Treatment queries are under the Query tab in Cleo’s Explore application; see Figure 1. Creating a Treatment query is a two step process. First the contents of the treatment table are selected. Then, the treatment table is filtered.

Figure 1
Queries Tab in Cleo’s Explore Application

Queries tab in Colabrativ’s Clinical Entry and Operations (Cleo) Explore application before the creation of any treatment tables, or any queries have been run.

Selecting Treatments Table Content

Treatments in the treatments tables are grouped by patient, and chronologically ordered by the start date of each treatment. There are a number of options that control the contents of a treatments table; each option is reviewed below.

Treatment Table Options

Option	Description
Treatments Included	Single Treatment adds a single treatment to each row in the treatments table, and is the default for the Treatments Included option. The Treatment and Post-treatment option adds both a treatment and the next treatment (post-treatment) to each row of the treatments table. If the treatment is the last treatment and if a Deceased or Last Contact or Lost to Follow Up event is after the last treatment, then the Deceased or Last Contact or Lost to Follow Up event is added as the post-treatment. The Pre-treatment to Post-treatment option adds three treatments to each row in the treatment table. As with the Treatment and Post-treatment option above, Deceased or Last Contact or Lost to Follow Up events can be the final “post-treatment” for a patient. The All Treatment option puts all of a patient’s treatments in a single row. As with the Treatment and Post-treatment and Pre-treatment to Post-treatment options above, Deceased, Last Contact or Lost to Follow Up events can be the final “post-treatment” for a patient.
There are five therapy types that can be included in a treatments table.
Include Chemotherapies	If checked, chemoetherapy events will be included in the treatments table.
Include Complementary Therapies	If checked, complementary therapy events will be included in the treatments table, such as treatments with Curcumin.
Hormone Therapies	If checked, hormone therapy events will be included in the treatments table, such as treatments with Tamoxifen.
Include Immunotherapies	If checked, immunotherapy events will be included in the treatments table.
Include Vaccines	If checked, vaccine events will be included in the treatments table, such as MUC1 Dendritic Cell Vaccine treatments.
The next four Include options add additional information to the treatment table, including the patient’s immunohistochemistry (IHC) and genetic results.
Include Agent 0 1 Columns	If checked, agent columns will be added to the treatments table. Each treatment agent in a treatment will have a 1 in the column labeled with that agent’s name. This option was designed to facilitate cluster analysis.
Include IHC Results	If checked, the H-score for each IHC test run on the patient’s specimen collected just prior to the treatment. e.g. pretreatment specimen, will be added to a column that uses the IHC test code as the column header.
Include Full IHC Results	If checked, the intensity, percent positive cells and H-score for each IHC test run on the patient’s pretreatment specimen will be added to the columns that use the IHC test code as prefix for the column header.
Include Genetic Results	If checked, the results for each genetic test, such as polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH) or next generation sequencing run on the patient’s pretreatment specimen will be added to a column that uses the test code as the column header.
There are a number of situations in which one might not want to include the next treatment in a table. The next five options allow one to merge a number of difference treatment types into the treatment added to the treatments table.
Merge Neoadjuvant Treatments	If checked, neoadjuvant treatments will be merged with the following treatment. The start date of the neoadjuvent treatment will be used as the start for the merged treatment, if it is before the start of the treatment. A Neo flag will be added to the Flag column when a neoadjuvent merge is performed.
Merge HIPEC Treatments	If checked, Heated Intraperitoneal Chemoperfusion (HIPEC) treatments will be merged with the following treatment. The start date of the HIPEC treatment will be used as the start for the merged treatment, if it is before the start of the treatment. A HIPEC flag will be added to the Flag column when a HIPEC merge is performed.
Merge Maintenance Treatments	If checked, maintenance treatments will be merged with the previous treatment. The end date of the maintenance treatment will be used as the end date for the merged treatment, if it is after the end date of the treatment. A Main flag is be added to the Flag column when a maintenance merge is performed.
Merge Continuation Treatments	If checked, continuation treatments will be merged with the previous treatment. The end date of the continuation treatment will be used as the end date for the merged treatment, if it is after the end date of the treatment. A Cont flag is be added to the Flag column when a continuation merge is performed.
Simultaneous Treatments	If checked, treatments that overlap in time, but are of different treatment event types, e.g. a chemotherapy and a hormone therapy, will be treated as simultaneous. The agents in the simultaneous treatment will be added to an inserted Simultaneous Agents column.

Treatments Table Creation

Once treatments table options have been selected, the table can be created without applying any filtering to it by clicking on the “Create” button; see Figure 2. This is the only action that can be taken for the “All Treatment” Treatments Option. The treatments table creation options are disabled after a treatments table has been created, but the options used to create the treatments table are still displayed.

Prior to the creating the treatments table it is a good idea to supply a title in the “Query Title” box. The title may also be added after creating the table by filling in the “Query Title” box and clicking the “Update Title” button.

Once the treatments table has been created, it can be downloaded as a tab separated values (TSV) table by clicking on the green link. For the All Treatments table in Figure 2, the link is PatientTherapies_2013-11-29_09-45-05.tsv.

Figure 2
Queries Tab in Cleo’s After Creating an All Treatments Table

The Queries tab in Colabrativ’s Clinical Entry and Operations (Cleo) application after creating an All Treatments table. The treatments table creation options have been disabled, but still display the options that were selected when creating the treatments table, PatientTherapies_2013-11-29_09-45-05.tsv.

Filtering the Treatments Table

Filters are applied to a treatments table by selecting a filter from the “Select Filter” pull-down menu. There are a number of filters that can be applied to a treatments table. Each filter is shown below.

