https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&user=Comm&feedformat=atomNCBO Wiki - User contributions [en]2024-03-29T00:10:21ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=NCBO_Widgets&diff=10314NCBO Widgets2010-10-29T17:43:42Z<p>Comm: /* Term-selection field on a form */</p>
<hr />
<div>NCBO widgets are the HTML or Javascript code that you can put on your Web site or Web form to use BioPortal functionality there. Using NCBO Widgets is just one of [[Using_NCBO_Technology_In_Your_Project|the ways in which you can use the NCBO technology directly on your Web site or in your application]].<br />
<br />
= Types of NCBO Widgets and use cases = <br />
* '''[[#Term-selection field on a form|Term-selection field on a form]]''': You can add a text field to your Web form that will let users enter a term from a controlled vocabulary (e.g., terms from a single ontology)<br />
** ''Example use case'': Suppose you are running a tissue microarray database and users upload sample descriptions to your database using a web form. There is usually a field for the user to enter the diagnosis for the tissue sample that she is entering. Usually, this field is a text-box or a drop down menu populated with a list of controlled terms. The free text-box is prone to errors, the drop-down gets too unwieldy with large terminologies. Using the NCBO term-selection widget to have users easily select a term from an ontology or controlled vocabulary (such as the NCI Thesaurus) to fill in the field. For example, when the user starts typing "cutaneous me", the term "cutaneous melanoma" pops up.<br />
** ''What does the term-selection field get you'': <br />
*** Look-ahead so that you don't need to type the whole term<br />
*** Controlled vocabulary provides consistency of the way different users use the term (If you want to put "Malignant melanoma", it will always be the same term from NCIT, regardless of how a user started typing it<br />
*** When a new version of your controlled vocabulary becomes available in BioPortal, the widget will automatically use that new version.<br />
*'''[[#Ontology search widget|Ontology search widget]]''': You can add to your Web site a search box that searches a specific BioPortal ontology. When the user selects the term of interest (with the help of the look-ahead feature), he can jump to the BioPortal page for the corresponding concept in BioPortal.<br />
*'''[[#Feed widget|Feed widget]]''': you can put a widget on your site that will have a live feed of all the changes to your ontology of interest, such as uploads of a new version, comments from other users, new mappings for concepts in your ontology.<br />
*'''[[#Ontology visualization widget|Ontology visualization widget]]''': You can put a widget on your Web site that visualizes your entire ontology of interest, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
*<font color="red">**NEW**</font> '''[[#OntologyTree Widget|OntologyTree Widget]]''': You can put a widget on your Web site that displays the ontology tree, or some part of it, as on the [http://bioportal.bioontology.org/visualize/39478#t_tab1: "Visualize" tab in BioPortal].<br />
<br />
= How to use NCBO Widgets=<br />
<br />
The easiest way to add any NCBO widget to your HTML page or Web form is by following these steps:<br />
* Find your ontology of interest in the [http://bioportal.bioontology.org/ontologies list of BioPortal ontologies] (e.g., NCI Thesaurus)<br />
* Click on the ontology name to get to the page with '''Details''' for that ontology (e.g., the [http://bioportal.bioontology.org/ontologies/39478 Details for NCI Thesaurus])<br />
* On the Ontology Details page, go to '''Ontology Widgets''' tab<br />
* Select the widget you want<br />
* Click the button below the widgets to get instructions for the specific widget<br />
<br />
== Term-selection field on a form ==<br />
<br />
To add a field to your form that lets the user fetch a term from your ontology of interest, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/form_complete.js <b>form_complete.js file</b>] and put it on your server<br />
</li><br />
<li>In the header for the page where you want the form field, include the <b>form_complete.js</b> file<br />
</li><br />
<li>On your form, for the fields where you want to use the term-selection widget, specify the field's class in the following format: <code>bp_form_complete-{ontology_id_list}-{value}</code><br />
<ul><br />
<li>For example, <code>bp_form_complete-1032-uri</code> will use NCI Thesaurus (ontology id is 1032) and will put the term URI in the field after the user selects the term from the pull-down list.<br />
<ul><br />
<li><br />
<b>Note:</b> In addition to single ontology ids, you can use a list:<br><br />
<code>bp_form_complete-1032,1089-uri</code><br />
</li><br />
<li><br />
<b>OR</b> use 'all' to search across all BioPortal ontologies:<br><br />
<code>bp_form_complete-all-uri</code><br />
</li><br />
</ul><br />
</li><br />
<li>You can use the following parameters to select which value will be placed into the user-visible input field:<br />
<ul><br />
<li><br />
<code>uri</code> put the complete URI of the term (e.g., <a rel="nofollow" title="http://bioportal.bioontology.org/visualize/39478/Common_Neoplasm" class="external free" href="http://bioportal.bioontology.org/visualize/39478/Common_Neoplasm">http://bioportal.bioontology.org/visualize/39478/Common_Neoplasm</a>);<br />
</li><br />
<li><br />
<code>shortid</code> put the short id of the term, as used in BioPortal (e.g., "Common_Neoplasm");<br />
</li><br />
<li><br />
<code>name</code> put the preferred name of the term (e.g., "Common Neoplasm");<br />
</li><br />
</ul><br />
</li><br />
<li>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 term from the list. For example, if you create a field with this code:<br />
<pre><br />
&lt;input type="text" name="a" class="bp_form_complete-all-uri" size="100"/&gt;<br />
</pre><br />
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):<br />
<ul><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_preferred_name"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_concept_id"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_ontology_id"&gt;<br />
</pre><br />
</li><br />
<li><br />
<pre><br />
&lt;input type="hidden" id="a_bioportal_full_id"&gt;<br />
</pre><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Ontology search widget ==<br />
<br />
To add a search widget to your HTML page that searches a specific ontology, do the following:<br />
<ul><br />
<li>Download the [http://bioportal.bioontology.org/javascripts/widgets/quick_jump.js <b>quick_jump.js file</b>] and put it on your server<br />
</li><br />
<li>Copy the code below and paste it to your HTML page. <br />
<pre><br />
<div id="bp_quick_jump"></div><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1016";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"><br />
</script><br />
</pre><br />
</li><br />
<li><br />
<b>Note:</b> If you would like to use Quick Jump across multiple ontologies:<br />
<ul><br />
<li>You can enter a comma-separated list of ontology ids:<br><br />
var BP_ontology_id = "1032,1089";<br />
</li><br />
<li>You cans set the variable to 'all' to search all ontologies in BioPortal:<br><br />
var BP_ontology_id = "all";<br />
</li><br />
</ul><br />
</li><br />
<li>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)<br />
<ul><br />
<li>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:<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032";<br />
</script><br />
<script src="quick_jump.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
== Feed widget ==<br />
<br />
To add a Feed widget to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<script type="text/javascript"><br />
var BP_ontology_id = "1032"<br />
</script><br />
<script src="http://bioportal.bioontology.org/javascripts/widgets/feed_widget.js" type="text/javascript" charset="utf-8"></script><br />
</pre><br />
<br />
== Ontology visualization widget ==<br />
To add a widget visualizing your ontology to your HTML page, simple copy the code from the Ontology Widget page for your ontology of interest. Here is a sample:<br />
<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="FlexoViz" width="100%" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf" bgcolor="#ffffff"<br />
width="100%" height="100%" name="FlexoViz" align="middle"<br />
play="true"<br />
loop="false"<br />
quality="high"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object> <br />
</pre><br />
<br />
If you want the visualization to be focused on a particular term in the ontology, you can add the term id to the parameters above. For example, to have the widget focus on Melanoma in NCI Thesaurus, replace the following line in the snippet above:<br />
<pre><br />
flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
with <br />
<pre><br />
flashVars="widget=true&ontology=39478&nodeid=Melanoma&server=http://rest.bioontology.org/bioportal/"<br />
</pre><br />
<br />
(''note "&nodeid=Melanoma"'')<br />
<br />
== OntologyTree Widget ==<br />
<br />
'''Description'''<br><br />
The OntologyTree widget is an embeddable Flex application that allows a user to interact with a tree browser for ontologies. The widget can be configured to display a list of all the ontologies in BioPortal, allowing the user to select which one to view, or can be setup to view a particular ontology. Additionally, there are several Javascript helper functions for the widget, allowing it to be utilized as a fully functional component in other applications.<br />
<br />
'''Location'''<br><br />
http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf<br />
<br />
'''Parameters'''<br />
* '''ontology''' = The id of the ontology to use, by default it assumes this value is the ontology version id<br />
* '''virtual''' [true|false] - If true then the above ontology parameter is assumed to be a virtual ontology id<br />
* '''canchangeontology''' [true|false] = If false then users can't change the current ontology<br />
* '''canchangeroot''' [true|false] = If true the the user can specify a root concept (using the context menu)<br />
* '''rootconceptid''' = The id of the root concept to show in the tree, leave out to show the ontology roots<br />
* '''server''' = The rest server to use. Defaults to "http://rest.bioontology.org/bioportal/".<br />
* '''redirecturl''' = The url to redirect to for terms and ontologies (in BioPortal). Defaults to "http://bioportal.bioontology.org/".<br />
* '''alerterrors''' [true|false] = If true then errors will be displayed in an annoying popup box.<br />
* '''title''' = The title for the browser window<br />
<br />
'''Embed Example'''<br><br />
Using Javascript (preferred):<br />
<pre><br />
<script src="http://keg.cs.uvic.ca/ncbo/ontologytree/AC_OETags.js" language="javascript"></script><br />
<!--<br />
// -----------------------------------------------------------------------------<br />
// Globals<br />
// Major version of Flash required<br />
var requiredMajorVersion = 9;<br />
// Minor version of Flash required<br />
var requiredMinorVersion = 0;<br />
// Minor version of Flash required<br />
var requiredRevision = 124;<br />
// -----------------------------------------------------------------------------<br />
// --><br />
<br />
// Version check for the Flash Player that has the ability to start Player Product Install (6.0r65)<br />
var hasProductInstall = DetectFlashVer(6, 0, 65);<br />
<br />
// Version check based upon the values defined in globals<br />
var hasRequestedVersion = DetectFlashVer(requiredMajorVersion, requiredMinorVersion, requiredRevision);<br />
<br />
if (hasProductInstall && !hasRequestedVersion) {<br />
// DO NOT MODIFY THE FOLLOWING FOUR LINES<br />
// Location visited after installation is complete if installation is required<br />
var MMPlayerType = (isIE == true) ? "ActiveX": "PlugIn";<br />
var MMredirectURL = window.location;<br />
document.title = document.title.slice(0, 47) + " - Flash Player Installation";<br />
var MMdoctitle = document.title;<br />
<br />
AC_FL_RunContent(<br />
"src", "playerProductInstall",<br />
"FlashVars", "MMredirectURL=" + MMredirectURL + '&MMplayerType=' + MMPlayerType + '&MMdoctitle=' + MMdoctitle + "",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else if (hasRequestedVersion) {<br />
// if we've detected an acceptable version<br />
// embed the Flash Content SWF when all tests are passed<br />
AC_FL_RunContent(<br />
"src", "http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf",<br />
"width", "300",<br />
"height", "100%",<br />
"align", "middle",<br />
"id", "OntologyTree",<br />
"quality", "high",<br />
"bgcolor", "#ffffff",<br />
"name", "OntologyTree",<br />
"allowScriptAccess", "always",<br />
"flashVars", "ontology=&virtual=false&alerterrors=false&canchangeontology=true&rootconceptid=",<br />
"type", "application/x-shockwave-flash",<br />
"pluginspage", "http://www.adobe.com/go/getflashplayer"<br />
);<br />
} else {<br />
// flash is too old or we can't detect the plugin<br />
var alternateContent = 'Alternate HTML content should be placed here. '<br />
+ 'This content requires the Adobe Flash Player. '<br />
+ '<a href=http://www.adobe.com/go/getflash/>Get Flash</a>';<br />
document.write(alternateContent);<br />
// insert non-flash content<br />
}<br />
</pre><br />
<br />
Using HTML:<br />
<pre><br />
<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"<br />
id="OntologyTree" width="300" height="100%"<br />
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"><br />
<param name="movie" value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" /><br />
<param name="quality" value="high" /><br />
<param name="bgcolor" value="#ffffff" /><br />
<param name="allowScriptAccess" value="always" /><br />
<param name="flashVars" value="ontology=&alerterrors=false&canchangeontology=true" /><br />
<embed src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" quality="high" bgcolor="#ffffff"<br />
width="300" height="100%" name="OntologyTree" align="middle"<br />
play="true"<br />
loop="false"<br />
allowScriptAccess="always"<br />
type="application/x-shockwave-flash"<br />
flashVars="ontology=&alerterrors=false&canchangeontology=true"<br />
pluginspage="http://www.adobe.com/go/getflashplayer"><br />
</embed><br />
</object><br />
</pre><br />
<br />
'''Javascript Examples'''<br><br />
You will need to copy/paste this code to a Javascript file or embed directly in the HTML for usage in your page.<br><br />
<pre><br />
/* <br />
* The following JavaScript functions allow you to interact with the Flash BioPortal Ontology Tree. <br />
* You can load an ontology by id, and get the current ontology id or name.<br />
* Once an ontology is loaded then you can get the currently selected concept by id or name,<br />
* and you can also select a concept by id or name. <br />
* You can also listen for one of these events by implementing the following functions (see the stubs below):<br />
* appComplete, treeSelectionChanged, treeNodeDoubleClicked, or errorLoadingOntology<br />
*<br />
* These are the parameters that you can pass into the application using the "flashVars" parameter:<br />
* (see the examples below):<br />
* - ontology: the id of the ontology (version or virtual)<br />
* - virtual: if false (default) then the ontology id above is the version id<br />
* if true then the above ontology id is assumed to be the virtual id <br />
* - alerterrors: (true/false) determines whether the application will display errors (default is false)<br />
* - server: defines the URL of the rest server (null by default)<br />
* - title: changes the default title for the page <br />
