundles are grouped into two categories, Favorites and All Available. The Favorites is a smaller subset of all potential Bundles that are available to you, so that you can have a smaller list to work with. Any Bundle that you make yourself will automatically be in your Favorites. Otherwise, to make a Bundle that is not yours into a Favorite simply click on the Favorite checkbox.

Selecting a Term Bundle is simple. Just click on the row in the table with the Bundle of interest, and EMERSE will display the contents of the Bundle. Then, just click on either Highlight Documents when using a Patient List or Find Patients when searching across All Patients.

Making a new term bundle is also very easy—​just click on the New Term Bundle button and give the Bundle a Name and a Description. A few other features of the Bundles are described below.

All Term Bundles have a concept of "ownership". That means that only the "owner" (the person who created the Bundle) can manage it, such as adding/editing terms and choosing how the Bundle should be shared. Others can use it with the right Sharing privileges but they cannot modify it.

Filtering Bundles

If you have trouble finding the right Bundles to use, you can try to use the Filter Bundles feature, which can be found in a small text box above the list of available Bundles. Just start typing what you are looking for and those matching what you type will remain and everything else will be hidden. Filtering looks across the Name, Description and Terms within the Bundle. Filtering does not look through the Owner of the bundle.

Adding New Terms

Adding terms can be done within the Manage Terms tab of a Term Bundle.

Unlike the Quick Terms (where all terms are entered together in a row within a text box), with a Bundle you enter terms or phrases one by one, with each term or phrase within it’s own colorful "bubble".

As you enter the term the system will assign it a color, but you can change the color to one of the 18 possible choices by clicking on the small color palette icon (three overlapping colored circles) and then selecting a different color. You can always change this color later by editing the Term.

Editing Terms

Editing terms can be done within the Manage Terms tab of a Term Bundle. Terms can be edited if you are the owner of the Bundle. If you are not the owner you will not be able to make any changes. To edit an existing term, just click on the term inside of its "bubble" and an editing box should appear. This is also how you would change the color of a term, by choosing the color palette icon to change the color.

Uploading Terms

If you have a large list of terms that you’d like to add into a Bundle, instead of adding them in one-by-one you can add them all at once using the Upload Terms feature. Click on the Upload Terms button which can be found on the Mange Terms tab for a specific Bundle. Then just type or paste in any list of terms or phrases, one per line. EMERSE will assign the colors to the terms, which you can change later (see the "Editing Terms" section in this guide, above).

Removing Terms

To remove a term from a Bundle, go to the Manage Terms tab, click on a term to edit it, and then click on the Remove button next to that term.

You can also remove terms by dragging them to the area between the Terms to include and Terms to exclude areas

If you want to remove all terms from a Bundle at once, click on the Clear/Delete tab and then click on the Clear All Terms from Bundle button. This will remove all of the terms but preserve any sharing preferences that you may have used with the bundle.

Deleting a Term Bundle

To delete a Term Bundle, go to the Clear/Delete tab of the Bundle and then choose the Delete Bundle button. This will completely remove the Bundle, but be careful because there is no undo option once it has been deleted.

Spell Checking

Spell checking of terms can also be done for terms entered in a Bundle. The main difference between spell checking for Term Bundles compared to Quick Terms is that spell checking will be done live, right below the term being entered. To fix the spelling, simply click on the suggested spelling and it will be entered into the term "bubble".

Exclude Terms

General details about how the Exclude Terms work can be found in the Quick Terms section of this guide.

Exclude Terms for Term Bundles are entered differently compared to how they are entered for Quick Terms. For a Bundle, there are two columns of terms that can be entered. The column on the left is for Terms to include, and the column on the right is for Terms to exclude. It is the column on the right where these Exclude Terms should be entered. Additionally, since that section already defines a term as being an Exclude Term a minus sign should not be placed in front of it.

Copying a bundle

If you are not the owner of a Term Bundle but wish to make edits, you can make your own copy and become the "owner" of this new Bundle. To access this feature, click on the View Terms tab of the Bundle and then click on the Copy Term Bundle button. This new Bundle will then be yours to modify and control, but it is important to know that any changes to the original Bundle will no longer be reflected in your new Bundles, as they have essentially been split off from one another. You can also make a copy of your own Bundle if you want to make some changes but leave the original one intact.

Copying a Bundle (even one of your own) only copies the terms but does not copy any sharing preferences that you have set with the original bundle.
When you copy another user’s Bundle, the copied Bundle is available only to you by default.

Sharing Term Bundles

Similar to Patient Lists, Term Bundles can be shared with other users. In fact, to encourage sharing, any new Term Bundle is automatically made publicly available to everyone unless you specifically choose for it to not be, with the exception of Bundles that are copied. To access this Sharing feature click on the Sharing tab. You can make the Bundle private to only you, share it with others on your team (by entering their EMERSE usernames), or make it available to everyone who uses EMERSE.

Advanced Terms

The Advanced Terms feature is meant to be used by "power users" or those who need more flexibility and control in their searches. This feature leverages the underlying core of EMERSE which is Apache Lucene/Solr. Lucene/Solr is a highly regarded, and very powerful, open source search engine which has its own query syntax. In fact, all queries in EMERSE utilize Lucene/Solr but the other two ways to search (Quick Terms and Term Bundles) utilize a simplified approach for searching. With Advanced Terms you can take advantage of the full power of the Lucene/Solr search syntax. Complete details about the Lucene/Solr search syntax can be found on the Lucene Query Parser Syntax page.

