BioPAX Ontology of Biological Pathways - Control - Classes | NCBO BioPortal

BioPAX Ontology of Biological Pathways

Last uploaded: July 29, 2010

Details

Acronym	BP
Visibility	Public
Description	The BioPAX ontology (www.biopax.org) is a standard language for formally representing biological pathways. BioPAX Level 3 supports the representation of metabolic pathways, signal transduction pathways, protein-protein interaction networks, gene regulatory networks and genetic interactions.
Status
Format	OWL
Contact	Dr Emek Demir, demir@cbio.mskcc.org
Categories	Biological Process

Version	Released	Uploaded	Downloads
Level3 v1.0 (Parsed, Indexed, Metrics, Annotator)	07/02/2010	07/29/2010	OWL \| CSV \| RDF/XML

No views of BP available

Classes	69
Individuals	0
Properties	96
Maximum depth	4
Maximum number of children	15
Average number of children	4
Classes with a single child	5
Classes with more than 25 children	0
Classes with no definition	2

Id	http://www.biopax.org/release/biopax-level3.owl#Control http://www.biopax.org/release/biopax-level3.owl#Control
Preferred Name	Control
Definitions	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e. pathway or interaction. Usage: Conceptually, physical entities are involved in interactions (or events) and the events should be controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction, called "Activity Flow" representation, that can be ambiguous without context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a Biochemical Reaction in which the substrate is phosphorylated. Subclasses of control define types specific to the biological process that is being controlled and should be used instead of the generic "control" class when applicable. A control can potentially have multiple controllers. This acts as a logical AND, i.e. both controllers are needed to regulate the controlled event. Alternatively multiple controllers can control the same event and this acts as a logical OR, i.e. any one of them is sufficient to regulate the controlled event. Using this structure it is possible to describe arbitrary control logic using BioPAX. Rationale: Control can be temporally non-atomic, for example a pathway can control another pathway in BioPAX. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism.
Type	http://www.w3.org/2002/07/owl#Class

comment	Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e. pathway or interaction. Usage: Conceptually, physical entities are involved in interactions (or events) and the events should be controlled or modified, not the physical entities themselves. For example, a kinase activating a protein is a frequent event in signaling pathways and is usually represented as an 'activation' arrow from the kinase to the substrate in signaling diagrams. This is an abstraction, called "Activity Flow" representation, that can be ambiguous without context. In BioPAX, this information should be captured as the kinase catalyzing (via an instance of the catalysis class) a Biochemical Reaction in which the substrate is phosphorylated. Subclasses of control define types specific to the biological process that is being controlled and should be used instead of the generic "control" class when applicable. A control can potentially have multiple controllers. This acts as a logical AND, i.e. both controllers are needed to regulate the controlled event. Alternatively multiple controllers can control the same event and this acts as a logical OR, i.e. any one of them is sufficient to regulate the controlled event. Using this structure it is possible to describe arbitrary control logic using BioPAX. Rationale: Control can be temporally non-atomic, for example a pathway can control another pathway in BioPAX. Synonyms: regulation, mediation Examples: A small molecule that inhibits a pathway by an unknown mechanism.
prefLabel	Control
prefixIRI	Control
subClassOf	http://www.biopax.org/release/biopax-level3.owl#Interaction
type	http://www.w3.org/2002/07/owl#Class
disjointWith	http://www.biopax.org/release/biopax-level3.owl#GeneticInteraction

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Delete	Subject	Author	Type	Created
	Incorrect mapping	ariutta	Comment	2014-10-28
	Duplication	ariutta	Comment	2014-10-28

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Subject	Author	Type	Class	Created
Incorrect mapping	ariutta	Comment	http://www.biopax.org/release/biopax-level3.owl#Control	2014-10-28
Duplication	ariutta	Comment	http://www.biopax.org/release/biopax-level3.owl#Control	2014-10-28

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Add NCBO Web Widgets to your site for BP

Widget type	Widget demonstration
Jump To Type a class name from BP and jump to it in BioPortal Get code	Step 2: Follow the Instructions Download the quick_jump.js file and put it on your server Copy the code below and paste it to your HTML page Note: If you would like to use Quick Jump across multiple ontologies: You can enter a comma-separated list of ontology ids: var BP_ontology_id = "NCIt,SNOMEDCT"; You can set the variable to 'all' to search all ontologies in BioPortal: var BP_ontology_id = "all"; To include definitions in the Jump To drop-down, add the following variable in Javascript: var BP_include_definitions = true; In the code that you just pasted, make sure to change the path to the quick_jump.js file to point to the location where you put the file (relative to your HTML file) For example, if you put the quick_jump.js file in the same directory as your HTML file, this is the code you would use: <div id="bp_quick_jump"></div> <script type="text/javascript"> var BP_ontology_id = "BP";</script> <script src="quick_jump.js" type="text/javascript" charset="utf-8"></script> For more help visit NCBO Widget Wiki
Form Autocomplete Fill your form fields with classes from BP Get code	Example 1 (start typing the class name to get its full URI) Example 2 (get the ID for a class) Example 3 (get the preferred name for a class) Step 2: Follow the Instructions Download the form_complete.js file and put it on your server. In the header for the page where you want the form field, include the form_complete.js file. On your form, for the fields where you want to use the class-selection widget, specify the field's class in the following format: `bp_form_complete-{ontology_id_list}-{value}` For example, `bp_form_complete-NCIT-uri` will use NCI Thesaurus (ontology id is NCIT) and will put the class URI in the field after the user selects the class from the pull-down list. Note: In addition to single ontology ids, you can use a list: `bp_form_complete-NCIT,NCBITAXON-uri` OR use 'all' to search across all BioPortal ontologies: `bp_form_complete-all-uri` The autocomplete widget accesses ontology content from the latest version of the ontology. You can use the following parameters to select which value will be placed into the user-visible input field: `uri` put the complete URI of the class (e.g., http://www.biopax.org/release/biopax-level3.owl#EntityReference ) `shortid` put the short id of the class, as used in BioPortal (e.g., "Common_Neoplasm"); `name` put the preferred name of the class (e.g., "Common Neoplasm"); In addition to the input element you defined, there are four hidden form elements that are created and then set when a user selects a class from the list. For example, if you create a field with this code: <input type="text" name="a" class="bp_form_complete-all-uri" size="100"/> The 'name' attribute is used to create the four following fields (note how the 'a' from the name attribute is appended to the id attribute): <input type="hidden" id="a_bioportal_preferred_name"> <input type="hidden" id="a_bioportal_concept_id"> <input type="hidden" id="a_bioportal_ontology_id"> <input type="hidden" id="a_bioportal_full_id"> Additional parameters are documented on the NCBO Widget Wiki For more help visit NCBO Widget Wiki
Visualization Display a visualization for a given class in BP Get code	Step 2: Follow the Instructions Copy the code below and paste it to your HTML page <iframe frameborder="0" src="/widgets/visualization?ontology=BP&class=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23EntityReference&apikey=YOUR_API_KEY"></iframe> For more help visit NCBO Widget Wiki
Tree Widget Display a class tree with a search field for BP Get code	Step 2: Follow the Instructions Copy the code below and paste it to your HTML page <link rel="stylesheet" type="text/css" href="/widgets/jquery.ncbo.tree.css"> <script src="/widgets/jquery.ncbo.tree-2.0.2.js"></script> <div id="widget_tree"></div> var widget_tree = $("#widget_tree").NCBOTree({ apikey: "YOUR_API_KEY", ontology: "BP" }); You can also view a detailed demonstration For more help visit NCBO Widget Wiki