BioGRID ORCS - Example Searches

When searching BioGRID ORCS, you have a number of different options available to help you narrow down exactly what you're searching for. You can select the type of search you want to do, by choosing it from the “dropdown” list in the top right of the search box, as depicted in the image to the right. All searches can be restricted by organism.

Search Types

BioGRID ORCS Searches are broken down into two categories. Keyword searches and Ontology Term Searches. With keyword searches, you can search by plain text keywords and phrases to return results (search tips, advanced searching). For ontology term searches, you must choose specific ontology terms from a list of options.

Keyword Searches

There are three main types of keyword searches. By Screen (to search screen annotation), By Protein/Gene (to search protein/gene results) and By Publication (to search for entire publications). Each one can be used to find specific results within the BioGRID ORCS CRISPR Database.

BY SCREEN - Examples
  • CAS9 - Search for screens using the enzyme “CAS9”
  • Etoposide,Bleomycin - Search for screens involving the chemotherapy medication “Etoposide” or the cancer medication “Bleomycin”
  • cell proliferation - Search for screens with the phenotype “cell proliferation”
  • MAGeCK,EdgeR - Search for screens using the “Mageck” or “EdgeR” analysis method
  • Gecko - Search for screens using the “Gecko” CRISPR library
  • Leukemia - Search for screens in “Leukemia” cell types
  • A549,A2780 - Search for screens in “A549” or “A2780” cells
  • Toxin Exposure - Search for “Toxin Exposure” experiment screens
  • Virus - Search for screen's containing the word “Virus”
  • STE*,CDC* - Search for any protein/gene name that starts with either STE or CDC.
  • P22079 - Search for Uniprot Identifiers and other external database identifiers.
  • MAP7,CLN*,SULT1E1 - Search for multiple names together, including wildcards mixed in.
  • 6869,1328328 - Search by model organism ids like MGI and HGNC.

Ontology Term Searches

There are 13 different ontology term searches. For each of these, you simply have to select one or more of the available ontology terms, to limit your results. The following is a brief description of each ontology term search category.

  • By Cell Type - Search by cell types such as “acute myeloid leukemia” or “breast cancer”
  • By Cell Line - Search by cell line such as “HEK-293” or “CAMA-1”
  • By Experiment - Search by experiment such as “Timecourse” or “Toxin Exposure”
  • By Library Type - Search by library type such as “CRISPRa” or “CRISPRn”
  • By Enzyme - Search by enzyme such as “CAS9” or “SunCAS9”
  • By Condition/Drug - Search by condition/drug such as “Virus: Ebola” or “Methotrexate”
  • By Phenotype - Search by phenotype such as “autophagy” or “Response to Virus”
  • By Library Name - Search by Library name such as “Gecko” or “TKO”
  • By Format - Search by format such as “Pool”
  • By Analysis - Search by Analysis Method such as “MaGeCK”, “RANKS”, or “STARS”
  • By Methodology - Search by methodology such as “Activation” or “Knockout”
orcs/example_searches.txt · Last modified: 2020/08/07 21:29 by biogridadmin