It’s important to keep in mind that searches using Advanced Terms are really conducted at the level of a single document. So you if you are looking for two terms that occur together, those terms must exist in the same document. Additionally, since Advanced Search leverages the standard Solr search apparatus, you will not have access to multiple color highlighting or the use of Synonyms from this page. Terms will only be highlighted in yellow.

It is important to point out that Advanced Terms works differently from the Quick Terms and Term Bundles. A query using Quick Terms will be unlikely to give you the same result if you put the same query into Advanced Terms, and vice versa, because they way each functions is different.

Examples of what can be done with Advanced Terms is summarized in the Feature Comparison Table above, and explained in additional detail below.

Boolean searches

Boolean searches use the operators AND, OR, and NOT. They must be capitalized or they will be considered as regular terms. NOT in this context means that a document should not be identified/returned if it contains that term. For example:

chest AND xray NOT abdomen

The query above would identify documents that have the words chest and xray in the same document (anywhere in the document), but if the word abdomen was also in the document it would not be considered a hit even if the first two words (chest and xray) were there.

You can also group booleans together using parentheses, for example:

(chest AND pneumonia AND headache) OR (kidneys AND reflux AND "back pain")

This query will return documents that have the terms chest, pneumonia and headache all together in the same document in any order, or documents that have kidneys, reflux, and back pain all together in the same document in any order.

Boolean operators can only be used as described above with the Advanced Terms feature. The other two search features (Quick Terms and Term Bundles) have a type of implicit Boolean operator assigned to terms based on whether one is searching among a Patient List ( Highlight Documents ) where the OR operator is assumed, or among All Patients ( Find Patients ) where the AND operator is assumed if the colors of the terms different and the OR operator is assumed if the colors of the terms are the same. This is explained in more detail in the section about Search.

Wildcard searches

Two basic types of wildcards are supported (? and *). Wildcards can only be applied to single words, and cannot be applied to phrases.

? is used to match a single character. For example:


Would match words like beam, beat, bear, bean, bead, etc.

* is used to match zero or more characters:


Would match terms like hypertension and hypertensive, as well as just hyperten.

Fuzzy Searches

A fuzzy search allows you to search for terms that are similar to the term of interest. This can be way to look for possible misspellings. A fuzzy search can only be applied to a single word at a time. To use a fuzzy search you append the term of interest with a tilde (~) followed by a number between 0 and 2. These numbers represent the number of potential character substitutions that would have to occur to match the new term.

For example:


Would match beats as well as the word breast, since both of those terms can be created from the word beast by changing just one character. (Note that the original term beast would also be highlighted in this example).

Proximity Searches

A proximity search looks for two words within a certain maximum distance from one another, regardless of their order. Separate the two words by a space and wrap them in double quotes, then add a tilde (~) followed by a number representing the maximum distance in words that they can be separated.

For example:

"ct mass"~10

Would match phrases like …​a CT scan showed a mass in his left…​

as well as …​a 12x12x8 cm mass in her L upper lung found on CT…​.

and even simply mass CT

Regular Expressions

A Regular Expression is powerful way to match text using complex patterns. Regular Expressions are commonly used by computer programmers, and it is expected that only those with a certain level of technical expertise would ever use this feature. The syntax for creating Regular Expressions can be complex and difficult to understand, and can vary between programming languages. To create a Regular Expression with EMERSE follow the guidelines for Java regular expressions.

Regular Expressions within EMERSE can be created for single words/tokens only (not multi-word phrases). Nevertheless, there may not be much advantage to using this featured compared to simple wildcard matching. Wrap the regular expression within a forward slash at the beginning and end to tell the query parse that it is a regular expression. For example,


Would match 100mg, 150mg, 400mg, 650mg, etc.

By default EMERSE will use the case-insensitive index when identifying a regular expression. That means even if you specify a mix of uppercase or lowercase letters, they will all be treated as lowercase for the search. It is possible to specify that the regular expression search is Case-sensitive. Details on how to do this can be found in the section on Case Sensitive Searches, below.

Case Sensitive Searches

By default, all searches using the Advanced Terms feature are case-insensitive. However, it is possible to specify that a term be Case-sensitive using the Advanced Terms feature. This is done by using the case-sensitive index instead. Add RPT_TEXT_NOIC: in front of the term and that term will be searched in a case-sensitive manner that exactly matches the case of the term entered. For example,


Would match ALL but not All or all

You can also use Regular Expressions (see above) with Case-sensitive searches. For example,


Would find either EcG or EkG but not ECG, EKG, ecg, ekg, etc., since the Regular Expression specifies that the first and last letters are upper-case and the middle character is lower-case.

One more example using the the Boolean feature along with a Case-Sensitive search:


This search looks for the case-sensitive SAM as well as the case-insensitive term mitral in the same document. SAM is an acronym for 'systolic anterior motion' which can refer to the mitral valve. The query also excludes documents that contain the case-sensitive Sam which could refer to someone’s name, and excludes the case-insensitive "sam-e" which can be the name of a supplement some people may be taking.

