Protein-protein interactions (ppi
)¶
PPIDatabase
is an abstract class defining a common interface
for accessing protein-protein interaction databases.
Classes implementing this interface are:
The common interface¶
-
class
orangecontrib.bio.ppi.
PPIDatabase
¶ A general interface for protein-protein interaction database access.
An example:
>>> ppidb = MySuperPPIDatabase() >>> ppidb.organisms() # List all organisms (taxids) ['... >>> ppidb.ids() # List all protein ids ['... >>> ppidb.ids(taxid="9606") # List all human protein ids. ['... >>> ppidb.links() # List all links [('...
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organisms
()¶ Return all organism ncbi taxonomy ids contained in this database.
-
ids
(taxid=None)¶ Return a list of all protein ids. If taxid (as returned by organisms()) is not
None
limit the results to ids to this organism only.
-
synonyms
(id)¶ Return a list of synonyms for primary id (as returned by ids).
-
all_edges
(taxid=None)¶ Return a list of all edges. If taxid is not
None
return the edges for this organism only.
-
edges
(id1, id2=None)¶ Return a list of all edges (a list of 3-tuples (id1, id2, score)).
-
all_edges_annotated
(taxid=None)¶ Return a list of all edges annotated. If taxid is not None return the edges for this organism only.
-
edges_annotated
(id=None)¶ Return a list of all edges annotated.
-
search_id
(name, taxid=None)¶ Search the database for protein name. Return a list of matching primary ids. Use taxid to limit the results to a single organism.
-
extract_network
(ids)¶
-
classmethod
download_data
()¶ Download the latest PPI data for local work.
-
PPI databases¶
-
class
orangecontrib.bio.ppi.
BioGRID
¶ Bases:
orangecontrib.bio.ppi.PPIDatabase
Access BioGRID PPI data.
Example
>>> biogrid = BioGRID() >>> print biogrid.organism() # Print a list of all organism ncbi taxis in BioGRID [u'10090',... >>> print biogrid.ids(taxid="9606") # Print a set of all human protein ids [u'110004' >>> print biogrid.synonyms("110004") # Print a list of all synonyms for protein id '110004' as reported by BioGRID [u'3803', u'CU464060.2', u'CD158b', u'p58.2', u'CD158B1', u'NKAT6'] >>>
-
ids
(taxid=None)¶ Return a list of all protein ids (biogrid_id_interactors). If taxid is not None limit the results to ids from this organism only.
-
synonyms
(id)¶ Return a list of synonyms for primary id.
-
all_edges
(taxid=None)¶ Return a list of all edges. If taxid is not None return the edges for this organism only.
-
edges
(id)¶ Return a list of all interactions where id is a participant (a list of 3-tuples (id_a, id_b, score)).
-
all_edges_annotated
(taxid=None)¶ Return a list of all edges annotated. If taxid is not None return the edges for this organism only.
-
edges_annotated
(id)¶ Return a list of all links
-
search_id
(name, taxid=None)¶ Search the database for protein name. Return a list of matching primary ids. Use taxid to limit the results to a single organism.
-
classmethod
download_data
(address)¶ Pass the address of the latest BIOGRID-ALL release (in tab2 format).
-
classmethod
init_db
(filepath)¶ Initialize the sqlite data base from a BIOGRID-ALL.*tab2.txt file format.
-
init_db_index
()¶ Will create an indexes (if not already present) in the database for faster searching by primary ids.
-
extract_network
(ids)¶
-
-
class
orangecontrib.bio.ppi.
STRING
(taxid=None, database=None)¶ Bases:
orangecontrib.bio.ppi.PPIDatabase
Access STRING PPI database.
-
organisms
()¶ Return all organism taxids contained in this database.
-
ids
(taxid=None)¶ Return a list of all protein ids. If taxid is not None limit the results to ids from this organism only.
-
synonyms
(id)¶ Return a list of synonyms for primary id as reported by STRING (proteins.aliases.{version}.txt file)
-
synonyms_with_source
(id)¶ Return a list of synonyms for primary id along with its source as reported by STRING (proteins.aliases.{version}.txt file)
-
all_edges
(taxid=None)¶ Return a list of all edges. If taxid is not None return the edges for this organism only.
Note
This may take some time (and memory).
-
edges
(id)¶ Return a list of all edges (a list of 3-tuples (id1, id2, score)).
-
classmethod
download_data
(version, taxids=None)¶ Download the PPI data for local work (this may take some time). Pass the version of the STRING release e.g. v9.1.
-
extract_network
(ids)¶
-
-
class
orangecontrib.bio.ppi.
STRINGDetailed
(taxid=None, database=None, detailed_database=None)¶ Bases:
orangecontrib.bio.ppi.STRING
Access STRING PPI database. This class also allows access to subscores per channel.
Note
This data is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License.
If you want to use this data for commercial purposes you must get a license from STRING.
-
all_edges
(taxid=None)¶ Return a list of all edges. If taxid is not None return the edges for this organism only.
Note
This may take some time (and memory).
-
edges
(id)¶ Return a list of all edges (a list of 3-tuples (id1, id2, score)).
-
extract_network
(ids)¶
-
ids
(taxid=None)¶ Return a list of all protein ids. If taxid is not None limit the results to ids from this organism only.
-
organisms
()¶ Return all organism taxids contained in this database.
-
synonyms
(id)¶ Return a list of synonyms for primary id as reported by STRING (proteins.aliases.{version}.txt file)
-
synonyms_with_source
(id)¶ Return a list of synonyms for primary id along with its source as reported by STRING (proteins.aliases.{version}.txt file)
-