Treatment Table Filters

Once an agent name has been entered in the Chemotherapy Agents box, a new box will be created for an additional agent name. If the wild-card (*) is added as an agent then the filter will not remove treatment rows that match the agents supplied, but table row may have additional agents. Without a wildcard, the number of agents must match the number of agents supplied in the filter.

After setting up the desired filters for treatments table click on the “Run Query” button. The filtering will be applied to a preexisting treatments table, or a new treatments table will be created from the treatments table options which have been selected. The starting treatments table can be downloaded using the green link supplied for it. See Figure 3, in which the start treatment table link is Treatments_2013-11-28_11-08-16.tsv. The number of patients, specimens and treatments are provided for before and after the filtering. The filtered table can also be downloaded using the green link supplied for it. See again Figure 3, in which the query results table link is Query_2013-11-28_11-08-16.tsv.

Figure 3
Queries Tab in Cleo’s After Filtering Treatments Table

The Queries Builder after using a specimen type filter of O and P on a treatments table. The treatments tables created before and after filtering are Treatments_2013-11-28_11-08-16.tsv, and Query_2013-11-28_11-08-16.tsv, respectively.

Multiple filters can be run at the same time by simply selecting another filter from the “Select Filter” pull-down menu. After a Query has been run, additional filtering can be performed. For example, one might want to first filter on Cancer Codes and then Patient Histologies initially, and then to use the resulting filtered treatments table as the starting table for several treatment agents filterings.

Select Query

Just below the Query Builder banner is the “Select Query” pull-down menu (see Figure 3). All of the queries that have been run are displayed in this pull-down menu with their time-stamps plus their queries titles. To clear the query, an empty query can be selected from the “Select Query” pull-down menu. When a query is selected, the Query Builder panel will be cleared and replaced with the selected query’s information.

 

iExperiment electronic notebook search user interface showing a carboxypeptidase purification example.

iExperiment’s new search interface is shown above. Like all search interfaces, ours has a query box and a submit query button. You can search specific fields in your experiment results. The specific fields are provided for you in the Add Field pull-down menu. In the example above, a general search is being performed on “carboxypeptidase” and a specific search on “purification” in the category “technique”. For your convenience a “Clear Query” button is provided to begin new searches. Each result contains the title and authors of the experiments found in the search, along with text fragments highlighting the search words. The record title is linked to the full record.

Search Fields are arranged in a hierarchical manner. The basis for the hierarchy is as follows:

 
The top portion of the Add Field pull down menu.

Meta Data:

• title, authors, institutions, last modified, projects,
• state, and categories

Sections:

• purpose, introduction, plan, methods, results,
• summary, and conclusions

Materials:

• animals, strain, species, consumables, lot number,
• expiration date, equipment, serial number,
• reagents, formula, pH, samples, part number,
• suppliers names, address and URL

Content:

• attachment, figure, file name, caption, sample set,
• and data category

Search Tips: The Lucene query parser syntax used in iExperiment’s search function is summarized in the table below.

Qurey Type	Example	Discussion
Single Term	protein	For a single term like “protein”, the program will be searched for the word “protein” in all of the records the user has permission to view.
Single Character Wildcard	te?t	The single character wildcard is a question mark (?). Our example “te?t” will match both “test” or “text”. A wildcard cannot be the first character of a search term. If you do place a wildcard at the beginning of a word, you will receive a message reminding you about this limitation.
Multiple Character Wildcard	carbo*	The multiple character wildcard is an asterisk (*). Our example “carbo*” will match “carbon”, “carbonic”, “carbonyl”, and many other similar words.
Fuzzy Searches	carbo~	Lucene fuzzy search uses the tilde character (~). Our example “carbo~” will match both “carbon” and “harbor”.
Phrase	“protein purification”	A phrase is a group of words enclosed within quotes. The search returns exact matches to the phrase. Without the quotes, the search looks for any records that contain any of the words.
Proximity Searches	“phosphate sodium”~3	A proximity search contains a group of words in quotes with a tilde character (~) after the last quote mark, followed by an integer. The integer is the number of hops a word must make to match the phrase. Our example will find “phosphate sodium”, “sodium phosphate”, and “sodium dihydrogen phosphate”.
Field	author:david	A field is denoted by a colon (:) after the field name followed by the field search term. Field names must match exactly. If the field is not exact, the search will return no matches. We have provided an “Add Field” pull down menu, so the user do not have to remember the field names.
Range Searches	[2011-01-01 TO 2011-01-31]	Range searches are contained in a pair of square brackets[], and include a pair of terms separated by a “TO”. Range searches are useful for searching dates. Due to the lexigraphical ordering of words the year must proceed the month which proceeds the day. Dates in iExperiment are stored as YYYY-MM-DD, where the YYYY is the year, MM is the numerical month, and DD is the numerical day. Our example search will return experiments that have dates in January 2011.
AND Operator	protein AND purification	The default operator between search terms is OR. Using the AND operator requires that the search return results that match both terms.
Required (+) Operator	protein +purification	The required operator is a plus sign (+) before a search term. Our example will return results that contain “purification”, and may contain “protein”.
NOT Operator	purification NOT “lipid purification”	The NOT operator allows you to exclude terms from your searches. A minus sign (-) can also be used as a NOT operator. The example could be expressed as ‘purification -”lipid purification”.’
Grouping	title:(carboxypeptidae AND purification)	Terms can be grouped by enclosing the terms with parentheses (). This is useful for performing both multiple term field searches, as shown in the example, and for controlling the logic of a search with AND and OR operators.

For more details see http://lucene.apache.org/java/3_0_3/queryparsersyntax.html.

]]> http://www.colabrativ.com/introduction-of-iexperiment-search/feed/ 7