* - canchangeontology: if true then the ontology can be changed<br />
* - rootconceptid: sets the optional root node of the tree<br />
* - canchangeroot: if false then the root of the tree cannot be changed by the user (using context menu items)<br />
*/<br />
<br />
// get a handle for the flash application<br />
function getApp() {<br />
if (navigator.appName.indexOf ("Microsoft") != -1) {<br />
app = window["OntologyTree"];<br />
} else {<br />
app = document["OntologyTree"];<br />
}<br />
if (app == null) {<br />
app = document.getElementById("OntologyTree");<br />
}<br />
if (app == null) {<br />
alert("Could not get Flash object, JavaScript/Flex communication failed.");<br />
}<br />
return app;<br />
}<br />
<br />
// these are the available functions that you can call ONCE the <br />
// flash SWF has finished loading<br />
<br />
/** Loads a new ontology by id. */<br />
function loadOntology(ontologyID) {<br />
var app = getApp();<br />
if (app && app.loadOntology) {<br />
app.loadOntology(ontologyID);<br />
}<br />
}<br />
<br />
/** Gets the id of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyID() {<br />
var ontologyID = null;<br />
var app = getApp();<br />
if (app && app.getOntologyID) {<br />
ontologyID = app.getOntologyID();<br />
}<br />
return ontologyID;<br />
}<br />
<br />
/** Gets the name of the current ontology, will be null if no ontology is loaded. */<br />
function getOntologyName() {<br />
var ontologyName = null;<br />
var app = getApp();<br />
if (app && app.getOntologyName) {<br />
ontologyName = app.getOntologyName();<br />
}<br />
return ontologyName;<br />
}<br />
<br />
/** Gets the id of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptID) {<br />
conceptID = app.getSelectedConceptID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** <br />
* Gets the full id (not all ontologies support this) of the currently selected concept. <br />
* Will be null if nothing is selected, will be the same as the conceptID if no fullID exists. <br />
*/<br />
function getSelectedConceptFullID() {<br />
var conceptID = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptFullID) {<br />
conceptID = app.getSelectedConceptFullID();<br />
}<br />
return conceptID;<br />
}<br />
<br />
/** Gets the name of the currently selected concept, will be null if nothing is selected. */<br />
function getSelectedConceptName() {<br />
var conceptName = null;<br />
var app = getApp();<br />
if (app && app.getSelectedConceptName) {<br />
conceptName = app.getSelectedConceptName();<br />
}<br />
return conceptName;<br />
}<br />
<br />
/** Loads and selects a concept (by id) in the current ontology. */<br />
function loadConceptByID(conceptID) {<br />
var app = getApp();<br />
if (app && app.loadConceptByID) {<br />
app.loadConceptByID(conceptID);<br />
}<br />
}<br />
<br />
/** Attempts to load and select a concept (by name) in the current ontology. */<br />
function loadConceptByName(conceptName) {<br />
var app = getApp();<br />
if (app && app.loadConceptByName) {<br />
app.loadConceptByName(conceptName);<br />
}<br />
}<br />
<br />
/** This function gets call by flash when the swf has finished loading. */<br />
function appComplete(swfID) {<br />
// alert("flash app finished loading: " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree selection changes */<br />
function treeSelectionChanged(nodeID, nodeName, swfID) {<br />
// alert("tree selection: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for tree double click events */<br />
function treeNodeDoubleClicked(nodeID, nodeName, swfID) {<br />
alert("tree node double clicked: " + nodeID + " - " + nodeName + " - " + swfID);<br />
}<br />
<br />
/** Implement this function to listen for error messages when loading an ontology */<br />
function errorLoadingOntology(errorMsg, swfID) {<br />
// alert("Error: " + errorMsg);<br />
}<br />
</pre><br />
<br />
'''GWT'''<br />
* See http://code.google.com/p/gwt2swf/ for information on how to embed SWF in GWT.<br />
<br />
= Referencing your ontology of interest in the widgets = <br />
<br />
Most of the time you would want your widget to use the latest version of your ontology of interest that is available in BioPortal. Thus, you would want to use the ontology id and not the version is in your widget. To find the ontology id, go to the "Ontology Details" page for your ontology of interest in BioPortal (e.g., the page for [http://bioportal.bioontology.org/ontologies/39478 NCI Thesaurus]). You will find the ontology id on the Metadata tab there (e.g., the ontology id for NCI Thesaurus is 1032).</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=10238BioPortal REST services2010-10-21T22:10:40Z<p>Comm: /* Hierarchy Services */</p>
<hr />
<div>This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/<br />
<br />
* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter. <br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''<br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Code Examples = <br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Signature''': ./ontologies?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do <br />
work for ontology views also with the same signature.<br />
<br />
For example to get a specific ontology view based on a version id would be possible by using the signature:<br />
<br />
'''./ontologies/download/{view version id}?email={email_address}'''<br />
<br />
or for getting all view versions of a virtual view can be achieved called using the signature:<br />
<br />
'''./ontologies/versions/{view id}?email={email_address}'''<br />
<br />
However, there are a couple of services that are special for views:<br />
<br />
== List all the latest version of views ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./views?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org<br />
<br />
== Get all versions of views from a virtual ontology id ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}<br />
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org<br />
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]<br />
* '''Optional arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource><br />
/bioportal/search/cutaneous%20mela<br />
</accessedResource><br />
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>3</pageSize><br />
<numResultsPage>3</numResultsPage><br />
<numResultsTotal>3</numResultsTotal><br />
<contents<br />
class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://www.ebi.ac.uk/efo/EFO_0000389<br />
</conceptId><br />
<conceptIdShort>EFO_0000389</conceptIdShort><br />
<preferredName><br />
cutaneous melanoma<br />
</preferredName><br />
<contents>cutaneous melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma<br />
</conceptId><br />
<conceptIdShort><br />
Cutaneous_Melanoma<br />
</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanoma<br />
</preferredName><br />
<contents>Cutaneous Melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId>DOID:2418</conceptId><br />
<conceptIdShort>DOID:2418</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanocytic Neoplasm<br />
</preferredName><br />
<contents><br />
Cutaneous Melanocytic Neoplasm<br />
</contents><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
* '''Examples''':<br />
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/40644/</accessedResource><br />
<accessDate>2009-12-16 10:06:10.727 PST</accessDate><br />
<data><br />
<classBean><br />
<id>Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId><br />
<label>Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Malignant Melanoma</string><br />
<string>Melanoma</string><br />
<string>melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>A malignant, usually aggressive tumor composed of atypical,<br />
neoplastic melanocytes.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0025202</string><br />
</list><br />
</entry><br />
<entry><br />
<string>owl:equivalentClass</string><br />
<list><br />
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and<br />
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ALT_DEFINITION</string><br />
<list><br />
<string><br />
<def-source>NCI-GLOSS</def-source><br />
<def-definition>A form of skin cancer that arises in<br />
melanocytes, the cells that produce pigment.</def-definition><br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ICD-O-3_Code</string><br />
<list><br />
<string>8720/3</string><br />
</list><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Neoplastic Process</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<id>Non-Cutaneous_Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId><br />
<label>Non-Cutaneous Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Extracutaneous Melanoma</string><br />
<string>Non-Cutaneous Melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>Melanoma is a malignant tumor of melanocytes,<br />
cells that are derived from the neural crest.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>code</string><br />
<list><br />
<string>C8711</string><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org<br />
<br />
== Get term for latest ontology version id ==<br />
'''NOTE''': ''This signature will change in BioPortal release 2.2''<br />
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}<br />
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org<br />
<br />
<br />
* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services only work on the latest version of the ontology (the "virtual ontology").<br />
<br />
'''<font color='red'>NOTE: To see which ontology versions have been processed for use with the Hierarchy Services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.</font>''' <br />
<br />
<br />
<br />
== Get parents/children of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
= Prototypes =<br />
<br />
== RDF Term Service ==<br />
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file. <br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"<br />
<br />
...<br />
<br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf"><br />
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description><br />
<bioportal:abbreviation>NEMO</bioportal:abbreviation><br />
<bioportal:format>OWL</bioportal:format><br />
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date><br />
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri><br />
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel><br />
<bioportal:versionNumber>.95</bioportal:versionNumber><br />
<bioportal:id>42743</bioportal:id><br />
<bioportal:ontologyId>1321</bioportal:ontologyId><br />
</owl:Ontology><br />
<br />
...<br />
<br />
<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023"><br />
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/><br />
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader><br />
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation><br />
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1447) http://owlapi.sourceforge.net --><br />
</pre><br />
<br />
== RDF Download Service ==<br />
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.<br />
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
== Notes Service ==<br />
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].<br />
<br />
== Mapping Service ==<br />
* '''Prototype'''<br />
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}<br />
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/<br />
** '''Required arguments:''' <br />
*** ontology_id<br />
** '''Optional arguments:''' <br />
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept<br />
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]<br />
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]<br />
** '''Sample Output:'''<br />
<pre><br />
<hash><br />
<mapping-from type="array"><br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:25:23</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<br />
<source-name>Carbon</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:27594</destination-id><br />
<id>98216</id><br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Carbon</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Carbon</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from> <br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:27:05</created-at><br />
<br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Gold</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:29287</destination-id><br />
<id>98218</id><br />
<user-id>38139</user-id><br />
<br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Gold</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Gold</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from><br />
</mapping-from><br />
<mapping-to type="array"><br />
<mapping-to><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<br />
<created-at>2008-05-09 08:35:27</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Carbohydrate</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>Carbohydrate</destination-id><br />
<id>98219</id><br />
<br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name><br />
<destination-name>Carbohydrate</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1083</destination-ont><br />
<source-id>Carbohydrate</source-id><br />
<br />
<destination-version-id>29531</destination-version-id><br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-to><br />
</mapping-to><br />
</hash><br />
<br />
</pre><br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=10237BioPortal REST services2010-10-21T22:10:21Z<p>Comm: /* Hierarchy Services */</p>
<hr />
<div>This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/<br />
<br />
* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter. <br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''<br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Code Examples = <br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Signature''': ./ontologies?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do <br />
work for ontology views also with the same signature.<br />
<br />
For example to get a specific ontology view based on a version id would be possible by using the signature:<br />
<br />
'''./ontologies/download/{view version id}?email={email_address}'''<br />
<br />
or for getting all view versions of a virtual view can be achieved called using the signature:<br />
<br />
'''./ontologies/versions/{view id}?email={email_address}'''<br />
<br />
However, there are a couple of services that are special for views:<br />
<br />
== List all the latest version of views ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./views?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org<br />
<br />
== Get all versions of views from a virtual ontology id ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}<br />
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org<br />
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]<br />
* '''Optional arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource><br />
/bioportal/search/cutaneous%20mela<br />
</accessedResource><br />
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>3</pageSize><br />
<numResultsPage>3</numResultsPage><br />
<numResultsTotal>3</numResultsTotal><br />
<contents<br />
class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://www.ebi.ac.uk/efo/EFO_0000389<br />
</conceptId><br />
<conceptIdShort>EFO_0000389</conceptIdShort><br />
<preferredName><br />
cutaneous melanoma<br />
</preferredName><br />
<contents>cutaneous melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma<br />
</conceptId><br />
<conceptIdShort><br />
Cutaneous_Melanoma<br />
</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanoma<br />
</preferredName><br />
<contents>Cutaneous Melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId>DOID:2418</conceptId><br />
