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How to Search

Overview

While the bioassay data made available by BARD are vast and complex, searching those data is simple and flexible. To begin, just start typing to perform a free-text search. (Note: case is ignored in all searches.) By the time you type the third character, BARD’s auto-suggest feature will begin guiding you to the most relevant data. If one of the suggestions is close to what you’re looking for, you can select it to perform a constrained search for your input exclusively within the data category shown in bold. If you prefer a more open-ended exploration, simply click “SEARCH BARD” to perform an unconstrained search across all data categories. As an alternative to searching by text you can search by one or more ID numbers. You can even search by molecular structure by drawing or pasting a structure.

With BARD, one simple search box is your gateway to the high-quality bioassay data you need to accelerate your research.

Free-Text Search

BARD is powered by state-of-the-art database management systems as well as a high-speed, free-text SOLR search engine that scours every entry in the system. What you get are reliably comprehensive results organized by assay definitions, compounds and projects.

The goal of BARD is to help you find what you are looking for as quickly as possible, from the simplest search possible. Here are some of the categories of data that are searchable:

  • Target name
  • Description
  • GO biological process term
  • GO molecular function term
  • KEGG disease category
  • KEGG disease name
  • MeSH term
  • Panther class description
  • Title
  • Protocol
  • Readout technologies (e.g. fluorescence, bioluminescence)
  • Cell lines
  • Assay components

Auto-Suggest

Almost as soon as you start typing BARD will start giving you results. As you enter the third character of your search, a drop-down list of possible matches will appear. As you continue to type, that list will shorten to focus on the most relevant results, perhaps even the exact result you are seeking.

You’ll notice that in bold type at the end of each auto-suggest match is the data category in which the match occurs. So even if auto-suggest doesn’t display exactly what you are looking for, you’ll have some idea if the term you are searching is bringing you any closer to what you need.

Unconstrained and Constrained Searches

If none of the auto-suggest matches or categories shown in bold type are what you are searching for, you can simply click the “SEARCH BARD” button to perform an unconstrained search of all categories. This will likely generate more results, which might be useful if you wish to perform a more open-ended exploration of your search term.

If you do select one of the auto-suggest matches, you will initiate a constrained search where the results will be limited to the category shown in bold type. For example, if you were to type the search term “ras” then clicked on the auto-suggest line “ras protein signal transduction as GO Biological Process”, your results will be exclusively of entries where “ras protein signal transduction" is the GO Biological Process targeted by a particular assay definition or project.

You’ll notice that when you select one of the auto-suggest matches to perform a constrained search, BARD changes the text in the search box. So for our above example, the search box would read: gobp_term:“ras protein signal transduction". You can use this formula – category:“search term” – to perform constrained searches by typing them directly into the search box. There are many more advanced search formulas.

Search by One or More ID Numbers

Every assay definition, project, and compound has a searchable ID number in BARD. For example, the assay definition named “Additional SAR compounds tested via Multiplex dose response to identify specific small-molecule inhibitors of Ras and Ras-related GTPases specifically Rac1 wildtype” has been assigned the ADID number 4159. So if you wish to revisit this specific entry, instead of typing its long name, you can just type “4159”. Partial ID searches are not possible, thus typing in “41” or “415” would not find the above assay definition.

You can also search multiple ID numbers of the same type of data (assay definition, project or compound) simply by separating them with commas. For a more convenient way to search multiple IDs, click “IDs” near the search box to open a larger search box. In this box, you can paste a carriage return-separated list of ID numbers copied from a spreadsheet.

Search by Molecular Structure

To search by molecular structure, click “Structure” near the search box. This will open a structure editor where you can paste or draw a structure to search. To learn more about this full-featured editor’s many capabilities, visit http://www.scilligence.com/web/jsdraw.aspx.

With BARD, you can perform a variety molecular structure searches: substructure, superstructure, exact structure, and similarity. Similarity searches require a numeric parameter describing the degree of similarity required for matches, and can be set between 0 and 100%. For more details on BARD’s molecular structure search, please visit http://tripod.nih.gov/?p=427.

Advanced Search Formulas

As you can see below, there are a wide variety of search formulas available. Advanced users can use these to quickly target specific categories within a particular type of data.

