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Searching the ELN

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 marked in the text with (new!) 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.  Some ways to refine your text search follow.

  1. Searching for a word finds only occurrences of that whole word.  Example:  searching for the word cytoplasm finds only that word and not cytoplasmic.
  2. Searching is not case sensitive.
  3. The asterisk (*) can be used as a wild card so that searching for the text cytoplasm* will return Entries that have cytoplasm and cytoplasmic.
  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 cytoplasmic loop. Entries found contain the word cytoplasmic or loop. search-OR.png
  5. Putting multiple words in “double quotes” will return only Entries containing that exact phrase.  In the example above only the third of the three entries would be returned if you did a search for the exact phrase “cytoplasmic loop”.
  6. Keyword text searches will search over text found within the ELN entry (title, ELN fields, and the body of the ELN entry) as well as text found within any readable file attached to an ELN entry.

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 will 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 magnesium sulfate was found in both the body of one Entry and in a pdf attached document in a different Entry.


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 analysis. The word was found in the ELN Field Lab: as well as in the title and body of ELN Entries.


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 ChemAxon.  Marvin for JavaScript is used by CDD to add structures to the database through the web interface.  Marvin JS is web-based so it requires no installation or licensing of chemical drawing/rendering tools, it just works.

General structure-based querying within CDD Vault using Marvin-JS is documented in this Knowledge Base article.

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.  

  • Drawing the structure directly into the window using Marvin’s drawing tools.  
  • Drag and drop a structure file into the MarvinJS 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.  Note that many browsers do not allow Javascript applications to have access directly to the clipboard.  If you try to paste using the mouse you may get a nudge to use ctrl-V instead making the action available via browser actions.
  • Import the structure using the open/import folder icon at the top of MarvinJS.  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.  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’ (highlighted in green below).  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 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. 


Filtering Search Results:

Filters allow the user to narrow their hit lists to show only a portion of the search results.  From the drop-down lists below the search window select any number of authors whose Entries you wish to be in your hit list.  Clicking a username in the author list will turn the name rusty orange and you will see results written by that author.  If no authors are selected, all Entries across your project team will be available in the hit list.

Status of an Entry can be filtered the same way.  Select to see only Any, Open, or Finalized entries.  

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.

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 BioTech Collaborator project, uncheck all other projects to view the filtered hit list.

The figure below shows a query and query results from a combined search for text and substructure with results filtered by project and Entry status.

  1. Text search for trifluoro*:  returns any Entry with the word fragment in it.  This search initially brought back many results, there are three trifluoros in the body of this entry alone.  Note the yellow highlighted word fragments.
  2. Substructure search for phenol: This part of the query returned all chemical structures from Entries that had a benzene ring with an oxygen 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 by Project and Status:  Search results are narrowed even further by selecting only two Projects and filtering to view only Entries that are still Open.  See highlighted filter criteria in red.



Searching for Molecules from the Vault (new!)

To search for an existing CDD vault Molecule using the Molecule name/ID, simply clicking the “Insert Link” icon in the header bar of your ELN entry.  Then, start typing the Molecule Name/ID into the text box, and you will see a list of matching Molecule names/IDs presented to you.  Next, click the Molecule Name you wish to insert.


Finally, you can configure what’s displayed within your ELN entry by selecting the appropriate radio button. Select the top radio button to type in the custom text you desire or select the 2nd radio button to display only the Molecule Name.



Searching for Other ELN Entries (new!)

To search for an existing CDD Vault ELN entry, simply click the “Insert Link” icon in the header bar of your ELN entry.  Then, start typing any text from the title of an existing ELN entry into the text box, and you will see a list of matching ELN entries presented to you.  Next, click the ELN entry you wish to insert.


Finally, you can configure what’s displayed within your ELN entry by selecting the appropriate radio button. Select the top radio button to type in the custom text you desire or select the 2nd radio button to display only the title of the ELN entry.