Filtering by Metadata

Metadata are additional pieces of data about a document that can potentially be used to help with searching. Examples of metadata might be the source of the document (e.g. the main EHR, radiology, pathology, etc), the type of test (e.g., MRI report, CT report, plain film report, etc), the clinical service (e.g., nephrology, cardiology, rheumatology, etc) and others. While it is possible to search based on metadata, the specific types of metadata and names of the possible elements will vary from one installation/site to another and will depend completely on how the system was configured locally, what data have been loaded, etc. Therefore, if you are interested in this option you will likely need to contact your local EMERSE administrators to get more information. Below is simply an example of the type of query that could be run if specific metadata elements were captured and stored within EMERSE:


The query above will search for the phrase motor vehicle accident and it will limit the search to a locally named source that is called EHR and a locally named department called ADULT EMERGENCY. As mentioned above, the specific names of sources, departments, and other metdata will be unique to each installation, so it is not possible to provide specific details on what options will be available at each site.

Date Ranges and Date Math

Searches can be limited by date ranges using the Advanced Terms feature. Currently, due to technical constraints for how EMERSE was designed, this date feature can only be used when searching across All Patients using the Find Patients function. It will not work when searching across a Patient List with the Highlight Documents function. At some point the system may be re-designed to allow these Advanced Terms date ranges to be used everywhere.

It is worth pointing out that there may be no real need to use a date range within an Advanced Search query, since a date range can already be applied to any search (even searches using Advanced Terms) by using the Dates button available in the Navigation Panel, in the upper left corner of the screen. However, if using dates in the query is desirable, they should be in the standard Solr date syntax, which can be somewhat complex to use. It is also worth pointing out that if you set a specific date range using the Dates button in the Navigation Panel AND you also set a custom date in your Advanced Terms query, an error will occur and 0 patients will be returned. In other words, if you want to use the date options within an Advanced Terms query, you need to leave the standard EMERSE date fields blank.

A basic example of how a date range can be included in a search is below. This query will search for the term trabeculotomy and it will limit the search to the date range January 20, 2015 through May 20, 2015.

RPT_TEXT:"trabeculotomy" AND RPT_DATE:[2015-01-20T00:00:00Z TO 2015-05-20T23:59:59Z]

The following query is similar to the one above, but shows how some basic date math can be used. In this query the same date is used for both the initial and final dates (2015-01-20), but the second instance of the date is followed by +4MONTHS which essentially adds 4 months to the date, and thus is equivalent to the previously shown query that includes the date range of January 20, 2015 through May 20, 2015.

RPT_TEXT:"trabeculotomy" AND RPT_DATE:[2015-01-20T00:00:00Z TO 2015-01-20T23:59:59Z+4MONTHS]

A few more examples, using the special NOW option are below.

Search for trabeculotomy between January 20, 2015 and the current date:

RPT_TEXT:"trabeculotomy" AND RPT_DATE:[2015-01-20T00:00:00Z TO NOW]

Search for trabeculotomy between 12 months prior to the current date and the current date:


Search for trabeculotomy between 30 days prior to the current date and the current date:


Search for trabeculotomy between 60 days prior to the current date and 30 days prior to the current date:



The Synonyms feature in EMERSE can help you conduct more thorough searches by providing suggestions for additional terms or phrases that are related to the terms you entered. One of the great things about Synonyms is that you have full control over what is included in your search. Synonyms are essentially system-provided suggestions about additional words or phrases that you may want to include in your searches, based on the words/phrases you have already entered. You can incorporate the suggestions into your own search terms, either with the Quick Terms feature or the Term Bundles feature. Because these are system-wide suggestions, these terms are available to all users in the system.

The term Synonym is used loosely here. In fact, these can include many types of related terms that might be useful for a search, outlined in the table below.

Table 4. Examples of the types of Synonyms provided within EMERSE




  • ALL, acute lymphoblastic leukemia

  • ESRD, end stage renal disease

  • CXR, chest x-ray


  • chemotherapy, chemo

  • ventilator, vent

  • shoulder pain, shld pain

Professional and consumer terms

  • myocardial infarction, heart attack

  • alopecia, hair loss

  • emesis, puking


  • ventilator, ventilater ventalator

  • pneumoina, pneuomnia, pneuomonia

  • diarriea, diahhrea, diarhea

Trade and generic drug names

  • Tylenol, acetaminophen

  • Prilosec, omeprazole

  • Zoloft, sertraline

Chemotherapy regimens

  • CHOP, cyclophosphamide, hydroxydaunorubicin, oncovin, prednisone

  • CFAR, cytoxan, fludarabine, alemtuzumab, rituximab

  • FOLFOX, folinic acid, fluorouracil, oxaliplatin

Word stems

  • pain, painful, painfully

  • sleep, sleeping, sleepy

  • test, tested, testing

True synonyms

  • frigid, cold, freezing

  • break, shatter, fracture

  • sandal, shoe, footwear

Phrasing variations

  • lidocaine with epineprhine

  • lido w/ epi

  • epi-lidocaine

Accessing the Synonyms feature is easy. In Quick Terms, simply click on the list of terms already entered that are highlighted in various colors in the Navigation Panel. After clicking on the term(s) you will reach another screen where each term/phrase will be shown in a colored bubble. If a synonym exists for that term, a Synonyms button will appear in the bubble. The Synonyms for a Term Bundle can be accessed in the same manner. In addition, for Term Bundles the Synonyms can be reached by selecting the bundle, and then clicking on the Manage Terms tab. Once the Synonyms button is clicked, a small pop-up window appears that displays the terms in three categories.

  1. Synonyms: These are the "standard" synonyms suggestions

  2. Related Terms: These are terms related to the synonyms but considered different enough from the original term that it should not be included in the former category. For example, a Related Term of acalabrutinib is mantle cell lymphoma since acalabrutinib is meant to treat mantle cell lymphona. The two terms are related, but not really the same. Sometimes, however, other related terms may seem more related but were placed in that category to prevent too many matches from being displayed for an initial term that was very generic.