<conceptIdShort>DOID:2418</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanocytic Neoplasm<br />
</preferredName><br />
<contents><br />
Cutaneous Melanocytic Neoplasm<br />
</contents><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
* '''Examples''':<br />
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/40644/</accessedResource><br />
<accessDate>2009-12-16 10:06:10.727 PST</accessDate><br />
<data><br />
<classBean><br />
<id>Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId><br />
<label>Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Malignant Melanoma</string><br />
<string>Melanoma</string><br />
<string>melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>A malignant, usually aggressive tumor composed of atypical,<br />
neoplastic melanocytes.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0025202</string><br />
</list><br />
</entry><br />
<entry><br />
<string>owl:equivalentClass</string><br />
<list><br />
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and<br />
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ALT_DEFINITION</string><br />
<list><br />
<string><br />
<def-source>NCI-GLOSS</def-source><br />
<def-definition>A form of skin cancer that arises in<br />
melanocytes, the cells that produce pigment.</def-definition><br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ICD-O-3_Code</string><br />
<list><br />
<string>8720/3</string><br />
</list><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Neoplastic Process</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<id>Non-Cutaneous_Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId><br />
<label>Non-Cutaneous Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Extracutaneous Melanoma</string><br />
<string>Non-Cutaneous Melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>Melanoma is a malignant tumor of melanocytes,<br />
cells that are derived from the neural crest.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>code</string><br />
<list><br />
<string>C8711</string><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org<br />
<br />
== Get term for latest ontology version id ==<br />
'''NOTE''': ''This signature will change in BioPortal release 2.2''<br />
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}<br />
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org<br />
<br />
<br />
* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
The Hierarchy Services only work on the latest version of ontology (the "virtual ontology").<br />
<br />
'''<font color='red'>NOTE: To see which ontology versions have been processed for use with the Hierarchy Services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.</font>''' <br />
<br />
<br />
<br />
== Get parents/children of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
= Prototypes =<br />
<br />
== RDF Term Service ==<br />
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file. <br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"<br />
<br />
...<br />
<br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf"><br />
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description><br />
<bioportal:abbreviation>NEMO</bioportal:abbreviation><br />
<bioportal:format>OWL</bioportal:format><br />
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date><br />
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri><br />
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel><br />
<bioportal:versionNumber>.95</bioportal:versionNumber><br />
<bioportal:id>42743</bioportal:id><br />
<bioportal:ontologyId>1321</bioportal:ontologyId><br />
</owl:Ontology><br />
<br />
...<br />
<br />
<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023"><br />
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/><br />
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader><br />
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation><br />
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1447) http://owlapi.sourceforge.net --><br />
</pre><br />
<br />
== RDF Download Service ==<br />
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.<br />
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
== Notes Service ==<br />
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].<br />
<br />
== Mapping Service ==<br />
* '''Prototype'''<br />
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}<br />
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/<br />
** '''Required arguments:''' <br />
*** ontology_id<br />
** '''Optional arguments:''' <br />
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept<br />
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]<br />
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]<br />
** '''Sample Output:'''<br />
<pre><br />
<hash><br />
<mapping-from type="array"><br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:25:23</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<br />
<source-name>Carbon</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:27594</destination-id><br />
<id>98216</id><br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Carbon</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Carbon</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from> <br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:27:05</created-at><br />
<br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Gold</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:29287</destination-id><br />
<id>98218</id><br />
<user-id>38139</user-id><br />
<br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Gold</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Gold</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from><br />
</mapping-from><br />
<mapping-to type="array"><br />
<mapping-to><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<br />
<created-at>2008-05-09 08:35:27</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Carbohydrate</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>Carbohydrate</destination-id><br />
<id>98219</id><br />
<br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name><br />
<destination-name>Carbohydrate</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1083</destination-ont><br />
<source-id>Carbohydrate</source-id><br />
<br />
<destination-version-id>29531</destination-version-id><br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-to><br />
</mapping-to><br />
</hash><br />
<br />
</pre><br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=10236BioPortal REST services2010-10-21T22:05:01Z<p>Comm: </p>
<hr />
<div>This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/<br />
<br />
* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter. <br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''<br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Code Examples = <br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Signature''': ./ontologies?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do <br />
work for ontology views also with the same signature.<br />
<br />
For example to get a specific ontology view based on a version id would be possible by using the signature:<br />
<br />
'''./ontologies/download/{view version id}?email={email_address}'''<br />
<br />
or for getting all view versions of a virtual view can be achieved called using the signature:<br />
<br />
'''./ontologies/versions/{view id}?email={email_address}'''<br />
<br />
However, there are a couple of services that are special for views:<br />
<br />
== List all the latest version of views ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./views?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org<br />
<br />
== Get all versions of views from a virtual ontology id ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}<br />
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org<br />
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]<br />
* '''Optional arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource><br />
/bioportal/search/cutaneous%20mela<br />
</accessedResource><br />
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>3</pageSize><br />
<numResultsPage>3</numResultsPage><br />
<numResultsTotal>3</numResultsTotal><br />
<contents<br />
class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://www.ebi.ac.uk/efo/EFO_0000389<br />
</conceptId><br />
<conceptIdShort>EFO_0000389</conceptIdShort><br />
<preferredName><br />
cutaneous melanoma<br />
</preferredName><br />
<contents>cutaneous melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma<br />
</conceptId><br />
<conceptIdShort><br />
Cutaneous_Melanoma<br />
</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanoma<br />
</preferredName><br />
<contents>Cutaneous Melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId>DOID:2418</conceptId><br />
<conceptIdShort>DOID:2418</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanocytic Neoplasm<br />
</preferredName><br />
<contents><br />
Cutaneous Melanocytic Neoplasm<br />
</contents><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
* '''Examples''':<br />
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/40644/</accessedResource><br />
<accessDate>2009-12-16 10:06:10.727 PST</accessDate><br />
<data><br />
<classBean><br />
<id>Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId><br />
<label>Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Malignant Melanoma</string><br />
<string>Melanoma</string><br />
<string>melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>A malignant, usually aggressive tumor composed of atypical,<br />
neoplastic melanocytes.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0025202</string><br />
</list><br />
</entry><br />
<entry><br />
<string>owl:equivalentClass</string><br />
<list><br />
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and<br />
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ALT_DEFINITION</string><br />
<list><br />
<string><br />
<def-source>NCI-GLOSS</def-source><br />
<def-definition>A form of skin cancer that arises in<br />
melanocytes, the cells that produce pigment.</def-definition><br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ICD-O-3_Code</string><br />
<list><br />
<string>8720/3</string><br />
</list><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Neoplastic Process</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<id>Non-Cutaneous_Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId><br />
<label>Non-Cutaneous Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Extracutaneous Melanoma</string><br />
<string>Non-Cutaneous Melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>Melanoma is a malignant tumor of melanocytes,<br />
cells that are derived from the neural crest.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>code</string><br />
<list><br />
<string>C8711</string><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org<br />
<br />
== Get term for latest ontology version id ==<br />
'''NOTE''': ''This signature will change in BioPortal release 2.2''<br />
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}<br />
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org<br />
<br />
<br />
* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
'''<font color='red'>NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.</font>''' <br />
<br />
<br />
<br />
== Get parents/children of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
= Prototypes =<br />
<br />
== RDF Term Service ==<br />
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file. <br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"<br />
<br />
...<br />
<br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf"><br />
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description><br />
<bioportal:abbreviation>NEMO</bioportal:abbreviation><br />
<bioportal:format>OWL</bioportal:format><br />
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date><br />
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri><br />
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel><br />
<bioportal:versionNumber>.95</bioportal:versionNumber><br />
<bioportal:id>42743</bioportal:id><br />
<bioportal:ontologyId>1321</bioportal:ontologyId><br />
</owl:Ontology><br />
<br />
...<br />
<br />
<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023"><br />
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/><br />
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader><br />
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation><br />
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1447) http://owlapi.sourceforge.net --><br />
</pre><br />
<br />
== RDF Download Service ==<br />
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.<br />
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
== Notes Service ==<br />
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].<br />
<br />
== Mapping Service ==<br />
* '''Prototype'''<br />
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}<br />
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/<br />
** '''Required arguments:''' <br />
*** ontology_id<br />
** '''Optional arguments:''' <br />
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept<br />
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]<br />
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]<br />
** '''Sample Output:'''<br />
<pre><br />
<hash><br />
<mapping-from type="array"><br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:25:23</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<br />
<source-name>Carbon</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:27594</destination-id><br />
<id>98216</id><br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Carbon</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Carbon</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from> <br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:27:05</created-at><br />
<br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Gold</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:29287</destination-id><br />
<id>98218</id><br />
<user-id>38139</user-id><br />
<br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Gold</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Gold</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from><br />
</mapping-from><br />
<mapping-to type="array"><br />
<mapping-to><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<br />
<created-at>2008-05-09 08:35:27</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Carbohydrate</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>Carbohydrate</destination-id><br />
<id>98219</id><br />
<br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name><br />
<destination-name>Carbohydrate</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1083</destination-ont><br />
<source-id>Carbohydrate</source-id><br />
<br />
<destination-version-id>29531</destination-version-id><br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-to><br />
</mapping-to><br />
</hash><br />
<br />
</pre><br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=10235BioPortal REST services2010-10-21T22:04:30Z<p>Comm: </p>
<hr />
<div>This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/<br />
<br />
* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter. <br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''<br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Code Examples = <br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Signature''': ./ontologies?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do <br />
work for ontology views also with the same signature.<br />
<br />
