Searching PID
Search database
Two simple database queries can be performed on the PID home page:
Biomolecule and/or biological process search
The query text can be:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifier
- UniProt identifier
- CAS number or compound name in literature
- Gene Ontology (GO) Biological process term or identifier (entered as GO:0000000)
- NCI thesaurus term or identifier
- a comma-separated list of any of the above.
Search results
- the search is performed as a Boolean "OR" of the matched terms.
- the search result summary is separated by data source; includes a hyperlink to view all interactions containing the found search terms; and displays a table listing terms found and their corresponding pathways
- users can view predefined pathways containing found search terms by clicking on the pathway links in the table
- users can view individual Molecule Pages for search terms found by clicking on the terms in the table
- users can click on the link "complete network maps for your search terms" which will display interaction network maps for the found search terms
- network maps are displayed in GIF format by default. However, users can switch to one of the other three output formats: SVG, XML and BioPAX. For more information about understanding and using the network graphics, please refer to the Network maps and Output Formats sections.
Advanced search
This search can be performed separately on NCI-Nature curated data, BioCarta data or Reactome data (see Database content).
For searches of NCI-Nature curated or Reactome data, the biomolecule name or identifier query text can be:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifier
- UniProt identifier
- CAS number or compound name in literature
- a comma-separated list of any of the above.
For BioCarta data, the biomolecule name or identifier search can be:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifier
- CAS number or compound name in literature
- a comma-separated list of any of the above.
The following options can be used to modify the search:
To search specific pathways, enter:
- a pathway name
- any substring of a pathway name
- a comma-separated list of any of the above.
The Browse Pathways page allows users to view all pathways in the database.
To search specific biological processes, enter:
- a GO biological process term or identifier (entered as GO:0000123)
- an NCI thesaurus term or identifier
- any substring of a process name
- a comma-separated list of any of the above
Searches of NCI-Nature curated data can be limited by evidence code; the default is to include data with any or no evidence code.
Check boxes are provided to expand the initial search results by interactions one degree upstream or downstream. Selecting these options might allow the search results to be combined into a single network map when connections between otherwise distinct networks are found during the search.
Search Results
- the search is performed as a Boolean "OR" of the matched terms.
- the result is a set of interactions that can be displayed as a single connected network or a set of distinct networks.
- the search results are displayed in GIF format by default. However, users can switch to one of the other three output formats: SVG, XML and BioPAX. For more information about understanding and using the network graphics, please refer to the Network maps and Output Formats sections.
Connected Molecules Search
For the set of query biomolecules, this search will attempt to construct a single network with the fewest connecting interactions.
The search can be performed separately on NCI-Nature Curated data or BioCarta data (see Database content).
For searches of NCI-Nature Curated or Reactome data, the seach text can be:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifier
- UniProt identifier
- CAS number or compound name in literature
- a comma-separated list of any of the above.
For BioCarta data, the search text can be:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifier
- CAS number or compound name in literature
- a comma-separated list of any of the above.
Search results
- the search is performed as a Boolean "OR" of the matched terms.
- the result is a set of interactions that can be displayed as a single connected network. If a single network containing all the queried molecules cannot be constructed, the search results will contain several disconnected networks.
- the search results are displayed in GIF format by default. However, users can switch to one of the other three output formats: SVG, XML and BioPAX. For more information about understanding and using the network graphics, please refer to the Network maps and Output Formats sections.
Batch Query
This query can be performed separately on NCI-Nature curated data, BioCarta data or Reactome data (see Database content). The user can upload one or two files containing molecule names or identifiers listed in a single column.
For queries of NCI-Nature Curated or Reactome data, the uploaded lists can contain any combination of:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifier
- UniProt identifier
For BioCarta data, the uploaded lists can contain any combination of:
- HUGO gene symbol (or any alias listed in Entrez Gene)
- Entrez Gene identifiers
Search results
- the search is performed as a Boolean "OR" of the matched terms.
- the Batch query results page includes a hyperlink to view all interactions containing the found search terms, and displays a table listing terms found and their corresponding pathways
- users can click on the link "complete network maps for your search terms" which will display interaction network maps for the found search terms
- users can view their query list terms overlaid onto predefined pathways by clicking on the pathway links in the table
- the pathways are ranked by the probability that they include biomolecules from the query list. The lower the p-value the greater the probability that the query list is biased towards a given pathway. The parameters for generating the p-value are the size of the query set, the number of biomolecules in a given pathway and the number of molecules in the database as a whole.
- the query results are displayed in GIF format by default. However, users can switch to one of the other three output formats: SVG, XML and BioPAX. For more information about understanding and using the network graphics, please refer to the Network maps and Output Formats sections.