  3. Spelling Alternatives: These are generally misspellings of the terms of interest. They are not always actually misspelled words, as these can include correctly spelled words that are not the right ones. For example beast instead of breast.

In the Synonyms pop-up window each term will be highlighted with the same color as the original term that prompted the Synonym suggestion. If the term is highlighted it means that it is already selected and ready to be added into the list of search terms to be used. It is possible to click on each individual term to highlight or de-highlight the term for inclusion (highlighted) or exclusion (not highlighted). Or, one can use the provided buttons to Highlight All or De-Highlight All. For example, if a large list of terms is provided but you only want to include a single suggestion, first click on the De-Highlight All button, and then click on the single term of interest to highlight it. Once the selection is complete, click on the Add Highlighted Terms button to add those selected (highlighted) terms.

If Synonyms are used within Quick Terms, the added terms are assigned random colors, and there is no control over what colors the terms will be. If Synonyms are used with a Term Bundle, then all of the added terms will be assigned the same color as the original term that displayed the Synonyms button. These colors can be changed later if desired.

The ability to control the colors of the added Synonyms (Term Bundle) versus no control over the colors (Quick Terms) has important implications when conducting an All Patient search using the Find Patients search mode, since the colors of the terms are used to define how the search is conducted (Details can be found in the section on Searching). When conducting a search across a Patient List the colors of the terms should not affect how the highlighting occurs within the documents.

Once additional terms are added via the Synonyms feature, it may be worth checking if those newly added terms also have Synonym suggestions. For example, if the word fruit is originally entered by a user, then the Synonyms feature might suggest apple as an additional term. Once apple is added, then apple cider might be suggested, and so on. Note that if a term/phrase is already included in your list of Quick Terms or the Term Bundle you are working with, then the Synonyms feature will not suggest those terms since they have already been included. Only new terms will be provided as suggestions.

Users are not able to add new terms to the system-provided Synonym suggestions, but users are always free to add as many terms as needed to their own Quick Terms or Term Bundles. Only system administrators can add additional terms to the system-wide Synonym suggestions, so please contact your local EMERSE system administrator for terms that you think are missing but should be included.

It is also worth noting that other datasets can be imported into EMERSE that can add to the list of available Synonym suggestions. Examples of such datasets can be found here, and directions for formatting a Synonyms dataset for importing into EMERSE can be found in our Administrator Guide.


Searching is really the core of what EMERSE does. But conducting an effective search can be complex and depends on more than just the search terms used. EMERSE provides two basic types of searching modes which are, in turn, dependent on the scope of the population that will be searched.

Searching in EMERSE is an action invoked by clicking a button either called Find Patients or Highlight Documents (which will change depending on the Search Mode, described below). These buttons are available from the Terms screens. However a search cannot be carried out until parameters have been set, including:

  1. The patients to be searched through (All Patients or a Patient List)

  2. The date range (Note that if no specific date range is defined, the system will default to the full date range of all documents in the system).

  3. The Terms.

Find Patients Search Mode

The Find Patients search mode is used when searching across All Patients. It’s the equivalent of trying to identify a cohort based on search terms, and it is the search mode you would use when you want to identify patients of interest from among all of the patients in the system.

Data displayed with the Find Patients mode

When in the Find Patients mode, EMERSE will provide results including:

  1. Patient count: Total number of patients found in the system meeting the criteria

  2. Demographics summary: Charts showing the demographic breakdown of the patients, including their current age.

  3. Text snippets: Brief Text Snippets from the 100 top-ranked documents. This is to provide some context for what was found to help ensure that the search retrieved what you were looking for.

If you are satisfied with the search results, you can then explore the list of patients in more detail, or save the list for later use by clicking on the button Move patients to Temporary Patient List. Note that to actually save the list for later use you would then need to click on the Convert to Saved Patient List button after converting it to a Temporary Patient List. Once the patients have been moved to a Temporary Patient List, you can also search through their documents using the Highlight Documents button, because at this point you have switched from the Find Patients mode to the Highlight Documents mode by selecting a subset of patients in the system to look through.

Searching with the Find Patients mode

Perhaps the most important aspect of the Find Patients mode is how the search is conducted to identify the patients. This is described below.

Using the Find Patients mode, with either Quick Terms or a Term Bundle:

  • Terms that are the same color are searched using the OR operator.

  • Terms are that are different colors are searched using the AND operator.

  • A patient will be identified if the search query matches at least one document for that patient, and searches are done on a per-document basis. That is, if one is searching for heart "chest pain", then the query is translated behind the scenes to find all patients who have a document that contains heart AND chest pain in the same document. Alternatively, if one searches for heart "chest pain" then the query is translated behind the scenes to heart OR "chest pain". In this second case, any patient will be retrieved if they have at least one document that contains either the term heart or the term chest pain. The document would not have to contain both.

Using the Find Patients mode, with Advanced Terms:

  • Terms separated by a space are searched using the OR operator, unless actual Boolean operators are included, and Advanced Terms supports the inclusion of Booleans.

  • Only one color (yellow) is used with Advanced Terms to highlight, so there is no distinction made using colors.

Search Strategies with the Find Patients Mode

Because of how searches are conducted, and how patients are identified, in the Find Patients mode, it is best to use a Term Bundle when using multiple terms, and to ensure that true synonyms for a concept are highlighted in the same color. Using Quick Terms may result in no patients being found when multiple terms are being used since Quick Terms assigns different colors to each term and, as a result, the system would be looking for patients that have all of the distinct terms in a single document. With a Term Bundle you have full control over the colors that the terms are highlighted in, so it is much easier to form a more complex/broad query with multiple terms.