For example to get a specific ontology view based on a version id would be possible by using the signature:<br />
<br />
'''./ontologies/download/{view version id}?email={email_address}'''<br />
<br />
or for getting all view versions of a virtual view can be achieved called using the signature:<br />
<br />
'''./ontologies/versions/{view id}?email={email_address}'''<br />
<br />
However, there are a couple of services that are special for views:<br />
<br />
== List all the latest version of views ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./views?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org<br />
<br />
== Get all versions of views from a virtual ontology id ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}<br />
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org<br />
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]<br />
* '''Optional arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource><br />
/bioportal/search/cutaneous%20mela<br />
</accessedResource><br />
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>3</pageSize><br />
<numResultsPage>3</numResultsPage><br />
<numResultsTotal>3</numResultsTotal><br />
<contents<br />
class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://www.ebi.ac.uk/efo/EFO_0000389<br />
</conceptId><br />
<conceptIdShort>EFO_0000389</conceptIdShort><br />
<preferredName><br />
cutaneous melanoma<br />
</preferredName><br />
<contents>cutaneous melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma<br />
</conceptId><br />
<conceptIdShort><br />
Cutaneous_Melanoma<br />
</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanoma<br />
</preferredName><br />
<contents>Cutaneous Melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId>DOID:2418</conceptId><br />
<conceptIdShort>DOID:2418</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanocytic Neoplasm<br />
</preferredName><br />
<contents><br />
Cutaneous Melanocytic Neoplasm<br />
</contents><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
* '''Examples''':<br />
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/40644/</accessedResource><br />
<accessDate>2009-12-16 10:06:10.727 PST</accessDate><br />
<data><br />
<classBean><br />
<id>Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId><br />
<label>Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Malignant Melanoma</string><br />
<string>Melanoma</string><br />
<string>melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>A malignant, usually aggressive tumor composed of atypical,<br />
neoplastic melanocytes.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0025202</string><br />
</list><br />
</entry><br />
<entry><br />
<string>owl:equivalentClass</string><br />
<list><br />
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and<br />
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ALT_DEFINITION</string><br />
<list><br />
<string><br />
<def-source>NCI-GLOSS</def-source><br />
<def-definition>A form of skin cancer that arises in<br />
melanocytes, the cells that produce pigment.</def-definition><br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ICD-O-3_Code</string><br />
<list><br />
<string>8720/3</string><br />
</list><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Neoplastic Process</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<id>Non-Cutaneous_Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId><br />
<label>Non-Cutaneous Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Extracutaneous Melanoma</string><br />
<string>Non-Cutaneous Melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>Melanoma is a malignant tumor of melanocytes,<br />
cells that are derived from the neural crest.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>code</string><br />
<list><br />
<string>C8711</string><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org<br />
<br />
== Get term for latest ontology version id ==<br />
'''NOTE''': ''This signature will change in BioPortal release 2.2''<br />
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}<br />
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org<br />
<br />
<br />
* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
'''<font color='red'>NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.</font>''' <br />
<br />
<br />
<br />
== Get parents/children of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
<br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
== Get siblings of a given concept in a specific ontology version ==<br />
* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies <br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/42331/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/siblings/42331/Melanoma<br />
</accessedResource><br />
<accessDate>20100408 18:06:16.868 PDT</accessDate><br />
<data><br />
<list><br />
<classBean><br />
<ontologyVersionId>42331</ontologyVersionId><br />
<id>Common_Germ_Cell_Neoplasm</id><br />
<fullId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Germ_Cell_Neoplasm<br />
</fullId><br />
<label>Common Germ Cell Tumor</label><br />
<synonyms><br />
<string>Common Germ Cell Tumor</string><br />
<string>Common Germ Cell Neoplasm</string><br />
</synonyms><br />
<relations><br />
<entry><br />
<string>Level</string><br />
<int>1</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<ontologyVersionId>42331</ontologyVersionId><br />
<id>Common_Hematopoietic_Neoplasm</id><br />
<fullId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Hematopoietic_Neoplasm<br />
</fullId><br />
<label>Common Hematopoietic Neoplasm</label><br />
<synonyms><br />
<string>Common Hematopoietic Neoplasm</string><br />
<string>Common Hematopoietic Tumor</string><br />
</synonyms><br />
<relations><br />
<entry><br />
<string>Level</string><br />
<int>1</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
= Prototypes =<br />
<br />
== RDF Term Service ==<br />
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file. <br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"<br />
<br />
...<br />
<br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf"><br />
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description><br />
<bioportal:abbreviation>NEMO</bioportal:abbreviation><br />
<bioportal:format>OWL</bioportal:format><br />
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date><br />
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri><br />
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel><br />
<bioportal:versionNumber>.95</bioportal:versionNumber><br />
<bioportal:id>42743</bioportal:id><br />
<bioportal:ontologyId>1321</bioportal:ontologyId><br />
</owl:Ontology><br />
<br />
...<br />
<br />
<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023"><br />
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/><br />
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader><br />
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation><br />
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1447) http://owlapi.sourceforge.net --><br />
</pre><br />
<br />
== RDF Download Service ==<br />
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.<br />
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
== Notes Service ==<br />
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].<br />
<br />
== Mapping Service ==<br />
* '''Prototype'''<br />
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}<br />
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/<br />
** '''Required arguments:''' <br />
*** ontology_id<br />
** '''Optional arguments:''' <br />
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept<br />
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]<br />
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]<br />
** '''Sample Output:'''<br />
<pre><br />
<hash><br />
<mapping-from type="array"><br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:25:23</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<br />
<source-name>Carbon</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:27594</destination-id><br />
<id>98216</id><br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Carbon</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Carbon</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from> <br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:27:05</created-at><br />
<br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Gold</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:29287</destination-id><br />
<id>98218</id><br />
<user-id>38139</user-id><br />
<br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Gold</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Gold</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from><br />
</mapping-from><br />
<mapping-to type="array"><br />
<mapping-to><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<br />
<created-at>2008-05-09 08:35:27</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Carbohydrate</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>Carbohydrate</destination-id><br />
<id>98219</id><br />
<br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name><br />
<destination-name>Carbohydrate</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1083</destination-ont><br />
<source-id>Carbohydrate</source-id><br />
<br />
<destination-version-id>29531</destination-version-id><br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-to><br />
</mapping-to><br />
</hash><br />
<br />
</pre><br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_REST_services&diff=10234BioPortal REST services2010-10-21T22:03:47Z<p>Comm: </p>
<hr />
<div>This page documents BioPortal Web Service signatures. The list below contains commonly accessed BioPortal Web services and is not intended to be an exhaustive list. If a feature you are interested in is not in the list below, please contact [mailto:support@bioontology.org BioPortal Support] to request the service or ask for more details on the full list of services. <br />
<br />
The '''prefix''' for all production service URLs in the table below is http://rest.bioontology.org/bioportal/<br />
<br />
* '''Note''': All NCBO REST web service calls MUST append a user identification query parameter with the pattern of "email=UserEmail" (note some clients may need to use URL encoding). For example, email=example@example.org or email=example%40example.org as an encoded email. Please start adding the user identification URL parameter to all your web service invocations. Later in 2009, we may start challenging REST service calls that do not have this parameter. <br />
<br />
* '''Note''': ''Signatures for BioPortal services have changed in BioPortal 2.0.4 release on January 13th, 2009. This page has the new service URLs. If you have any questions, please contact [mailto:support@bioontology.org BioPortal Support].''<br />
<br />
= Overview - Using NCBO Technology in Your Project =<br />
See [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in your Project] for general information and widgets available for use.<br />
<br />
= Code Examples = <br />
*Code examples for the ontology web services, developed in FlexViz, is available at: https://bmir-gforge.stanford.edu/gf/project/flexviz/frs/?action=index. To see the code in action, visit the [http://keg.cs.uvic.ca/ncbo/restservicestest/TestUI.html Test User Interface] that has been set-up using the FlexViz code.<br />
<br />
*Code examples for the [http://bioontology.org/wiki/index.php/Annotator_Web_service Annotator] and [http://www.bioontology.org/wiki/index.php/Resource_Index Resource Index] can be found on pages specific for those tools.<br />
<br />
= BioPortal Announce Mailing List =<br />
To receive notices of new BioPortal releases, changes to web services, or planned downtime subscribe to the [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-annouce] list.<br />
<br />
= Services to access ontologies and ontology versions =<br />
<br />
== List all the latest version of ontologies ==<br />
<br />
* '''Signature''': ./ontologies?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies?email=example@example.org<br />
<br />
== Get a specific ontology based on a version id ==<br />
* '''Signature''': ./ontologies/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/39002?email=example@example.org<br />
<br />
== Download an ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given ontology version id.<br />
* '''Signature''': ./ontologies/download/{ontology version id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/download/39002?email=example@example.org<br />
<br />
== Download the latest ontology file ==<br />
* '''Description''': Download the file (.obo, .owl) corresponding to the given virtual ontology id.<br />
* '''Signature''': ./virtual/download/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/download/1090?email=example@example.org<br />
<br />
== Get all versions of an ontology from a virtual ontology id ==<br />
* '''Signature''': ./ontologies/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontologies/versions/1104?email=example@example.org<br />
<br />
== Get latest version of an ontology id ==<br />
* '''Signature''': ./virtual/ontology/{ontology_id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104?email=example@example.org<br />
<br />
== List all ontology categories ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./categories?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/categories<br />
<br />
== List all ontology groups ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2''<br />
* '''Signature''': ./groups?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/groups<br />
<br />
= Services to access ontology views and ontology view versions =<br />
<br />
Since all the views on ontologies are ontologies themselves all the services that work on ontologies do <br />
work for ontology views also with the same signature.<br />
<br />
For example to get a specific ontology view based on a version id would be possible by using the signature:<br />
<br />
'''./ontologies/download/{view version id}?email={email_address}'''<br />
<br />
or for getting all view versions of a virtual view can be achieved called using the signature:<br />
<br />
'''./ontologies/versions/{view id}?email={email_address}'''<br />
<br />
However, there are a couple of services that are special for views:<br />
<br />
== List all the latest version of views ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Signature''': ./views?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views?email=example@example.org<br />
<br />
== Get all versions of views from a virtual ontology id ==<br />
'''NOTE''': ''To be released in BioPortal version 2.2'' <br />
* '''Description''': Returns all versions of views defined on the latest version a virtual ontology, grouped by virtual view ids.<br />
* '''Signature''': ./views/versions/{ontology id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/views/versions/1104?email=example@example.org<br />
<br />
= Search services =<br />
<br />
== Search BioPortal ==<br />
* '''Signature''': ./search/{query}[?{optional args}]&email={email_address}<br />
* '''Alt Signature''': ./search/?query={uri-encoded query}[&{optional args}]&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/Gene?email=example@example.org<br />
* You can use multiple query terms, separated by a space, for example: [http://rest.bioontology.org/bioportal/search/lung%20disease http://rest.bioontology.org/bioportal/search/lung disease?email=example@example.org]<br />
* '''Optional arguments:''' <br />
