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Search by Molecule Keyword

The Search page of the Explore Data tab offers a keyword option to search any of the fields associated with molecules and batches. Protocol data can not be searched in this section, but is available in a "By protocol" section of the Search interface, and may be combined with the keyword search.

 

General search rules

  • Search values are not case-sensitive.
  • As long as a keyword is stored in one of the molecule or batch fields defined below, a search can include any combination of terms in any order.
  • A specific molecule or batch field can be searched by choosing it from the drop-down.
  • Molecule and Batch fields are indexed using rules described for each data type in the Available Molecule Keyword Search Fields table below.
  • Boolean logical operators and parentheses can be used to compose complex queries which can be saved for future use. We will show some typical examples below.
  • Search results will contain molecules that match the search criteria, with will include all batches per molecule regardless of search criteria.
  • When the results table is loaded, additional fields may be added via the Change Display Options link at the top of the table.

  

Exact Match or Partial Match Search

By default, the search will return results that match your terms exactly, allowing you to find a precise list of molecules, user-defined fields, or any combination of keywords.

 

Star *

  1. To compose flexible, partial match searches, use “ * ” wild-card to match 1 or more additional characters. For example " Ben* " will find anything that starts with "ben": benzene, benzodiazepine, benadryl, etc.
    • Molecule keyword search is prefix based, meaning that the search term must include initial characters, and can not start with the middle or tail of a term. e.g. to find benzodiazepine, the search must include "ben" or "benzo". Nothing will be found by looking for "diazepine", even if a wild card is included ("*diazepine" will not work).
  2. Star * search can be used without any additional keywords to find molecules that have any value for a specific batch field. For example, selecting "batch note" from the keyword drop-down, and entering *, will return all molecules that have a value in the batch "note" field.Screen_Shot_2013-01-30_at_11.27.53_AM.png

 

Dash -

A dash "-" is a special character which is not included in any search. Dashes divide an alpha-numeric string into sections that may be searched independently (e.g. "ABD-123873-old-5" is broken up into separate terms "ABD" and "123873" and "old" and "5"). In this case, it is possible to search for the middle fragment (e.g. "123873") and still find the matching record.

  

Available Molecule Keyword Search Fields

Field NameDescription
 any field

 Default setting of the Keyword Search.

If no specific field is selected, the search will look across all available fields.  Restricting the search to any of the fields below will limit the search context to that field.

        E.g. Search for "CT-460 or CT-510" will return two molecules CT-0000460 and CT-0000510.

 

name and synonyms 

The search will only look at Molecule Name and Synonyms. Identifiers assigned as molecule names or as synonyms will be normalized prior to searching so that:

        • Text-based prefix is separated from the numeric sequence. The prefix is separated if it precedes the numeric sequence directly (e.g. ABC001), or if it's separated by one of the following delimiters, the delimiter is removed for the purposes of searching and uniqueness validation.
        • :  /  .  ,  \  ~  !  @  #  $  % ^  &  (  )  -  _  +  =  <  > ?
          (e.g. ABC-001 ABC.001 ABC/001 all represent the same ID)

Leading zeros are removed from the numeric sequence, which is then searched independently of the prefix.

* The

Neither the leading zero padding or the ID prefix is necessary to include in this search.

         E.g. If full Molecule Name is CT-0000460, searching for "460" will return this molecule.

description

 Free text molecule description. This field is most commonly left blank, and will not yield any search results.

 data set

 Search the data set name for publicly available molecules. Make sure to select the data-sets from the Explore Data side-bar prior to executing your search.

        E.g. Select all data-sets and search for "Malaria". Molecules returned will belong to Malaria-related data-sets.

 CDD#

 Search the CDD# assigned to all publicly registered molecules either independently or alongside any privately assigned molecule names or synonyms.

        E.g. Searching for "CDD" or "CDD-" with only your vault data selected, will return any molecules in your projects that have been registered in CDD public.

 (If a private molecule in your vault appears with a CDD#, this means it is also available in CDD's public domain. Your private information is never shared)

 batch fields

  This is a general section heading that can be searched if you don't know the name of the specific batch field. 

  We describe a generic batch field. Depending on the business rules, there may be no batch fields beyond batch name, or may be any number of pre-defined fields. Look at the full list of fields in the keyword drop-down, and search specific field's values. If you are not able to find what you need under a specific field, try expanding your search to include all "batch fields" or "all fields".

     -name

 Search the Batch ID assigned by CDD. This is a required, and automatically generated field during compound registration. In prefix-based databases, this ID will be formatted as XX-000, where the prefix reflects a salt-code, and suffix is the sequence number for this salt form. The search will return a complete molecule record that includes this Batch ID. To view available batches, change display options to "Batch/Run" mode.

