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Contains methods to load supplementary data and export networks into
Petri nets.
Overview
Protein annotations
Opens a window in which the user manages protein annotations. Protein
annotations are key/value pairs associated with a given protein
identifier. Annotations must be loaded from the file system (note: the
Java API contains methods to generate such annotation file). These
protein annotations can be used to create filtered protein sets
to restrict networks or complex sets to the filtered protein space.
See also:
Name mappings
Opens a window for managing name mappings. Name mappings are loaded as directed networks from the file system.
See also: Name mappings
GO settings
Manages Gene Ontology (GO) functional similarity calculators. A GO setting consists of the following parameters:
- GO network - Gene Ontology network loaded from an .obo format file
- Namespace - GO namespace: "biological process", "cellular component" or "molecular function"
- Relationships - the
relationships followed in the ontology used to construct the network
("is_a" relationships, "part_of" relationships or both)
- Annotations - a set of gene to GO-term annotations loaded from an annotations file
- Term similarity - a measure for the similarity between two given GO terms
- Functional similarity - a measure for the functionaly similarity of two proteins based on the term similarities of their annotated terms
Ontology and annotation files can be downloaded from the Gene Ontology website.
Important note: The protein
identifier types used in the GO files might not be the same as in the
other data files. You might have to use a name mapping file. ProCope
provides such a name mapping file for yeast in data/yeastmappings_YYMMDD.txt
.
See also:
Localization data
Manages localization data for proteins. Localization data must be loaded from files in a specific format.
See also:
Petri nets
Contains methods to export and convert Petri nets.
Generate Petri net
Generates a Petri net which integrates information from all selected
networks, complex sets and purification datasets. The Petri net is
stored in a GZIPed file.
See also: Petri nets
Convert to
Cytoscape/XGMML
Converts a given Petri net file to a Cytoscape-compatible XGMML format file.
See also: Petri nets
Convert to ToPNet
Converts a given Petri net file to a pair of ToPNet .places/.interactions files.
See also: Petri nets