** ontologyids=<ontologyid>,<ontologyid>… - limits the search to specific ontologies (default: all ontologies)<br />
** isexactmatch=[1/0] – match the entire concept name (default: 0)<br />
** includeproperties=[1/0] – include attributes in the search (default: 0)<br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
** maxnumhits=<maxnumhits> - the maximum number of top matching results to return (default: 1000)<br />
** subtreerootconceptid=<uri-encoded conceptid> - narrow the search to concepts residing in a sub-tree, where the "subtreerootconceptid" is the root node. This feature requires a SINGLE <ontologyid> passed in using the "onotlogyids" parameter.<br />
* '''Description:''' <br />
The search attempts to match both partial and exact queries, giving more weight to exact matches. In single-word searches, the wildcard character (*) is automatically appended to the end of the word. For example, searching for "lun" would return all concepts whose name contains a word that begins with "lun" (i.e. "Lung", "Murine Lunate Bone", "Base of the Lung", etc).<br />
<br />
In phrase searches (multiple words), the wildcard character is appended to the end of each word. For example, searching for "cut mela" would return all concepts whose name contains a word starting with "cut", followed by any word that begins with "mela" (i.e. "Cutaneous Melanoma", "Metastatic Non-Cutaneous Melanoma", "Cutaneous Melanoma Clinical TNM Finding", etc).<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/search/software/?ontologyids=1104&isexactmatch=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource><br />
/bioportal/search/cutaneous%20mela<br />
</accessedResource><br />
<accessDate>2009-05-07 16:17:46.182 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>1</numPages><br />
<pageSize>3</pageSize><br />
<numResultsPage>3</numResultsPage><br />
<numResultsTotal>3</numResultsTotal><br />
<contents<br />
class="org.ncbo.stanford.bean.search.SearchResultListBean"><br />
<searchResultList><br />
<searchBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://www.ebi.ac.uk/efo/EFO_0000389<br />
</conceptId><br />
<conceptIdShort>EFO_0000389</conceptIdShort><br />
<preferredName><br />
cutaneous melanoma<br />
</preferredName><br />
<contents>cutaneous melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Cutaneous_Melanoma<br />
</conceptId><br />
<conceptIdShort><br />
Cutaneous_Melanoma<br />
</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanoma<br />
</preferredName><br />
<contents>Cutaneous Melanoma</contents><br />
</searchBean><br />
<searchBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<recordType><br />
RECORD_TYPE_PREFERRED_NAME<br />
</recordType><br />
<conceptId>DOID:2418</conceptId><br />
<conceptIdShort>DOID:2418</conceptIdShort><br />
<preferredName><br />
Cutaneous Melanocytic Neoplasm<br />
</preferredName><br />
<contents><br />
Cutaneous Melanocytic Neoplasm<br />
</contents><br />
</searchBean><br />
</searchResultList><br />
<ontologyHitList><br />
<ontologyHitBean><br />
<ontologyVersionId>39715</ontologyVersionId><br />
<ontologyId>1136</ontologyId><br />
<ontologyDisplayLabel><br />
Experimental Factor Ontology<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39833</ontologyVersionId><br />
<ontologyId>1009</ontologyId><br />
<ontologyDisplayLabel><br />
Human disease<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
<ontologyHitBean><br />
<ontologyVersionId>39478</ontologyVersionId><br />
<ontologyId>1032</ontologyId><br />
<ontologyDisplayLabel><br />
NCI Thesaurus<br />
</ontologyDisplayLabel><br />
<numHits>1</numHits><br />
</ontologyHitBean><br />
</ontologyHitList><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
= Term services =<br />
(formerly referred to as Concept services)<br />
<br />
== Get term ==<br />
* '''Signature''': ./concepts/{ontology version id}/{concept id}?email={email_address}<br />
* '''Alt Signature''': ./concepts/{ontology version id}?conceptid={uri-encoded concept id}&email={email_address}<br />
**To ensure that the Web service works within your application, use the Alt signature as some ontologies may contain terms where the concept id is a URI. <br />
* '''Optional arguments:''' <br />
** light=[1/0] - when set to 1, returns the "light" version of XML with only a basic info for the concept and its immediate children<br />
** norelations=[1/0] - when set to 1, returns only the requested term information (id, label, fullid, type, synonyms, definitions) without the "relations" map. This is useful when you need to quickly retrieve just the base information about a term.<br />
* '''Examples''':<br />
http://rest.bioontology.org/bioportal/concepts/39002/BRO:Resource?email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&light=0&email=example@example.org<br/><br />
http://rest.bioontology.org/bioportal/concepts/41009?conceptid=http%3A%2F%2Fihtsdo.owl%2Fsnomedct%2Fanatomy%23302509004&norelations=1&email=example@example.org<br />
* '''Sample Output''':<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/40644/</accessedResource><br />
<accessDate>2009-12-16 10:06:10.727 PST</accessDate><br />
<data><br />
<classBean><br />
<id>Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Melanoma</fullId><br />
<label>Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Malignant Melanoma</string><br />
<string>Melanoma</string><br />
<string>melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>A malignant, usually aggressive tumor composed of atypical,<br />
neoplastic melanocytes.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>UMLS_CUI</string><br />
<list><br />
<string>C0025202</string><br />
</list><br />
</entry><br />
<entry><br />
<string>owl:equivalentClass</string><br />
<list><br />
<string>'Common Neoplasm' and 'Melanocytic Neoplasm' and<br />
(Disease_Has_Abnormal_Cell only 'Melanoma Cell')</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ALT_DEFINITION</string><br />
<list><br />
<string><br />
<def-source>NCI-GLOSS</def-source><br />
<def-definition>A form of skin cancer that arises in<br />
melanocytes, the cells that produce pigment.</def-definition><br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<string>ICD-O-3_Code</string><br />
<list><br />
<string>8720/3</string><br />
</list><br />
</entry><br />
<entry><br />
<string>Semantic_Type</string><br />
<list><br />
<string>Neoplastic Process</string><br />
</list><br />
</entry><br />
<entry><br />
<string>SubClass</string><br />
<list><br />
<classBean><br />
<id>Non-Cutaneous_Melanoma</id><br />
<fullId>http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Non-Cutaneous_Melanoma</fullId><br />
<label>Non-Cutaneous Melanoma</label><br />
<type>Class</type><br />
<synonyms><br />
<string>Extracutaneous Melanoma</string><br />
<string>Non-Cutaneous Melanoma</string><br />
</synonyms><br />
<definitions><br />
<string>Melanoma is a malignant tumor of melanocytes,<br />
cells that are derived from the neural crest.</string><br />
</definitions><br />
<relations><br />
<entry><br />
<string>code</string><br />
<list><br />
<string>C8711</string><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</entry><br />
</relations><br />
</classBean><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get all root terms for an ontology version id ==<br />
* '''Signature''': ./concepts/{ontology version id}/root?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/39002/root?email=example@example.org<br />
<br />
== Get term for latest ontology version id ==<br />
'''NOTE''': ''This signature will change in BioPortal release 2.2''<br />
* '''New Signature''': ./virtual/ontology/{ontology id}/{concept id}?email={email_address}<br />
* '''New Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/BRO:Resource?email=example@example.org<br />
<br />
<br />
* '''Signature''': ./virtual/{ontology id}/{concept id}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/1104/BRO:Resource?email=example@example.org<br />
<br />
== Get all terms using the specific ontology version id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./concepts/{ontology version id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1&email=example@example.org<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Get all terms using the virtual ontology id ==<br />
<br />
'''NOTE:''' 'Get all terms' service has changed. The new signature and examples are reflected below. See [[#Changes_to_the_Get_all_terms_service]] for more information.<br />
<br />
* '''Signature''': ./virtual/ontology/{ontology id}/all?pagesize={pagesize}&pagenum={pagenum}&email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/ontology/1104/all?&pagesize=50&pagenum=1&email=example@example.org<br />
* '''Arguments:''' <br />
** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
== Changes to the Get all terms service ==<br />
<br />
Starting in BioPortal 2.3.1 (released March 15, 2010), the 'Get all terms' service has changed to support speedier and more complete term retrieval. To support this, several changes to the response XML and service signature are being made. Please see the following notes to update your existing applications to support these changes.<br />
<br />
* '''Examples''': A preview of the new service can be seen on the NCBO staging site:<br />
** http://rest.bioontology.org/bioportal/concepts/40644/all?pagesize=50&pagenum=1<br />
** http://rest.bioontology.org/bioportal/concepts/42431/all?pagesize=50&pagenum=500<br />
<br />
* '''Signature'''<br />
** '''New parameters:''' Previously, offset and limit were used to control pagination of results. These parameters have been replaced as follows:<br />
*** '''pagesize:''' An integer limiting how many results will be returned on a single page (a 'page' is equivalent to a single call to the REST service)<br />
*** '''pagenum:''' An integer indicating which page of results to return.<br />
<br />
* '''Response''': The structure of the new 'Get all terms' response XML has been brought into line with other BioPortal REST term services. In addition, to assist in paging through result sets, 'page' metadata is provided. A list of classBeans is provided in the classBeanResultList element, which includes each classes' set of relations (examples of relations include SuperClass, SubClass, and rdfs:label). Please see the example below for a full demonstration of the new response.<br />
<br />
= View Extraction Service = <br />
* This web service can be used to extract a subtree from an ontology. See [http://www.bioontology.org/wiki/index.php/View_Extraction View Extraction] for usage details. <br />
<br />
= Instance Services =<br />
<br />
== Get all direct instances for a given term ==<br />
* '''Signature''': ./concepts/instances/{ontlogyVersionId}[?conceptid={uri-encoded concept id}[&{optional args}]&email={email_address} <br />
* '''Optional arguments:''' <br />
** pagesize=<pagesize> - the number of results to display in a single request (default: all)<br />
** pagenum=<pagenum> - the page number to display (pages are calculated using <total results>/<pagesize>) (default: 1)<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/instances/38801?conceptid=SubstrateType&pagesize=1&pagenum=1&email=example@example.org<br />
* '''Description''': returns all direct instances for a given term.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/instances/38801<br />
</accessedResource><br />
<accessDate>20100408 18:17:21.226 PDT</accessDate><br />
<data><br />
<page><br />
<pageNum>1</pageNum><br />
<numPages>5</numPages><br />
<pageSize>1</pageSize><br />
<numResultsPage>1</numResultsPage><br />
<numResultsTotal>5</numResultsTotal><br />
<contents class="org.ncbo.stanford.bean.concept.InstanceBeanResultListBean"><br />
<list><br />
<instanceBean><br />
<id>unknown_substrate_type</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</fullId><br />
<label>unknown_substrate_type</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unknown_substrate_type<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_484</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<br />
<list><br />
<string>SubstrateType of unknown type.</string><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</contents><br />
</page><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get an instance and its property/value pairs ==<br />
* '''Signature''': ./instance/{ontlogyVersionId}[?instanceid={instanceid}&email={email_address}]<br />
<br />
* '''Example''': http://rest.bioontology.org/bioportal/instance/38801?instanceid=glass&email=example@example.org<br />
* '''Description''': returns information about an instance and a list of property/value pairs.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/instance/38801<br />
</accessedResource><br />
<accessDate>20100408 18:10:48.760 PDT</accessDate><br />
<data><br />
<instanceBean><br />
<id>glass</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</fullId><br />
<label>glass</label><br />
<relations><br />
<entry><br />
<propertyBean><br />
<id>:NAME</id><br />
<fullId>:NAME</fullId><br />
<label>:NAME</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#glass<br />
</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>unique_identifier</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#unique_identifier<br />
</fullId><br />
<label>unique_identifier</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>MO_742</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdfs:comment</id><br />
<fullId>http://www.w3.org/2000/01/rdfschema#comment<br />
</fullId><br />
<label>rdfs:comment</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<string>The array is made on a glass slide.</string><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>:DIRECTTYPE</id><br />
<fullId>:DIRECTTYPE</fullId><br />
<label>:DIRECTTYPE</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
<entry><br />
<propertyBean><br />
<id>rdf:type</id><br />
<fullId>http://www.w3.org/1999/02/22rdfsyntaxns#type<br />
</fullId><br />
<label>rdf:type</label><br />
<relations /><br />
</propertyBean><br />
<list><br />
<instanceBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<relations /><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>owl:Class</id><br />
<fullId>http://www.w3.org/2002/07/owl#Class<br />
</fullId><br />
<label>owl:Class</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</list><br />
</entry><br />
</relations><br />
<instanceType><br />
<list><br />
<classBean><br />
<id>SubstrateType</id><br />
<fullId><br />
http://mged.sourceforge.net/ontologies/MGEDOntology.owl#SubstrateType<br />
</fullId><br />
<label>SubstrateType</label><br />
<type>Class</type><br />
<relations /><br />
</classBean><br />
</list><br />
</instanceType><br />
</instanceBean><br />
</data><br />
</success><br />
</pre><br />
<br />
= Hierarchy Services =<br />
<br />
'''<font color='red'>NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies for ontologies with STATUS=28.</font>''' <br />
<br />
<br />
<br />
== Get parents/children of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[parents|children]/{ontlogyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/children/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
** '''Example''': http://rest.bioontology.org/bioportal/virtual/parents/1032/Melanoma?level=1&offset=1&limit=3&email=example@example.org<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
== Get paths to roots/leaves from a concept in a specific ontology version ==<br />
* '''Signature''': ./concepts/[rootpath|leafpath]/{ontologyVersionId}/{conceptId}[?email={email_address}&{optional args}]<br />
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies <br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/rootpath/42693/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/leafpath/42693/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