Additionally, be careful about adding too many terms, especially if a term is a different color from the others, since it means that the additional term must also be in the document for the document to be retrieved. Adding an extraneous term that isn’t very important for identifying the right patient population has the potential to result in no patients being found. For example, if the following query is used, the query will only find patients that have at least one document with all three of those terms in the same document:

heart chest pain chest tightness

Thus, it is better to use only those terms that are absolutely necessary to find the right patients, or to use a Term Bundle and set the color of the terms more strategically, such as:

heart chest pain chest tightness

In this case, the above query will look for documents that contain heart AND either chest pain or chest tightness, but chest pain and chest tightness do not have to both be present, only one of them.

Highlight Documents Search Mode

The Highlight Documents search mode is used when searching across a known set of patients, using either a Temporary Patient List or a Saved Patient List. This mode is equivalent to a chart review where you want to highlight all of the terms of interest, because you already know what patients you are interested in looking through.

Data displayed with the Highlight Documents mode

When in the Highlight Documents mode, EMERSE will provide results including:

  1. Overview: The Overview is a table where every patient is shown in a row and the document sources are shown in the columns. This Overview provides a high level view of what was found for each patient, with each cell providing specifics about what was found on a per-patient, per-document source basis. There are several viewing options for the Overview table.

    1. Numbers: Numbers are displayed in cells that have search "hits". (In search jargon, a "hit" means that the search query matched a document in the system). The numbers represent the total number of documents with at least one hit and the total number of documents for that specific patient and document source. For example, if a cell says "21 of 92" it means that the patient has 21 documents containing a search hit out of a total of 92 documents for that source. Cells that are blank have no hits. Clicking on the Numbers icon will toggle between showing the numbers for cells that have hits and numbers for all of the cells, even those that do not have a hit. This can be useful if you are interested in knowing if a patient has any documents for a specific source, even if there are no hits for that source. For example, a cell might say "0 of 12" or even "0 of 0".

    2. Grayscale: The Grayscale option will shade a cell in a gray color, with darker colors representing more documents with a hit. This provides a rapid visual overview similar to a "heat map" which is commonly used in some disciplines. Darker shades may help point out areas in which to focus, since they have more documents and thus more mentions of the terms of interest. The general rule of thumb is that cells with no hits are white, cells with 1-5 document hits are a light gray, 6-10 hits a slightly darker gray, and so on. The Grayscale option can be toggle on or off by clicking on the icon, and it can be used in conjunction with the Numbers option and the Mosaic Option, described below.

    3. Mosaic: The Mosaic option provides another way to view the data at a high level. It displays a color-coded grid representing the terms found for each patient based on document source, where the colors are shown in specific locations within a 6 x 3 grid (because there are 18 possible colors for terms). Each color corresponds to the color of a term as it is displayed in the Navigation Panel.

  2. Summaries: Clicking on a specific cell on the Overview page will take you to a drill-down view of all documents for that specific user and document source. This is known as the Summaries page, since it displays the high level summaries, or text snippets, of what was found based on the search. Each row in the Summaries view represents a document for that patient. By default these documents are sorted in reverse chronological order, with the most recent documents on top, but the table is sortable in both directions by clicking on the header column of interest. A row that is blank means that there were no hits for that document, whereas a row that is not blank will show a snippet, or Summary, of what was found for that document with the search terms of interest. This allows for rapidly skimming the notes at a high level to see if it is worth drilling down further to open the actual note for more details.

  3. Documents: Clicking on a specific row on the Summaries page will take you to a drill-down view of the actual document. The entire document will be shown, with the terms of interest highlighted in the document. Above the document two smaller tables are shown. One is a table of metadata, which is information about the document. This information might include a unique document ID, the clinical service, the authoring clinician, etc. but it will different depending the local configuration of EMERSE. The other table shows the Summaries for that document, with the terms highlighted within a short snippet of text. This is to provide another way to quickly skim the results for anything of interest. It is also worth noting that clicking on any of the highlighted terms in this table will take you to that specific place in the document, which is basically a hidden shortcut. The Documents page has variation navigation options to skip to the next document, or next patient, or even to print the document if permitted. There is no way to save the document—​however, it can always be accessed again at a later time by going back to EMERSE.

Searching with the Highlight Documents mode

The Highlight Documents mode is simpler than the Find Patients mode. This is because all terms are treated as being separated by the OR operator, regardless of the color in which the terms are highlighted (unless otherwise specified using actual Boolean operators with the Advanced Terms). The general idea is that since the patients of interest have already been identified, the goal with Highlight Documents is to simply highlight any terms of interest anywhere in the documents to support a rapid, efficient chart review process. As a result, there is no harm in including additional terms even if they are not present anywhere in the documents, since their absensce will not affect the highlighting of the other terms.

Search Strategies with the Highlight Documents Mode

In general, no specific search strategies are needed when searching in the Highlight Documents mode. Even so, it may still be advantageous to use a Term Bundle to group terms with similar meaning by the same color to aid in more rapid chart reviews. In other words, if you are searching for a list of narcotic medications and the resulting constipation that they might cause, it may be useful to set all of the narcotic medications to be green, all of the constipation terms to be orange, and all of the stool softeners/laxatives to be purple. Then, someone reviewing the charts would only have to recognize one of three colors to know what kind of concept was being highlighted.