Data Type Category Use Quotes for Term? Description Example Formula
All name Y Search for assay definitions, compounds and projects with the given string in their name name:"ras"
Assay Definition accession_gene Y Search for assay definitions with gene target ID numbers matching the given string accession_gene:"12381848"
Assay Definition accession_process Y Search for assay definitions with process target ID numbers matching the given string accession_process:"GO:0010468"
Assay Definition accession_protein YSearch for assay definitions with protein target ID numbers matching the given string accession_protein:"P17861"
Assay Definition ADID N Search for assay definitions by one or more ADIDs ADID:1121,1128
Assay Definition assay_format Y Search for assay definitions with the given assay format
Assay Definition assay_type Y Search for assay definitions with the given assay type assay_type:"direct enzyme activity assay"
Assay Definition comment Y Search for assay definitions containing the given string in their comment field comment:"genedata"
Assay Definition detection_method_type Y Search for assay definitions with the given detection method type detection_method_type:"absorbance"
Assay Definition protocol Y Search for assay definitions containing the given string in their protocol prototocol:"pyoverdine"
Assay Definition target_name_gene YSearch for assay definitions with gene target names matching the given string target_gene_process:"http://www.ncbi.nlm.nih.gov/gquery/?term=12381848"
Assay Definition target_name_process YSearch for assay definitions with process target names matching the given string target_name_process:"regulation of gene expression"
Assay Definition target_name_protein YSearch for assay definitions with protein target names matching the given string target_name_protein:"X-box-binding protein 1"
Assay Definition, Compound target_name YSearch for assay definitions with target names matching the given string target_name:"(GO:0008219) cell death"
Assay Definition, Project accession Y Search for assay definitions with gene target accession numbers that match the given string accession:"12381848"
Assay Definition, Project biology YSearch for assay definitions with a target biology matching the given string biology:"gene"
Assay Definition, Project biology_dict_label Y Search for assay definitions with a target biology matching the given string biology_dict_label:"process"
Assay Definition, Project description Y Search for assay definitions and projects containing the given string in their description description:"affiliation"
Assay Definition, Project gobp_id Y Search for assay definitions and projects annotated as being related to the given GO Biological Process ID gobp_id:"GO:0010468"
Assay Definition, Project gobp_term Y Search using a GO Biological Process term gobp_term:"accession"
Assay Definition, Project gocc_id Y Search using a GO Cellular Component ID gocc_id:"movement"
Assay Definition, Project gocc_term Y Search using a GO Cellular Component Term gocc_term:"nucleus"
Assay Definition, Project gomf_id Y Search using a GO Molecular Function ID gomf_id:"endoplasmic reticulum"
Assay Definition, Project gomf_term Y Search using a GO Molecular Function Term gomf_term:"binding"
Assay Definition, Project kegg_disease_cat YSearch by KEGG disease category kegg_disease_cat:"infectious disease"
Assay Definition, Project kegg_disease_names YSearch by KEGG disease name kegg_disease_names:"crohns disease"
Compound CID N Search for Compounds by one or more PubChem CIDs cid:11972586,16759566
Compound collection Y collection:"mlpcn"
Compound compound_class Y Search for compounds of a particular class. Options are: drug, probe compound_class:"drug"
Compound exact NSearch for compounds with the exact given structure specified using SMILES exact:OC(C1CCNCC1)(C2=CC=CC=C2)C3=CC=CC=C3
Compound iupacName Y Search for compounds having the given IUPAC name iupacName:"[4-[bis(4-chlorophenyl)methyl]piperazin-1-yl]-(5-methyl-4-nitro-1,2-oxazol-3-yl)methanone"
Compound similarity NSearch for Compound similar to the given structure specified by SMILES defaulting to a threshold of 90% similarity similarity:N.N.Cl[Pt]Cl
Compound substructure N Search for Compounds that contain the given substructure specified by SMILES substructure:Cl.OC(CCCN1CCCCC1)(C2=CC=CC=C2)C3=CC=CC=C3
Compound superstructure N Search for Compounds that the given structure specified by SMILES contains superstructure:Cl.OC(CCCN1CCCCC1)
Compound target_accession Y get search using target a session numbers target_accession:"12381848"
Compound target_description Y Search using description of target target_description:"Acetylcholinesterase"
Compound target_gene_id Y Search using gene target ID numbers target_gene_id:"12381848"
Compound threshold N Sets the percent similarity threshold for a Compound similarity search. Must be combined with a similarity search. similarity: NC(=O)NS(=O)(=O)C1=CC=C(N)C=C1 threshold:90
Compound, Project probeId Y Search for compounds with the given ML probe id probeid:"ML329"
Project PID N Search for Projects by one or more PIDs pid:1244
Project projectIdYFind a project by the project identifier assigned by the warehouse projectid:"17"