* '''Description''': return a set of path to the roots (resp. leaves) for a given concept in a specific ontology version. Paths are represented as a list of conceptIds, separated by periods (.) The first one in the list is a root (resp. leaf) in the hierarchy; the last one in the list is the direct parent (resp. direct child) of the concept.<br />
* '''Sample Output:''' <br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource><br />
/bioportal/concepts/rootpath/40644/Melanoma<br />
</accessedResource><br />
<accessDate>2009-04-21 11:06:23.439 PDT</accessDate><br />
<data><br />
<list><br />
<classBean><br />
<ontologyVersionId>40644</ontologyVersionId><br />
<id>Melanoma</id><br />
<relations><br />
<entry><br />
<string>Path</string><br />
<string><br />
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Morphology.Melanocytic_Neoplasm<br />
</string><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<ontologyVersionId>40644</ontologyVersionId><br />
<id>Melanoma</id><br />
<relations><br />
<entry><br />
<string>Path</string><br />
<string><br />
Getings_and_Disorders_Kind.Diseases_Disorders_and_Getings.Diseases_and_Disorders.Neoplasm.Neoplasm_by_Special_Category.Common_Neoplasm<br />
</string><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get paths to root/leaves from a concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/[rootpath|leafpath]/{ontologyId}/{conceptId}[?email={email_address}&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/rootpath/1032/Melanoma?email=example@example.org<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/leafpath/1032/Melanoma?email=example@example.org<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
** limit=<integer> – limits the number of results<br />
* '''Description''': The same as the previous services, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
== Get siblings of a given concept in a specific ontology version ==<br />
* '''Signature''': ./concepts/siblings/{ontlogyVersionId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
**NOTE: To see which ontology versions have been processed for use with the Hierarchy services, see http://rest.bioontology.org/obs/ontologies <br />
* '''Example''': http://rest.bioontology.org/bioportal/concepts/siblings/42331/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': returns the set of sibling concepts at the given level (i.e., siblings that have the same direct (level=1), grand-parents (level=2), etc.) for a given concept.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF8" ?><br />
<success><br />
<accessedResource>/bioportal/concepts/siblings/42331/Melanoma<br />
</accessedResource><br />
<accessDate>20100408 18:06:16.868 PDT</accessDate><br />
<data><br />
<list><br />
<classBean><br />
<ontologyVersionId>42331</ontologyVersionId><br />
<id>Common_Germ_Cell_Neoplasm</id><br />
<fullId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Germ_Cell_Neoplasm<br />
</fullId><br />
<label>Common Germ Cell Tumor</label><br />
<synonyms><br />
<string>Common Germ Cell Tumor</string><br />
<string>Common Germ Cell Neoplasm</string><br />
</synonyms><br />
<relations><br />
<entry><br />
<string>Level</string><br />
<int>1</int><br />
</entry><br />
</relations><br />
</classBean><br />
<classBean><br />
<ontologyVersionId>42331</ontologyVersionId><br />
<id>Common_Hematopoietic_Neoplasm</id><br />
<fullId><br />
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Common_Hematopoietic_Neoplasm<br />
</fullId><br />
<label>Common Hematopoietic Neoplasm</label><br />
<synonyms><br />
<string>Common Hematopoietic Neoplasm</string><br />
<string>Common Hematopoietic Tumor</string><br />
</synonyms><br />
<relations><br />
<entry><br />
<string>Level</string><br />
<int>1</int><br />
</entry><br />
</relations><br />
</classBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
<br />
== Get siblings of a given concept in the latest version of a given ontology ==<br />
* '''Signature''': ./virtual/siblings/{ontlogyId}/{conceptId}?level=<level>&email={email_address}&[&{optional args}]<br />
* '''Example''': http://rest.bioontology.org/bioportal/virtual/siblings/1032/Melanoma?level=1&email=example@example.org<br />
* '''Required arguments:''' <br />
** level=<integer> - limits results to a given level in the hierarchy<br />
* '''Optional arguments:''' <br />
** offset=<integer> – results offset (used for pagination)<br />
* '''Description''': The same as the previous service, but takes an ontology id and returns parents from the latest version of that ontology.<br />
<br />
= Bio2RDF Dump Service =<br />
<br />
This service allows you to output a given ontology from BioPortal in the form of a N3 RDF file conforming to the requirements for integrating into the [http://sourceforge.net/projects/bio2rdf/ Bio2RDF] collection.<br />
<br />
* '''Signature''': ./ontology/dump_n3/{ontlogyVersionId}?email={email_address}<br />
* '''Example''': http://rest.bioontology.org/bioportal/ontology/dump_n3/40865?email=example@example.org<br />
<br />
= Annotator Service =<br />
<br />
The NCBO Annotator is a Web service that can be used to annotate text metadata with biomedical ontology concepts. The concepts are from ontologies in BioPortal and includes the Unified Medical Language System (UMLS) Metathesaurus, OBO Foundry candidate ontologies and many others. <br />
<br />
The Annotator can be tested via a Web interface available through [http://bioportal.bioontology.org/annotate BioPortal]. For more information on using the Annotator Web service, see: http://bioontology.org/wiki/index.php/Annotator_Web_service.<br />
<br />
= Resource Index Service =<br />
<br />
The Resource Index provides a mechanism to search for biomedical data based on ontology concepts. For more information on using the Resource Index service, see http://www.bioontology.org/wiki/index.php/Resource_Index.<br />
<br />
= Prototypes =<br />
<br />
== RDF Term Service ==<br />
'''Coming in late May, 2010!''' This service allows you to output a snippet of an ontology from BioPortal in the form of an RDF file. <br />
* '''Signature''': ./bioportal/rdf/{ontology version id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/{ontology id}/{concept id},{concept id},...,{concept id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/1321/NEMO_spatial:NEMO_0000024?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/42743/NEMO_spatial:NEMO_0000023?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
** concept id<br />
* '''Description''': returns a BioPortal concept as RDF/XML ontology snippet. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': <nowiki>http://purl.bioontology.org/ontology/{ACRONYM}/{ID}</nowiki><br />
*** '''OBO''': <nowiki>http://purl.obolibrary.org/{IDSPACE}_{LOCALID}</nowiki><br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0"?><br />
<rdf:RDF xmlns="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf#"<br />
<br />
...<br />
<br />
<owl:Ontology rdf:about="http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf"><br />
<bioportal:description>Neural ElectroMagnetic Ontologies (NEMO) describe classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, functional (cognitive/behavioral) attributes, and data-level attributes (acquisition and analysis parameters).</bioportal:description><br />
<bioportal:abbreviation>NEMO</bioportal:abbreviation><br />
<bioportal:format>OWL</bioportal:format><br />
<bioportal:date>Wed May 19 09:56:21 PDT 2010</bioportal:date><br />
<bioportal:uri>http://purl.bioontology.org/ontology/NEMO/NEMO_spatial:NEMO_0000023.rdf</bioportal:uri><br />
<bioportal:displayLabel>Neural ElectroMagnetic Ontologies</bioportal:displayLabel><br />
<bioportal:versionNumber>.95</bioportal:versionNumber><br />
<bioportal:id>42743</bioportal:id><br />
<bioportal:ontologyId>1321</bioportal:ontologyId><br />
</owl:Ontology><br />
<br />
...<br />
<br />
<owl:Class rdf:about="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000023"><br />
<rdfs:label>right_parietal_scalp_surface_region</rdfs:label><br />
<rdfs:subClassOf rdf:resource="http://nemo.nic.uoregon.edu/ontologies/working/NEMO_spatial.owl#NEMO_0000006"/><br />
<skos:broader>NEMO_spatial:NEMO_0000006</skos:broader><br />
<skos:notation>NEMO_spatial:NEMO_0000023</skos:notation><br />
<skos:prefLabel>right_parietal_scalp_surface_region</skos:prefLabel><br />
</owl:Class><br />
</rdf:RDF><br />
<br />
<!-- Generated by the OWL API (version 3.0.0.1447) http://owlapi.sourceforge.net --><br />
</pre><br />
<br />
== RDF Download Service ==<br />
'''Coming in late July, 2010.''' This service allows you to download an entire ontology from BioPortal in the form of an RDF file.<br />
* '''Signature''': ./bioportal/rdf/download/{ontology version id}?email=example@example.org<br />
* '''Alt Signature''': ./bioportal/virtual/rdf/download/{ontology id}?email=example@example.org<br />
* '''Examples''': <br />
** http://rest.bioontology.org/bioportal/virtual/rdf/download/1321?email=example@example.org<br />
** http://rest.bioontology.org/bioportal/rdf/download/42743?email=example@example.org<br />
* '''Required arguments:''' <br />
** ontology version id<br />
* '''Description''': returns a BioPortal ontology as RDF/XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]. <br />
** The RDF dump will use URIs that are based on which format the ontology is in:<br />
*** '''OWL/RDF(S)''': preserve original URIs<br />
*** '''Protégé & RRF''': http://purl.bioontology.org/ontology/{abbreviation}/{concept_id}<br />
*** '''OBO''': http://purl.obolibrary.org/{idspace}_{localid}<br />
<br />
== Notes Service ==<br />
The prototype notes service has been replaced with a new [[Ontology_Notes|structured notes service]].<br />
<br />
== Mapping Service ==<br />
* '''Prototype'''<br />
** '''Signature''': ./mappings/service/{ontology_id}/{concept_id}<br />
** '''Example''': http://bioportal.bioontology.org/mappings/service/1083/<br />
** '''Required arguments:''' <br />
*** ontology_id<br />
** '''Optional arguments:''' <br />
*** concept_id=if concept_id is included, the service will return all mappings to and from the given concept<br />
** '''Description''': returns BioPortal Mappings as XML. This is a prototype web service, for updates subscribe to [https://mailman.stanford.edu/mailman/listinfo/bioportal-announce bioportal-announce]<br />
** '''Example Code:''' [http://www.bioontology.org/wiki/index.php/ExtractMappings Extract Mappings]<br />
** '''Sample Output:'''<br />
<pre><br />
<hash><br />
<mapping-from type="array"><br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:25:23</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<br />
<source-name>Carbon</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:27594</destination-id><br />
<id>98216</id><br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Carbon</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Carbon</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from> <br />
<mapping-from><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<created-at>2008-05-09 08:27:05</created-at><br />
<br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Gold</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>CHEBI:29287</destination-id><br />
<id>98218</id><br />
<user-id>38139</user-id><br />
<br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>Chemical entities of biological interest</destination-ont-name><br />
<destination-name>Gold</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1007</destination-ont><br />
<source-id>Gold</source-id><br />
<destination-version-id>38377</destination-version-id><br />
<br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-from><br />
</mapping-from><br />
<mapping-to type="array"><br />
<mapping-to><br />
<comment nil="true"></comment><br />
<map-type>Human</map-type><br />
<br />
<created-at>2008-05-09 08:35:27</created-at><br />
<updated-at>2008-08-05 17:26:06</updated-at><br />
<source-name>Carbohydrate</source-name><br />
<source-ont-name>NanoParticle Ontology (NPO)</source-ont-name><br />
<destination-id>Carbohydrate</destination-id><br />
<id>98219</id><br />
<br />
<user-id>38139</user-id><br />
<relationship-type nil="true"></relationship-type><br />
<destination-ont-name>NanoParticle Ontology (NPO)</destination-ont-name><br />
<destination-name>Carbohydrate</destination-name><br />
<map-source nil="true"></map-source><br />
<destination-ont>1083</destination-ont><br />
<source-id>Carbohydrate</source-id><br />
<br />
<destination-version-id>29531</destination-version-id><br />
<source-version-id>29531</source-version-id><br />
<source-ont>1083</source-ont><br />
</mapping-to><br />
</mapping-to><br />
</hash><br />
<br />
</pre><br />
<br />
<br />
<!--<br />
= Usage Logging =<br />
* '''Signature''': ./usage?{args}<br />
* '''Example''': http://rest.bioontology.org/bioportal/usage?requesturl=ontologies&resourceparameters=13578&email=example@example.org<br />
* '''Required arguments:''' <br />
** none specifically, but at least one optional argument is required<br />
* '''Optional arguments:''' <br />
** requesturl=<string contained in request url> – limit results to a given string contained in REST service request url. Unique values for the requesturl are: <br />
<pre><br />
/categories<br />
/concepts/{ontology version id}/{concept id}<br />
/concepts/{children or leafpath or parents or siblings}/{ontology version id}/{concept id}<br />
/diffs/{virtual id}<br />
/ontologies/{ontology version id} <br />
/ontologies/download/{ontology version id}<br />
/ontologies/versions/{ontology virtual id}<br />
/path/{ontology version id}/{concept id}<br />
/search/{search terms}<br />
/virtual/{virtual id}<br />
/virtual/ontology/{virtual id}/{concept id}<br />
/virtual/rootpath/{virtual id}/{concept id}<br />
/virtual/siblings/{virtual id}/{concept id}<br />
</pre><br />
** resourceparameters=<string contained in resource parameters> – limit results to a given string contained in resource parameters. For example, in the URL http://rest.bioontology.org/bioportal/search/melanoma, the word "melanoma" is considered a "resource parameter".<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given starting date (default: no starting date)<br />
** startdateaccessed=<date in format mm/dd/yyyy> – limit results to the given ending date (default: today's date)<br />
* '''Description''': returns BioPortal REST services usage data as XML.<br />
* '''Sample Output:'''<br />
<pre><br />
<?xml version="1.0" encoding="UTF-8" ?><br />
<success><br />
<accessedResource>/bioportal/usage</accessedResource><br />
<accessDate>2009-07-27 14:21:19.728 PDT</accessDate><br />
<data><br />
<list><br />
<usageLoggingBean><br />
<requestUrl><br />
/search/Certain infectious and parasitic diseases/<br />
</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Certain%20infectious%20and%20parasitic%20diseases<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>1</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Hypertension/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters><br />
query=Hypertension<br />
</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>2</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
<usageLoggingBean><br />
<requestUrl>/search/Melanoma/</requestUrl><br />
<httpMethod>GET</httpMethod><br />
<resourceParameters>query=Melanoma</resourceParameters><br />
<requestParameters><br />
pagenum=1&ontologyids=1265&pagesize=20<br />
</requestParameters><br />
<hitCount>3</hitCount><br />
<dateAccessed class="sql-timestamp"><br />
2009-07-27 00:00:00.0<br />
</dateAccessed><br />
</usageLoggingBean><br />
</list><br />
</data><br />
</success><br />
</pre><br />
--><br />
<br />
= XML Schema Definitions for the REST services =<br />
<br />