Some elements with the Advanced Terms will not work properly when in the Highlight Documents mode, and these limitations are detailed in the section on Advanced Terms.

Additional Search Strategies

In addition to the two general search strategies described above (Search Strategies with the Find Patients Mode and Search Strategies with the Highlight Documents Mode), there are other tips that are worth noting to ensure that you get the results you’re looking for.

Understand the differences between the two search modes

This is described elsewhere, but it is extremely important to understand the differences between the two search modes, Find Patients and Highlight Documents. The way EMERSE works differs depending on which search mode is being used, and therefore this difference must be understood to ensure effective search results.

Use the synonyms

EMERSE can provide a lot of suggestions for additional terms through the Synoyms feature. Use this to expand your search to cover more possibilities for how something was worded or phrased in the notes. Also be careful because EMERSE is a very literal search engine. If you want to look for antibiotics and that is what you type in, the system will look for the word antibiotics only. If what you really meant was to find any instance of any antibiotic mentioned in the notes, then you will have to include all of the possible terms for these, and there may be hundreds of them (e.g., cephalexin, Keflex, Ancef, Ciprodex, amoxicillin, etc). The Synonyms feature can certainly help expand the breadth of the query terms, but it may not be complete.

While the Synonyms can be very useful and powerful, be careful about what Synonym suggestions you add. EMERSE has the potential to provide a very large list of options, but adding too many terms could slow things down without providing much benefit. And, for ambiguous terms, you might inadvertently include concepts you don’t even want. For example, if you are searching for synonyms of MI because you want to look for terms related to myocardial infarction, EMERSE will also suggest terms like Michigan since that is also a different meaning of MI.

Break up the query

Similar to trying multiple variations, be careful about how specific the query is. For example, if you enter "metastatic breast cancer", then the system will look for that specific phrase. It might be better to look for the phrase metastatic and the phrase "breast cancer" separately, so that you have a greater chance of finding other variations such as:

the breast cancer was found to be metastatic to the lungs

Note, however, that sometimes breaking up the query can lead to false positives if, for example there was text such as:

history of breast cancer as well as melanoma metastatic to the brain

Another approach for 'separating' the terms is to use the Proximity Search feature within the Advanced Terms section. This will allow you to search for two terms within a specified number of words from each other. For example, suppose you were looking for "sublingual nitroglycerin". A logical alternative phrase would also be "nitroglycerin sublingually". But if the phrase in the clinical note is actually "nitroglycerin was given sublingually" then the simpler, shorter phrase would miss it. Including a Proximity Search parameter like "nitroglycerin sublingually"~5 would capture the longer phrase, since it will look for the words nitroglycerin and sublingually within 5 words of each other. Example:

Search Term: "nitroglycerin sublingually"

The patient was given nitroglycerin sublingually upon arrival to the ED.

The nitroglycerin was given sublingually upon arrival to the ED.

Search Term: "nitroglycerin sublingually"~5

The patient was given nitroglycerin sublingually upon arrival to the ED.

The nitroglycerin was given sublingually upon arrival to the ED.

But similar to the prior example with breast cancer and metastatic, there are risks of false positives when the terms are more separated. There will likely be a tradeoff between how far apart you may allow the terms to be, and how likely there may be a false positive as a result. With a proximity distance set too small, you may also miss some terms, resulting in false negatives. Example:

Search Term: "nitroglycerin sublingually"~5

The nitroglycerin was given sublingually upon arrival to the ED.

The nitroglycerin was rapidly given to Mr. Jones-Smith sublingually upon arrival to the ED.

Beware of implicit concepts

A concept that you’re looking for may be implicitly described but not explicitly stated. An example of this would be looking for the concept of metastatic as it relates to breast cancer. If the phrase is…​

the breast cancer was also found in her lungs

…​this implies that the cancer was metastatic even though the term metastatic or its variants (metastasized, mets, etc.) was not explicitly mentioned. EMERSE, being a simple tool, is not able to interpret that phrase as being an example of a metastatic breast cancer.

Another example:

He had a raised, red patch on his arm that he didn’t even notice.

This is an example of an asymptomatic rash, even though neither of those two words (neither asymptomatic nor rash) appears in the sentence above. This can happen often, so it is important to be careful of what might be missed when only searching for specific phrases or concepts.

Beware of ambiguous terms

There are hundreds of terms that are used in the clinical notes that are ambiguous—​that is, it is hard to know what a term represents without understanding the context in which it appears, and some terms/abbreviations may have been completely made up locally by a single clinician or a small group of clinicians.

For example, diffs might mean differentials, or differences, or difficulties or even be a part of an abbreviation for Clostridium difficiles (C diffs).

Other common ambiguous abbreviations include CA which can mean cancer, calcium, or California, and MG could mean milligrams, myasthenia gravis, or magnesium.

Even terms that one might think are straightforward might not be. For example, imagine you are interested in exploring milk consumption to assess dairy intake, so you search for milk. Be careful because there can be terms like almond milk, carob milk, soy milk, rice milk, and others which are clearly not the right kind of milk. This is why reviewing the results carefully is very important.

Try multiple variations

You may be tempted to use the most standard, common phrasing for a particular concept, but it is best to consider all of the ways in which something might be phrased. Clinicians will sometimes even make up new terms. For example, scaphotrapeziotrapezoidal may be the official spelling, but clinicians have also used terms such as scaphotrapeziumtrapezoid, scapho-trapezoid-trapezium, and scaphoid-trapezium-trapezoidal. Clinical note creators also add hyphens or spaces (these are equivalent in EMERSE) into words where they might not be expected, as can be seen in the above examples, or even simple words like ham burger or yester-day. The system-suggested Synonyms can help capture this variability lot, but they may not be enough to cover all of the possibilities forwhat is mentioned in the notes.

