Ontology for Representing CDM Semantics - organization - Classes | NCBO BioPortal

Ontology for Representing CDM Semantics

Last uploaded: November 18, 2021

Details

Acronym	ORCS
Visibility	Public
Description	The Ontology for Representing CDM Semantics (ORCS) is an application ontology that was developed to transform common-data-model-based data into ontologically-based data such as RDF, RDF*, OWL2, or Referent Tracking tuples. Although initially developed for such transformations of PCORnet Common Data Model (CDM) based data, ongoing and future work involves other CDMs such as OMOP.
Status	Beta
Format	OWL
Contact	William R. Hogan, hoganwr@gmail.com
Categories	Health

Version	Released	Uploaded	Downloads
2021-11-13 (Parsed, Indexed, Metrics, Annotator)	11/18/2021	11/18/2021	OWL \| CSV \| RDF/XML

No views of ORCS available

Classes	861
Individuals	69
Properties	431
Maximum depth	13
Maximum number of children	53
Average number of children	3
Classes with a single child	117
Classes with more than 25 children	5
Classes with no definition	172

No projects using ORCS

Id	http://purl.obolibrary.org/obo/OBI_0000245 http://purl.obolibrary.org/obo/OBI_0000245
Preferred Name	organization
Definitions	An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
Type	http://www.w3.org/2002/07/owl#Class

definition	An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
prefLabel	organization
label	organization
editor preferred term	organization
editor note	BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor	PERSON: Alan Ruttenberg PERSON: Susanna Sansone PERSON: Philippe Rocca-Serra PERSON: Bjoern Peters
definition source	GROUP: OBI
prefixIRI	OBI:0000245
subClassOf	http://purl.obolibrary.org/obo/BFO_0000040
type	http://www.w3.org/2002/07/owl#Class
example of usage	PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status	http://purl.obolibrary.org/obo/IAO_0000122

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Delete	Subject	Author	Type	Created
	Organization Instances	malone%40ebi.ac.uk	Comment	2010-06-17

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Add NCBO Web Widgets to your site for ORCS

Widget type	Widget demonstration
Jump To Type a class name from ORCS 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 = "ORCS";</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 ORCS 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://purl.obolibrary.org/obo/OGMS_0000073 ) `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 ORCS 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=ORCS&class=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000073&apikey=YOUR_API_KEY"></iframe> For more help visit NCBO Widget Wiki
Tree Widget Display a class tree with a search field for ORCS 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: "ORCS" }); You can also view a detailed demonstration For more help visit NCBO Widget Wiki