XML Schema for [[#Term_services|concept]] and [[#Hierarchy_Services|hierarchy]] services have been provided courtesy Eamonn Maguire. An updated XML Schema document will be posted shortly.</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=10223Dissemination Wiki2010-10-08T20:46:11Z<p>Comm: /* NCBO Dissemination */</p>
<hr />
<div>==NCBO Dissemination ==<br />
<br />
'''Past Events'''<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (October 2005 - August 2010)]]'''<br />
<br />
'''Future Events'''<br />
<br />
*'''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_Workshop_-_Medinfo_2010 Medinfo Workshop on Infectious Disease Ontology]''', Cape Town, South Africa, September 9-15, 2010.<br />
<br />
*'''[http://www.bioontology.org/wiki/index.php/IDO_Workshop_2010 Infectious Disease Ontology Dissemination Workshop 2010]''', Baltimore, MD, December 8-9.<br />
<br />
*'''[http://ncorwiki.buffalo.edu/index.php/An_Introduction_to_Ontology_Building Introduction to Ontology Building]''', October 23, 2010, Tutorial, University at Buffalo.<br />
<br />
*'''[http://icbo.buffalo.edu ICBO - 2nd International Conference on Biomedical Ontology]''', Buffalo, NY. Workshops and tutorials: July 26-27, 2011. Conference: July 28-30, 2011. <br />
<br />
*For other forthcoming events pertaining to the NCBO's mission, see [http://www.bioontology.org/events.html here]<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/education.html here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations ]]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_User_Guide&diff=10171Annotator User Guide2010-09-09T15:55:58Z<p>Comm: /* Annotator Web Service Response */</p>
<hr />
<div>===Sample Clients for the Annotator===<br />
<br />
HTML Client: http://rest.bioontology.org/test_oba.html<br />
<br />
Code examples: http://www.bioontology.org/wiki/index.php/Annotator_Client_Examples<br />
<br />
===Annotator Web service endpoint===<br />
<br />
* Web service signature: http://rest.bioontology.org/obs/annotator?email=example@example.org<br />
* Type: POST<br />
<br />
=== Annotator Web Service Workflow===<br />
<br />
The Annotator Web service’s workflow is composed of two main steps (figure):<br />
<br />
[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]<br />
<br />
First, direct annotations are created from raw text. Annotations are based on syntactic concept recognition using a dictionary compiled from terms (concept names and synonyms) pulled from the ontologies. The Annotator enables the selection of ontologies from one of the largest sets of available biomedical ontologies. We implemented the service using a subset of the BioPortal ontologies which includes 16 ontologies from UMLS (12 in RRF format, 2 in OBO format, 2 in OWL format). These ontologies provide a dictionary of 1,594,785 concepts and 3,200,654 terms. <br />
<br />
In the second step, semantic expansion components leverage the semantics in ontologies (e.g., is_a relations and mappings) to create additional annotations. For example, the is_a transitive closure component traverses an ontology parent-child hierarchy to create new annotations with parent concepts of concepts in direct annotations. The ontology-mapping component creates new annotations based on existing mappings between different ontologies. Point-to-point mappings that link concepts one another are defined manually or by automatic algorithms in BioPortal.<br />
<br />
==== The is_a transitive closure expansion component ====<br />
An is_a transitive closure component traverses an ontology parent-child hierarchy to create new annotations with parent concepts. For instance, if data are annotated with a concept from the NCI Thesaurus, such as ''melanoma'', this component generates a new annotation with the concept ''skin neoplasm'', because the NCI Thesaurus provides the knowledge that ''melanoma'' is_a ''skin neoplasm.''<br />
The Annotator uses the is_a relations as they are defined by BioPortal in the <SubClass>/<SuperClass> information for a given concept (accessed via REST web service).<br />
<br />
==== The mapping expansion component ====<br />
An ontology-mapping component creates new annotations based on existing mappings between different ontologies. For example, an annotation done with concept ''40644/Melanoma'' in NCI Thesaurus can be expanded to another one with in SNOMED-CT because the BioPortal provides the mapping information.<br />
The Annotator uses the mapping as they are defined by the repositories: BioPortal mappings are defined in the BioPortal front-end and accessed in an ad-hoc manner.<br />
<br />
=== Annotator Web Service Parameters===<br />
<br />
*See http://www.bioontology.org/wiki/index.php/BioPortal_2.3_Release_Notes for changes in Annotator output and updated information on how to use UMLS ontologies with the Annotator. <br />
<br />
The Annotator Web service offers a set of parameters that allows a user to customize the Annotator workflow and filter the result. To customize the workflow and the result, the user can specify a set of ontologies and a specific set of semantic types. Plus, the two steps of the annotation workflow can be parametrized.<br />
<br />
The Annotator Web service response time depends on the selected components as each consumes resources at a different level. For example, the ''is_a'' transitive closure takes a long time to process, even when using a pre-computed hierarchy table. As another example, an annotation with ''wholeWordOnly=false'' will be significantly longer that with ''wholeWordOnly=true''.<br />
<br />
Please see below for the list of parameters and the possible values.<br />
<br />
<br />
{| border="1" cellpadding="2"<br />
|-valign="top"<br />
|width="10%"|'''longestOnly'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies either or not the concept recognition step (done with University of Michigan Mgrep tool) must match the longest words only if they are several concepts that match to an expression.<br />
<br />
* If ''longestOnly=true'', the Annotator selects only the longest term matching phrase. For example, if ''longestOnly=true'', the phrase ''breast cancer'' generates only ''breast cancer.'' If ''longestOnly=false'', it generates three annotations: ''breast'', ''cancer'' and ''breast cancer.'' <br />
<br />
* Attention, if the Annotator finds an annotation with the complete phrase in an ontology composing the dictionary, partial annotations with other ontologies will not be generated. For example, because ''breast cancer'' exists in Human Disease and the NCI Thesaurus, if ''longestOnly=true'', annotations generated with those terms will block annotations with the terms ''breast'' in the Vaccine Ontology or ''cancer'' in BIRNLex. For this reason, we discourage the uses of the '''longestOnly''' parameter when the Annotator is used with one or a small number of ontologies.<br />
<br />
|-valign="top"<br />
|width="10%"|'''wholeWordOnly'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies whether the concept recognition step must match whole words only or not, if they are several concepts that match to a given word.<br />
* For example: If ''wholeWordOnly=true'', the phrase 'neoplasms' will match the concept NCI/C0027651 (Neoplasms) only. If ''wholeWordOnly=false'', the concept NCI/C1551054 (S) or the concept NCI/C0242536 (ASM) will also match (~80 concepts in NCI) in addition.<br />
* Note that the concept recognition step does not consider text cast.<br />
<br />
|-valign="top"<br />
|width="10%"|'''filterNumber'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.<br />
<br />
|-valign="top"<br />
|width="10%"|'''stopWords'''<br />
|width="10%"|{stopWord1,...,stopWordN}<br />
|width="10%"|default: empty (i.e. none)<br />
|width="70%"|Specifies the list of stop words to use. <br />
|-valign="top"<br />
|width="10%"|'''withDefaultStopWords'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies whether to use the default stop words or not. The default stop word list is available from sample HTML page. If set to true, this override the value of stopWords given by the user.<br />
|-valign="top"<br />
|width="10%"|'''isStopWordsCaseSenstive '''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies whether stopwords are case-sensitive or not.<br />
|-valign="top"<br />
|width="10%"|'''minTermSize'''<br />
|width="10%"|{integer} <br />
|width="10%"|default: 0<br />
|width="70%"|Specifies the minimum length of the term to be included in the annotations. <br />
|-valign="top"<br />
|width="10%"|'''scored'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies either or not the annotations are scored. A score is a number assigned to an annotation that reflects the accuracy of the annotation. The higher the score is the better the annotation is. The scoring algorithm gives a specific weight to an annotation according to the context of this annotation. For instance, an annotation done by matching a concept preferred name will be given a higher weight than an annotation done by matching a concept synonym or than an annotation done with a parent level 3 in the is_a hierarchy. Details on the scoring algorithm are given in section Scoring algorithm.<br />
* For example, the phrase 'melanoma' is annotated both with the concept NCI/C0025202 (melanoma) and the concept NCI/C1522102 (Mouse Melanoma). The former annotation is scored 10 where as the latter is scored 8.<br />
|-valign="top"<br />
|width="10%"|'''withSynonyms'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name. <br />
|-valign="top"<br />
|width="10%"|'''ontologiesToExpand'''<br />
|width="10%"|{localOntology1,...,localOntologyN}<br />
|width="10%"|default: empty (i.e. all ontologies)<br />
|width="70%"|Specifies the list of ontologies to use with the mapping semantic expansion component. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces).<br />
* For example, 40403,40644,40401. <br />
* '''NOTE''': The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies<br />
|-valign="top"<br />
|width="10%"|'''ontologiesToKeepInResult'''<br />
|width="10%"|{localOntology1,...,localOntologyN}<br />
|width="10%"|default: empty (i.e. all ontologies)<br />
|width="70%"|Specifies the list of ontologies to keep in the result of the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces).<br />
* For example, 40403,40644,40401.<br />
* '''NOTE''': The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies<br />
|-valign="top"<br />
|width="10%"|'''isVirtualOntologyId'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies whether the input values are virtualOntologyId instead of localOntologyid. VirtualOntologyId is not version-specific.<br />
|-valign="top"<br />
|width="10%"|'''semanticTypes'''<br />
|width="10%"|{semanticType1,...,semanticTypeN} <br />
|width="10%"|default: empty (i.e. all semanticTypes)<br />
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available in the sample HTML page. The values are separated with comma (without spaces). Note that the restriction to semantic types is also applied during the semantic expansion steps.<br />
* For example, T047,T048,T191.<br />
|-valign="top"<br />
|width="10%"|'''levelMax'''<br />
|width="10%"|{integer} <br />
|width="10%"|default: 0<br />
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step. <br />
* For example, a call done with ''levelMax=3'' will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. A call done with ''levelMax=0'' is equivalent to disable the is_a transitive closure expansion step.<br />
|-valign="top"<br />
|width="10%"|'''mappingTypes'''<br />
|width="10%"|{null,mappingType1,...,mappingTypeN} <br />
|width="10%"|default: empty (i.e. all mappingTypes)<br />
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of semantic types that can be used is available in the sample HTML page. The values are separated with comma (without spaces). The current list is described hereafter.<br />
* For example, from-mrrel,Human.<br />
* Note that the use of the key word "'''null'''" in the '''mappingTypes''' list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.<br />
* The current list of mapping type is:<br />
** ''inter-cui'': This mapping type corresponds to the mappings available between CUIs in the UMLS Metathesaurus. For instance, NCI/C0025202 and MSH/C0025202 are mapped together because the share the same CUI in UMLS.<br />
** ''from-mrrel'': This mapping type corresponds to the mappings available in the MRREL table from UMLS.<br />
** ''Automatic'': This mapping type corresponds to the mappings automatically imported in BioPortal.<br />
** ''Manual'': This relation name corresponds to the mappings created by users in BioPortal.<br />
** ''Human'': This relation name corresponds to the mapping s [not used anymore] in BioPortal.<br />
<br />
|-valign="top"<br />
|width="10%"|'''textToAnnotate'''<br />
|width="10%"|<br />
|width="10%"|<br />
|width="70%"|Specifies the text to be annotated.<br />
|-valign="top"<br />
|width="10%"|'''format'''<br />
|width="10%"|{xml,text,tabDelimited}<br />
|width="10%"|default: xml<br />
|width="70%"|Specifies the desired format of the response from Annotator. For programmatic access, XML is strongly suggested. <br />
<br />
* ''xml'': returns XML representation of the annotatorResultBean.<br />
* ''text'': returns plain text representation of the annotatorResultBean.<br />
* ''tabDelimited'': shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').<br />
<br />
The elements of the Annotator response are described in next section.<br />
<br />
|}<br />
<br />
===Annotator Web Service Response===<br />
<br />
In this section we define the Annotator Web service model i.e., what the service returns to the user: the objects as well as their relations and the constraints that applies. Cf the UML class diagram here: http://obs.bioontology.org/docs/model/EARoot/EA3/EA46.htm<br />
<br />
'''Response Content: annotatorResultBean'''<br />
{| border="1" cellpadding="2"<br />
|-valign="top"<br />
|width="10%"|'''resultId'''<br />
|width="90%"| The id of the annotatorResultBean.<br />
|-valign="top"<br />
|width="10%"|'''dictionary'''<br />
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. ''dictionaryId'', ''dictionaryName'', and ''dictionaryDate'' identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator service on time.<br />
|-valign="top"<br />
|width="10%"|'''statistics'''<br />
|width="90%"| Statistics contains information on the number of annotations done for a given context. The ''contextName'' keyword identifies the type of context and ''nbAnnotation'' is the number of annotations of this type.<br />
|-valign="top"<br />
|width="10%"|'''parameters'''<br />
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator service. Those parameters are described in previous section.<br />
|-valign="top"<br />
|width="10%"|'''ontologies'''<br />
|width="90%"| To keep the model simple, we provide only the global ontology identifier, ''localOntologyId'' the name (''ontologyName'') and version (''ontologyVersion''). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: ''nbAnnotation'', the number of annotation that have been made with concepts from this ontology. ''score'', the sum of all the scores of the annotations done with concepts from this ontology (if parameter ''scored=true''). Therefore, score represents the most accurate ontology to annotate the given text.<br />
|-valign="top"<br />
|width="10%"|'''annotations'''<br />
|width="90%"| Annotation is a representation of one annotation. An annotation has a ''score'' which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a ''concept'' in a ''context''.<br />
<br />
{| border="2" <!-- The nested table must be on a new line --><br />
|-valign="top"<br />
|width="10%"|'''score'''<br />