Beware of word substitutions

Remember that the people who create clinical notes often have a difficult time spelling medical words, they make errors when they type, automated transcription systems can "hear" the wrong word, etc. For example, beast mass and prostrate cancer are phrases that contain correctly spelled words, but they are not the right words. In fact, many such word substitutions of correctly spelled (but incorrectly used) words appear. Often these are homonyms, but not always. Think carefully about how someone (or a computer) might hear a word and insert the wrong word. If you’re looking for people with a hoarse voice, be sure to search for horse voice because it’s almost guaranteed that someone will have used the wrong word at least once.

Following is a table containing examples of such word substitutions that have been found int he medical record. It is by no means complete.

Table 5. Examples of incorrect words used in clinical notes

Wrong Word (the word that was used in the note)

Correct Word (what the word was supposed to be)





























Understand the limitations of EMERSE

This has already been described in the section on Terms, but it is worth pointing out again. EMERSE ignores multiple characters such as ! ? . > < + - #. This means that some searches will not work. For example: BRCA1- will be interpreted by EMERSE as simply BRCA1, which means that although you can still search for BRCA1 you cannot distinguish between BRCA1- and BRCA1+. (If the phrase is "BRCA1 negative", or a similar variation, then EMERSE will be able to find the concept. Similarly, "150 pounds" when written as "150 #" or 150 # will simply be interpreted as 150 and a blood pressure written in the form of 120/90 will be interpreted the same as 120 90, meaning that you cannot use the slash symbol (/) as a way to look for a pattern that appears to be a blood pressure.

Understand the limitations of search in general

A search engine like EMERSE is great for finding concepts quickly, but it does not have any understanding of what it found, or the context in which a term was found. That is why it is important to carefully review the results for accuracy. Even in cases where you might think no error is possible, it just might be possible. The following is a real example of what was found in a clinical note:

A search for mesenteric polyarterisis nodosa should also include the abbreviation for polyarterisis nodosa which is PAN. Thus, an additional search term should be mesenteric PAN. By default EMERSE searches in a case-insensitive manner, so it will identify polyarteris pan as a 'hit'. However, the actual phrase highlighted was mesenteric pan niculitis. which is not the intended concept. In this case, an inadvertent space had been added into the word panniculitiis.

Similarly, terms like ular could represent a misspelling of the word ulnar or part of a word that had an inadvertent space such as ventric ular or fib ular.

Another example:

Suppose you are searching for lupus, so you include the abbreviation SLE which is a common abbreviation for systemic lupus erythematosus. The system will higlight something like:


In this case, it looks like there are two common medical abbreviations: [1] FE (iron), and [2] SLE (systemic lupus erythematosus). However, upon careful inspection, neither of those two abbreviation are correct. In fact, the word should have been FEMALE, but the person who typed the word accidentally shifted two of the letters to the right on the keyboard (, is directly to the right of m and s is directly to the right of a on a keyboard). Thus, what looks like two clinical concepts is really just the term female.

As a general rule of thumb, if you have found what you were looking for, and have verified that it is truly the correct concept then consider that to be a success. If you haven’t found what you were looking for, the concept may not be there at all, or it may be that you just haven’t figure out the unusual, or incorrect, way in which a term or concept was phrased.

Consult clinical experts

If possible, talk to someone who has clinical expertise in the area for which you are conducting your searches. They might be able to provide guidance about how certain concepts are likely to be phrased in the clinical notes.

Use the minimum necessary terms, sometimes

Queries that are too long or specific will generally not work well. For example, if you are looking for a positive depression screen based on a PHQ-9 test, do not search for "positive depression screen based on a PHQ-9 test". Instead it might be better to search for PHQ-9 since that alone will help narrow down the results because it is already very specific. This could perhaps be combined with terms such as positive to help narrow down the results.

With more general terms you may need to add more terms to help narrow the results. For example, if you are looking for type 1 diabetes and you just search for the word diabetes you will end up with far too many irrelevant hits because you will most likely be finding diabetes related to type 2 diabetes since it is much more common.

In other words, you will need to come up with a rational strategy for how to construct your search queries with search terms, and this will usually be very customized to your specific task.

Indeed, there may be times when using longer and more specific phrases can be useful. An example of this might be to look for wording used in a specific note template or report template, which can be useful when trying to identify specific notes needed for data abstraction. In such a situation, the specific text surround a concept of interest may be needed to narrow down the results to the desired one. The example below identifies very specific language used in a test result reported by the Mayo Clinic Medical Laboratories. Searching for this very specific language, which does not appear to vary between reports, helps to identify the actual lab report and not the mention of HIV-1 elsewhere in the notes.

This test was performed using the Abbott RealTime HIV-1 Qualitative assay (Abbott Molecular, Inc., Des Plaines, IL). This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

Search in stages

Sometimes it may not be an effective strategy to find your patients of interest with a single query. It may require several queries. For example, you may want to first identify your patient population using the Find Patients search mode just by searching for a rare disease. Once you have identified those potential patients, you can move them to a Patient List and then search them for more details (for medications, side effects, etc.) in a subsequent query using the Highlight Documents search mode.