       E.g. Search for "AQ" will return all molecules that have any batches with HCl salt form (AQ prefix represents HCl). Search for "AQ-002" Will return any molecules that have at least 2 HCl batches.

     -salt

 Search for molecules of a particular salt form, using the full salt name (rather than the salt code described by Batch Name). This is a required, and automatically generated field during compound registration.# Available CDD salt names and salt codes are listed here. Returned list will include all molecules that have a batch containing the specified salt. To view the salt data in the results table, change display options to include additional batch fields.

      E.g. Search for "Hydrochloride" will return any molecule that has an HCl salt-form. The batch names of these will begin with the AQ- prefix.

    -other fields

 Other common batch fields may include "Person", "Vendor", "External ID", "Date" and "Note". Batch fields will vary depending on your vault's business rules, so make sure to look in the keyword drop-down for your fields. Examples below refer only to the common fields.

       E.g. Searching for "John Smith" under the "Person" field, will return any molecules registered by, or assigned to John Smith. If the person entered initials "JS" when registering the molecule, the search will not return any results. Try searching J* S*, if you aren't sure how the name was actually entered. 

         E.g. Searching for "*" under the "Vendor" field, will return any molecules that have some kind of vendor information. If you have a specific vendor in mind, but are not sure of the exact spelling in the database, try a wild-card search such as "Sig*". 

         E.g. Searching for "2012-04-12 or 2012-05-03" under the "Date" field, will return any molecules with either of these two batch dates. Dates must be entered in this format: YYYY-MM-DD.

        E.g. Search for 3 specific molecule batches by their external IDs, by selecting "External ID" field: "BEI1 or BEI2 or BEI3"

 user defined fields  This is a general section heading which can be used if you don't know which user defined field contains the desired information. 
    -user defined field title  

This is a general section heading that can be searched if you don't know the name of the specific user defined field (UDF). 

We describe a generic UDF. Depending on the business rules, there may be no UDFs, or may be any number of pre-defined fields. Look at the full list of fields in the keyword drop-down, and search the specific field's values. If you are not able to find what you need under a specific field, try expanding your search to include all "user defined fields" or "all fields".

       E.g. a UDF called "Library" is added to some molecules that belong to specific compound libraries. There are multiple libraries present in the database. To find molecules that belong to at least one library, select "Library" from the drop-down, and run a wildcard search "*". To find molecules that belong to library A but not library B, select "Library" from the drop-down list, and search for "A and not B"

Boolean Operators and Search Term Precedence

Use Boolean logic to combine search terms, and parentheses to group terms and set precedence.

For example, "(mol1 OR mol2) AND (green OR red) AND NOT powder" would return compounds that match "mol1" or "mol2" and match "green" or "red" and do not match "powder".

Unlike regular Boolean queries, precedence of ANDs over ORs is not assured, so always use parentheses in your expressions. In place of typing "a AND b OR c", type "(a AND b) or C" or "a AND (b or C)" based on the desired outcome.

If you type multiple words without ANDs or ORs, AND is assumed.

Operator Description Venn Diagram Rules               Example
 OR Broadens the search to find records containing any of the words it separates. It means that one or the other, or both terms are true.   220px-VennOR.png   "MoleculeName1 OR MoleculeName2 or MoleculeName3" will return a list of 3 molecules
AND Narrows the search to find records containing all of the terms it separates. This is the default logic if no specific operator is used in the search. 220px-VennAND.png  

1. "Enantiomer Mixture AND DMSO soluble" search will mean "Enantiomer AND Mixture AND DMSO AND Soluble". Resulting compounds are labeled as both soluble in DMSO, and mixtures of enantiomers.

2. "(Library A AND Library B) OR Library C"  search finds compounds that are a part of libraries A and B, possibly part of all three A, B and C, or only part of C.

NOT Narrows the search to find records that do not contain the term following it. 220px-VennNOT.png  

1. "Enantiomer NOT DMSO" search will look for compounds that are enantiomer mixtures but not soluble in DMSO.

2. "Library A AND Library B NOT  (Library C) search will look for compounds that are a part of A and B, but not a part of C. Notice that we need parentheses in this example.

() Groups words or phrases when combining Boolean operators and shows the order in which relationships should be considered.   Terms that are included in parentheses are evaluated before other operations are performed.

1. "Library A AND  ( Library B or Library C)". This search is the same as "Library A and Library B, or Library A and Library C". We are looking for molecules that must be in Library A, and either in Libraries B or C.

 


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