Introduction: Searching with BioSpider

BioSpider was designed with simplicity in mind. Although you are able to specify explicit search options on the advanced search page, the simple search provides a single "smart" field.

Smart Search

Smart search is designed to guess your query type. It reduces the complexity of the search options making it ideal when performing a simple drug name lookup or structure search. The only specification that you need to include is the "Search Type". The search type is divided into three classes, outlined below:

  1. Drug:
    • Name (use the common active ingredient name for best results)
    • CAS Number
    • SMILES String (canonical or isomeric)
    • Pubchem ID (use cid= or sid= before the ID for compound and substance search, respectively)
    • KEGG ID (drug or compound ID)
    • InChI
    • MOL/SDF File
  2. Metabolite:
    • Name (use the common active ingredient name for best results)
    • CAS Number
    • SMILES String (canonical or isomeric)
    • Pubchem ID (use cid= or sid= before the ID for compound and substance search, respectively)
    • KEGG ID (compound ID)
    • InChI
    • MOL/SDF File
    • HMDB ID
  3. Protein:
    • Swiss-Prot Accession Number/ID

Some of these query types are explained in the table below:

Drug Name Generic or brand name (although generic may generate better results).
Example (generic): buspirone
Example (brand): tylenol
Chemical or Metabolite Name Common or IUPAC name.
Example (chemical): tetrahydrocannabinol
Example (metabolite): deoxyuridine
CAS Number CAS registry number - unique to every chemical.
Example (mesalamine): 89-57-6
SMILES String SMILES string in any format (Daylight, ISO).
Example (methimazole): CN1C=CN=C1S
SwissProt/Uniprot ID A unique UniProt identifier (primary accession number).
Example (accession number for Thyroid peroxidase): P07202
Example (accession number for Histamine H1 receptor): P35367

Advanced Search

Advanced Search provides a greater degree of control over the BioSpider search process. Although the simple search provides a good balance between speed and thoroughness, it is sometimes necessary to tweak some of the search options. These options are described below:

Option Explanation
Predict Targets/Enzymes for... This option controls whether enzyme/target prediction is enabled. As enzyme/target prediction can take a long time, you can disable it by turning off this option.
Identify common/general name If this option is enabled, BioSpider will attempt to identify the most general name for the given search compound (for small molecules). For example, if you search with a drug brand name, BioSpider will try to find the generic name. Disable this option if you find BioSpider is not guessing the common name correctly.
Search HMDB Disable this option to turn off HMDB searching.
Search DrugBank Disable this option to turn off DrugBank searching.
Search Wikipedia Some researchers consider Wikipedia a valuable general resource, while others may find it useless. To turn off searching of Wikipedia, disable this option.
Search for MSDS Files The search for MSDS files can take a long time depending on your query. If you don't need MSDS files, disable this option to speed up the search.
Max times to attempt a field before giving up By tweaking this value, you can increase or decrease the number of times a field is "hit" before further searching is declared useless by BioSpider. If you find that your search is showing many "Gave Up" messages in the search log, you can try increasing this value. Note that the higher the value, the longer the search will take in cases where information is sparse.
Output Search results for small molecules (drug, metabolite) can be displayed in either HTML or plain text. Although other formats will eventually be supported (XML), plain text output currently provides the best option if you need to process the results in a program.

Saving and Linking to Search Results

Search results for small molecules (drug, metabolite) can be saved for future linking or reference. To save a search, click the "Save Search Results" link in the search summary box at the top of the search results. You can then permanently link to your saved search using the given session ID (the link will be provided).

Metabolome Annotation

You can search for multiple compounds by entering each compound identifier (name, CAS, etc.) separated by newlines. You can let BioSpider run until completion in your browser window, or you can copy the given link and check back later (there is currently no email-notification system, which is planned for version 2).