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Searching ELN entries

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Charlie Weatherall
The ELN allows users to quickly search for text or chemical structures using a simple and intuitive interface. Searching can be done over text of the entries or by chemical structure. To refine search results filter them by the author name, status of the Entries or by the projects to which the Entries belong.

(In case you prefer a video tutorial instead, please view the embedded video from our YouTube channel CDD Academy - note: some of the latest enhancements might not be included in this video)

 

Searching ELN Entries by Text:

To do a keyword/text search type or paste the words you would like to find in the search window and hit the return key or click on the search icon at the right of the window. Here are some ways to perform a text search.

  1. Searching for a word finds only occurrences of that whole word (string). Example: searching for the text BRAF finds only that text and not BRAFV600E.
  2. Searching is not case sensitive.
  3. The asterisk (*) can be used as a wild card so that searching for the text BRAF* will return Entries that have BRAF and BRAFV600E.ELN_search_BRAF.png
  4. Putting two words into a search will bring back any Entry with either one of those words. See the figure below where the text query was knockout screening. Entries found contain the word knockout or screening. ELN_search_KO_screening.png
  5. Putting multiple words in “double quotes” will return only Entries containing that exact phrase. In this example if you did a search for the exact phrase “knockout screening” our search interface would return the one ELN entry that contains this exact phrase as part of an attached PDF file.ELN_search_KO_screening_exact.png
  6. As you may have noticed in the examples above, Keyword text searches will search over text found within the ELN entry (title, ELN fields, and the body of the ELN entry including Assay Annotations) as well as text found within any text readable file attached to an ELN entry (PDF, Word documents, PDB files).

Search results from text searches are displayed in a table below the query window. The first column in the results table is the Entry ID for the search results. Your Entry IDs may not be sequential although the oldest will be the smallest number. The last row in each search result points to the part of your ELN Entry where the text was found. See below where the phrase knockout screening was found in both the body of one Entry and in a PDF attached document in a different Entry.

ELN_search_KO_screening_exact_multiple_entries.png

If a keyword search is found in one of the custom ELN Fields, the hitlist will indicate the ELN field where the word was found. In the example below we searched for the keyword Templates. The word was found in the ELN Field Experiment Type: as well as in the PDF attachments of the ELN entries.

ELN_search_ELN_fields.png

Rank Ordering of the ELN Search Results

The ELN search relies on the Elasticsearch relevance ranking. It compares the term frequency, the inverse term frequency, and the field length. In short, it should match unique terms in smaller "fields" (body, title, file, etc.) higher.  Here is an example of the ordered rankings based on the location of the search term in the ELN entry:

(1) the search term in the BODY of an ELN entry
(2) the search term in the TITLE of an ELN entry
(3) the search term in a file that's attached in an ELN entry
(4) the search term in a meta-field of an ELN entry

If the keyword search term appears twice in an ELN entry, in any place, then that ELN entry prioritized higher in the search results.

Please visit the Elasticsearch relevance ranking documentation for further details.


Searching for Chemical Structures:

The chemical intelligence underneath CDD Vault and CDD ELN is handled by CDD Chemistry. The Ketcher Structure Editor is used by CDD to add structures to the database through the web interface. Ketcher is web-based so it requires no installation or licensing of chemical drawing/rendering tools, it just works.

 

To create a substructure query, click on the Filter by substructure search icon at the right side of the search window. This will bring up a query window where you can create a chemical structure for your search. Structures can be entered into the query window through several routes:  

ELN_search_substructure_button.png

  • Drawing the structure directly into the window using Ketcher’s drawing tools.  
  • Drag and drop a structure file into the  Ketcher window. All common structure file types are supported (list of allowable file types).
  • Copy and paste a text-based file like SMILES, InChi, Mol or CDXML into the window.
  • Import the structure using the open/import folder icon at the top of Ketcher. This will let you browse to a structure file or paste a text structure into the query.   

Searching by substructure also supports wild cards and a few special query groups. When drawing a structure for a query in the ELN use the codes below to search for specific types of atoms in a structure.

A or * :    These are general wild cards that will bring back ANY atom at that position.
M  :          Putting an M in a query will return any compound with a METAL at that position. (Na, Mg, Fe)
X   :          An X in the query structure will return any HALOGEN at that position.  (F, Cl, Br)
Q  :          A Q placed in the query will fetch any non-carbon, non-hydrogen HETEROATOM. (O, N)

Once you have run a substructure search, the results will be displayed below the search bar. We will search for the substructure in any molecule or reaction scheme that was entered in the body of the ELN entry.

  • If structure-searching was used as part of the query, a notice will be displayed next to the structure query icon that says ‘with structure’.
  • The list of ELN entries matching the query will be displayed below the query window and the substructure from your query will be highlighted.
  • If you would like to review or modify the structure from your query, click the Filter by substructure search icon again and the structure in the current query will be opened in the structure editor window. If you would like to toggle off the structure search, simply remove the molecule from the query window. 

ELN_search_substructure.png

Filtering Search Results:

Filters allow the user to narrow their hit lists to show only a portion of the search results. From the ELN search interface, click the Filter Entries icon, and add as many filters as you need in order to query your ELN entries.

ELN_add_filter.png

  • From the filter drop-down lists below the search window select any number of filtering categories. The filter categories under ELN are auto captured by the CDD Vault ELN such as the Author and Created Date. The filter categories below RalphieF Sandbox (current Vault that the entry below lives in) are custom ELN fields such as an Experiment Type drop down list which your vault administrator might add as metadata fields in an ELN entry.
    • Status of an Entry can be filtered the same way. Select to see only Any, Open, Finalized, In Review, or Discarded entries.
    • ProTip: these filters persist even if you log out of CDD Vault. They are a great way to maintain a search for your personal notebook (by Author = You).
  • The last way to filter search results is by Project. As always, the list of all projects you have permission to view are in the left column of the interface. Checking or unchecking projects in this list will show/hide results from Entries within those projects. In this example, all 10 projects in the vault are selected.

ELN_add_filter_view.png

Filtering of search results can be done either before or after a search. If you have too many results and want to filter out Entries from only the Selleck Chem project, uncheck all other projects to view the filtered hit list.

 

From the ELN search interface, you can also edit the display of the columns that are displayed by selecting the Edit Columns icon and checking off the columns that you wish to see displayed in the ELN search interface.

ELN_search_edit_columns.png

 

Bringing all of these concepts together

The figure below shows a query and query results from a combined search for text and substructure with results filtered by project. Author, Created date, and Experiment Type.

  1. Text search (1) for knockout screening: returns any Entry with either word in it. This search initially brought back many results.
  2. Substructure search (2) for chlorobenzene: This part of the query returned all chemical structures from Entries that had a benzene ring with a chlorine substituent.  The substructure from the query is highlighted in green. If a substructure search is part of the query, then a notification ‘with structure’ will appear next to the structure filter icon (note the green boxes below).  Remember if you want to review or modify the query molecule, click the structure search icon in the query bar. 
  3. Filter the results (3) by Project and Status: Search results are narrowed even further by selecting only one Project and filtering to view only Entries that are a specific Experiment Type, Created on a certain date by a certain Author.

ELN_search_all__together.png