Another example: Imagine you want to find a set of patients who have fibromyalgia and back pain but your query with the Find Patients mode returns almost none. This may be because with Find Patients the system is looking for documents that have the terms fibromyalgia and back pain in the same document. But what if the patients have these terms mentioned in different documents? One solution, among several, would be to first conduct a search for fibromyalgia using Find Patients and then saving the result as a Saved Patient List. Then conduct another, separate search for back pain using Find Patients, and saving this result as a Saved Patient List. Then, use the Merge Patients feature and select the patients that belong to both lists. The resulting set of patients would be ones that contain the terms fibromyalgia and back pain, but not necessarily within the same document. This smaller subset of patients could then be saved as a new list and searched further using the Highlight Documents feature.

Use multiple data resources

EMERSE was designed to work with unstructured, free text data. These clinical documents can be extremely valuable for finding the needed information, much of which might not be present anywhere else in the medical record. However, there are times when using structured data makes sense. For example, if you want to find all patients with a hemoglobin less than 6, you can’t type that into EMERSE and expect to get any sensibile results. It would be better to use a separate system designed for structured data (e.g., DataDirect at the University of Michigan, or the widely used i2b2 Workbench). It may also make sense to use structured data such as ICD-9 or ICD-10 billing codes as a first pass attempt to narrow down a patient cohort, and then search that subset of patients within EMERSE to do additional verifications within the clinical notes.

A patient list generated from a different system can be imported into EMERSE, or one can simply copy and paste a column of medical record numbers from an Excel sheet containing a list of patients generated in a different system. EMERSE also provides the technical capabilities for importing a list directly from another software system, but this functionality will depend on how it has been locally installed, configured, and connected to other systems.

It is best to think of EMERSE as being one tool among many in a toolbox of useful software to support your work. It is unlikely that any single tool will enable you to complete your task, but using multiple tools together will help you efficiently get your work done.

Plan your data entry with data extraction/search in mind

While this may not often be possible, if you have any control over how data are initially entered into the electronic health record, you can use strategies to help identify the note or concept later when searching. One example is to use standardized phrases that can be used in search later on that will positively identify only the notes of interest. Also, using more standardized language helps with ensuring that no unusual variations in wording are missed with the search.

Give thought to how you might want to identify and abstract data later on. It may be useful, for example, to include a unique "note identifier" in a note template, so that searching for just that identifier will identify all of the notes of interest. You can use something distinctive like stntv25; it can even be simple phrases like Strep throat note template version 2.5, as long as it is unique to that set of notes.

The Food and Drug Administration (FDA) has enabled just this type of searching with drug biosimilars. These drugs are required to have a generic name appended by a "distinguishing suffix that is devoid of meaning and composed of four lowercase letters" (Reference: Nonproprietary Naming of Biological Products). Examples include: emicizumab-kxwh, vestronidase alfa-vjbk, filgastrim-vkzt, filgastrim-sndz. Thus, searching for even the 4 letter suffix (kxwh, vjbk, vkzt, sndz) should positively identify the drug in most cases.

Be creative

Sometimes it helps to think 'outside the box' when conducting searches. For example, you may be interested in identifying patients based on structured ICD-10 codes. If your clinical notes contain such codes within the text of the document, they can be searched just like searching for any other word or phrase. If you’re interested in finding Ehlers-Danlos syndrome, which has an ICD-10 code of Q79.6, just search for that term and it will find any mention of that code in the notes. The main thing that you cannot do, as already mentioned above, is search for numeric data using comparitors such as greater than (>), less than (<) or equal to (=).

Solr API

This section is meant for highly technical groups who have a programmer/developer on the team.

An application programming interface (API) is available to teams needing to access the underlying EMERSE data store. This is based on the underlying Apache Solr infrastructure. This might be useful for groups wanting to utilize the very fast data retrieval mechanisms of Solr, but want to be able to retrieve the documents outside the constraints of the user interface so that additional processing/text mining can be done.

Details about utilizing this API can be found in the Solr documentation section on Client APIs.

The API access point should be locked down and secured by your IT Administrators, and you will need to be provisioned with a username/password for access.

A simple way to leverage the API is to use curl which is a tool available with almost any programming language. Using curl you can form an HTML query, with the results returned in JSON or XML format. Depending on how the query is formed, you can get back the medical record numbers (MRN), document metadata, or even the contents of the document itself. Remember that if the clinical document is in native HTML format, you may need to have a further cleanup process (e.g., strip HTML tags) to make the document usable for your projects.

Note that there is no way to access the EMERSE resources such as Synonym suggestions when using the Solr API.

Frequently Asked Questions

Can I export the data?

No. EMERSE was not designed for data export. It was designed to keep the data centralized and secure, but allow for easy access. If you need to download the data, consider using the Solr API.

You can, however, Export patient lists with the associated Comments and Tags if they were added. Access to the Export feature will depend on your specific privileges within the EMERSE system.

I can’t get into EMERSE, what am I doing wrong?

There are multiple reasons why you may be having trouble getting into the EMERSE application. A few are outlined below.

You haven’t been granted access

Or your access has been revoked. EMERSE contains patient data, so it is not the kind of system you can just log onto without someone providing an account. Talk to your system administrators if you think that is the issue.

You are not on the right network

If you can’t even see the login page (because the page is not found), this may be the reason you’re having trouble. In general, EMERSE will be available on a secured network available only to individuals on that internal, trusted network. There may be ways to get to this network from the outside using virtual private network (VPN) software. This is an issue to bring up to your local IT support teams.