|width="90%"| The scoring algorithm gives weight to each annotation according to the annotation context. The final score for an annotation is then calculated as the sum of all the scores of the annotations done with the same concept. Cf Recommender journal paper for more detail for now.<br />
<br />
|-valign="top"<br />
|width="10%"|'''concept'''<br />
|width="90%"| ''Concept'' is a representation of an ontology concept in the Annotator web service ontology model<br />
* ''localConceptId'' - global identifier for the concept in its original repository. <br />
* ''localOntologyId'' - identifier for the ontology in which the concept is defined. <br />
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology. <br />
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository). <br />
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred. <br />
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999). <br />
|-valign="top"<br />
|width="10%"|'''context'''<br />
|width="90%"| ''Context'' specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:<br />
{| border="2" style="background:#ABCDEF;" <!-- The nested table must be on a new line --><br />
|-valign="top"<br />
|width="10%"|'''MGREP'''<br />
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties: <br />
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep. <br />
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.<br />
|-valign="top"<br />
|width="10%"|'''ISA_CLOSURE'''<br />
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:<br />
* ''childConceptId'' - the concept from which the annotation was derived. <br />
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived. <br />
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.<br />
|-valign="top"<br />
|width="10%"|'''MAPPING'''<br />
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties: <br />
* mappedConceptId identifies the concept from which the annotation was derived. <br />
* mappingType specifies the type of mapping.<br />
|}<br />
|}<br />
|}</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_User_Guide&diff=10170Annotator User Guide2010-09-09T15:48:49Z<p>Comm: /* Annotator Web Service Parameters */</p>
<hr />
<div>===Sample Clients for the Annotator===<br />
<br />
HTML Client: http://rest.bioontology.org/test_oba.html<br />
<br />
Code examples: http://www.bioontology.org/wiki/index.php/Annotator_Client_Examples<br />
<br />
===Annotator Web service endpoint===<br />
<br />
* Web service signature: http://rest.bioontology.org/obs/annotator?email=example@example.org<br />
* Type: POST<br />
<br />
=== Annotator Web Service Workflow===<br />
<br />
The Annotator Web service’s workflow is composed of two main steps (figure):<br />
<br />
[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]<br />
<br />
First, direct annotations are created from raw text. Annotations are based on syntactic concept recognition using a dictionary compiled from terms (concept names and synonyms) pulled from the ontologies. The Annotator enables the selection of ontologies from one of the largest sets of available biomedical ontologies. We implemented the service using a subset of the BioPortal ontologies which includes 16 ontologies from UMLS (12 in RRF format, 2 in OBO format, 2 in OWL format). These ontologies provide a dictionary of 1,594,785 concepts and 3,200,654 terms. <br />
<br />
In the second step, semantic expansion components leverage the semantics in ontologies (e.g., is_a relations and mappings) to create additional annotations. For example, the is_a transitive closure component traverses an ontology parent-child hierarchy to create new annotations with parent concepts of concepts in direct annotations. The ontology-mapping component creates new annotations based on existing mappings between different ontologies. Point-to-point mappings that link concepts one another are defined manually or by automatic algorithms in BioPortal.<br />
<br />
==== The is_a transitive closure expansion component ====<br />
An is_a transitive closure component traverses an ontology parent-child hierarchy to create new annotations with parent concepts. For instance, if data are annotated with a concept from the NCI Thesaurus, such as ''melanoma'', this component generates a new annotation with the concept ''skin neoplasm'', because the NCI Thesaurus provides the knowledge that ''melanoma'' is_a ''skin neoplasm.''<br />
The Annotator uses the is_a relations as they are defined by BioPortal in the <SubClass>/<SuperClass> information for a given concept (accessed via REST web service).<br />
<br />
==== The mapping expansion component ====<br />
An ontology-mapping component creates new annotations based on existing mappings between different ontologies. For example, an annotation done with concept ''40644/Melanoma'' in NCI Thesaurus can be expanded to another one with in SNOMED-CT because the BioPortal provides the mapping information.<br />
The Annotator uses the mapping as they are defined by the repositories: BioPortal mappings are defined in the BioPortal front-end and accessed in an ad-hoc manner.<br />
<br />
=== Annotator Web Service Parameters===<br />
<br />
*See http://www.bioontology.org/wiki/index.php/BioPortal_2.3_Release_Notes for changes in Annotator output and updated information on how to use UMLS ontologies with the Annotator. <br />
<br />
The Annotator Web service offers a set of parameters that allows a user to customize the Annotator workflow and filter the result. To customize the workflow and the result, the user can specify a set of ontologies and a specific set of semantic types. Plus, the two steps of the annotation workflow can be parametrized.<br />
<br />
The Annotator Web service response time depends on the selected components as each consumes resources at a different level. For example, the ''is_a'' transitive closure takes a long time to process, even when using a pre-computed hierarchy table. As another example, an annotation with ''wholeWordOnly=false'' will be significantly longer that with ''wholeWordOnly=true''.<br />
<br />
Please see below for the list of parameters and the possible values.<br />
<br />
<br />
{| border="1" cellpadding="2"<br />
|-valign="top"<br />
|width="10%"|'''longestOnly'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies either or not the concept recognition step (done with University of Michigan Mgrep tool) must match the longest words only if they are several concepts that match to an expression.<br />
<br />
* If ''longestOnly=true'', the Annotator selects only the longest term matching phrase. For example, if ''longestOnly=true'', the phrase ''breast cancer'' generates only ''breast cancer.'' If ''longestOnly=false'', it generates three annotations: ''breast'', ''cancer'' and ''breast cancer.'' <br />
<br />
* Attention, if the Annotator finds an annotation with the complete phrase in an ontology composing the dictionary, partial annotations with other ontologies will not be generated. For example, because ''breast cancer'' exists in Human Disease and the NCI Thesaurus, if ''longestOnly=true'', annotations generated with those terms will block annotations with the terms ''breast'' in the Vaccine Ontology or ''cancer'' in BIRNLex. For this reason, we discourage the uses of the '''longestOnly''' parameter when the Annotator is used with one or a small number of ontologies.<br />
<br />
|-valign="top"<br />
|width="10%"|'''wholeWordOnly'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies whether the concept recognition step must match whole words only or not, if they are several concepts that match to a given word.<br />
* For example: If ''wholeWordOnly=true'', the phrase 'neoplasms' will match the concept NCI/C0027651 (Neoplasms) only. If ''wholeWordOnly=false'', the concept NCI/C1551054 (S) or the concept NCI/C0242536 (ASM) will also match (~80 concepts in NCI) in addition.<br />
* Note that the concept recognition step does not consider text cast.<br />
<br />
|-valign="top"<br />
|width="10%"|'''filterNumber'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies whether the concept recognition step to filter numbers or not.<br />
<br />
|-valign="top"<br />
|width="10%"|'''stopWords'''<br />
|width="10%"|{stopWord1,...,stopWordN}<br />
|width="10%"|default: empty (i.e. none)<br />
|width="70%"|Specifies the list of stop words to use. <br />
|-valign="top"<br />
|width="10%"|'''withDefaultStopWords'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies whether to use the default stop words or not. The default stop word list is available from sample HTML page. If set to true, this override the value of stopWords given by the user.<br />
|-valign="top"<br />
|width="10%"|'''isStopWordsCaseSenstive '''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies whether stopwords are case-sensitive or not.<br />
|-valign="top"<br />
|width="10%"|'''minTermSize'''<br />
|width="10%"|{integer} <br />
|width="10%"|default: 0<br />
|width="70%"|Specifies the minimum length of the term to be included in the annotations. <br />
|-valign="top"<br />
|width="10%"|'''scored'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies either or not the annotations are scored. A score is a number assigned to an annotation that reflects the accuracy of the annotation. The higher the score is the better the annotation is. The scoring algorithm gives a specific weight to an annotation according to the context of this annotation. For instance, an annotation done by matching a concept preferred name will be given a higher weight than an annotation done by matching a concept synonym or than an annotation done with a parent level 3 in the is_a hierarchy. Details on the scoring algorithm are given in section Scoring algorithm.<br />
* For example, the phrase 'melanoma' is annotated both with the concept NCI/C0025202 (melanoma) and the concept NCI/C1522102 (Mouse Melanoma). The former annotation is scored 10 where as the latter is scored 8.<br />
|-valign="top"<br />
|width="10%"|'''withSynonyms'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: true<br />
|width="70%"|Specifies either or not the direct annotations are done with or without Synonyms. By default it includes all the synonyms and preferred name. If 'false' is selected, the direct annotations are done with only preferred name. <br />
|-valign="top"<br />
|width="10%"|'''ontologiesToExpand'''<br />
|width="10%"|{localOntology1,...,localOntologyN}<br />
|width="10%"|default: empty (i.e. all ontologies)<br />
|width="70%"|Specifies the list of ontologies to use with the mapping semantic expansion component. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces).<br />
* For example, 40403,40644,40401. <br />
* '''NOTE''': The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies<br />
|-valign="top"<br />
|width="10%"|'''ontologiesToKeepInResult'''<br />
|width="10%"|{localOntology1,...,localOntologyN}<br />
|width="10%"|default: empty (i.e. all ontologies)<br />
|width="70%"|Specifies the list of ontologies to keep in the result of the annotation process. The list of ontologies that can be used is available in the sample HTML page. The values are separated with comma (without spaces).<br />
* For example, 40403,40644,40401.<br />
* '''NOTE''': The list of ontologies that are available via the Annotator Web service are those listed with <status>28</status> from this Web service call: http://rest.bioontology.org/obs/ontologies<br />
|-valign="top"<br />
|width="10%"|'''isVirtualOntologyId'''<br />
|width="10%"|{true, false}<br />
|width="10%"|default: false<br />
|width="70%"|Specifies whether the input values are virtualOntologyId instead of localOntologyid. VirtualOntologyId is not version-specific.<br />
|-valign="top"<br />
|width="10%"|'''semanticTypes'''<br />
|width="10%"|{semanticType1,...,semanticTypeN} <br />
|width="10%"|default: empty (i.e. all semanticTypes)<br />
|width="70%"|Specifies the list of semantic types to use in the annotation process. The list of semantic types that can be used is available in the sample HTML page. The values are separated with comma (without spaces). Note that the restriction to semantic types is also applied during the semantic expansion steps.<br />
* For example, T047,T048,T191.<br />
|-valign="top"<br />
|width="10%"|'''levelMax'''<br />
|width="10%"|{integer} <br />
|width="10%"|default: 0<br />
|width="70%"|Specifies the maximum level a parent concept must have to be considered for the is_a semantic closure expansion step. <br />
* For example, a call done with ''levelMax=3'' will expand a direct annotations done with a concept up to the 3rd level parent in the is_a hierarchy for this concept. A call done with ''levelMax=0'' is equivalent to disable the is_a transitive closure expansion step.<br />
|-valign="top"<br />
|width="10%"|'''mappingTypes'''<br />
|width="10%"|{null,mappingType1,...,mappingTypeN} <br />
|width="10%"|default: empty (i.e. all mappingTypes)<br />
|width="70%"|Specifies the list of mapping type to use during the mapping expansion step. The list of semantic types that can be used is available in the sample HTML page. The values are separated with comma (without spaces). The current list is described hereafter.<br />
* For example, from-mrrel,Human.<br />
* Note that the use of the key word "'''null'''" in the '''mappingTypes''' list disables the mapping expansion component. Note also that the mapping expansion is also limited by other parameters such as ''ontologiesToExpand'' and ''ontologiesToKeepInResult''.<br />
* The current list of mapping type is:<br />
** ''inter-cui'': This mapping type corresponds to the mappings available between CUIs in the UMLS Metathesaurus. For instance, NCI/C0025202 and MSH/C0025202 are mapped together because the share the same CUI in UMLS.<br />
** ''from-mrrel'': This mapping type corresponds to the mappings available in the MRREL table from UMLS.<br />
** ''Automatic'': This mapping type corresponds to the mappings automatically imported in BioPortal.<br />
** ''Manual'': This relation name corresponds to the mappings created by users in BioPortal.<br />
** ''Human'': This relation name corresponds to the mapping s [not used anymore] in BioPortal.<br />
<br />
|-valign="top"<br />
|width="10%"|'''textToAnnotate'''<br />
|width="10%"|<br />
|width="10%"|<br />
|width="70%"|Specifies the text to be annotated.<br />
|-valign="top"<br />
|width="10%"|'''format'''<br />
|width="10%"|{xml,text,tabDelimited}<br />
|width="10%"|default: xml<br />
|width="70%"|Specifies the desired format of the response from Annotator. For programmatic access, XML is strongly suggested. <br />
<br />
* ''xml'': returns XML representation of the annotatorResultBean.<br />
* ''text'': returns plain text representation of the annotatorResultBean.<br />
* ''tabDelimited'': shorter version of "Text" format. returns not the full result content but the annotations only (no statistics, etc.). The format of the tab delimited file is: score \t conceptId \t preferredName \t synonyms (separated by ' /// ') \t semanticType (separated by ' /// ') \t contextName \t isDirect \t other context information (e.g., childConceptId, mappedConceptId, level, mappingType) (separated by ' /// ').<br />
<br />
The elements of the Annotator response are described in next section.<br />
<br />
|}<br />
<br />
===Annotator Web Service Response===<br />
<br />
In this section we define the Annotator web service model i.e., what the service returns to the user: the objects as well as their relations and the constraints that applies. Cf the UML class diagram here: http://obs.bioontology.org/docs/model/EARoot/EA3/EA46.htm<br />
<br />
'''Response Content: annotatorResultBean'''<br />
{| border="1" cellpadding="2"<br />
|-valign="top"<br />
|width="10%"|'''resultId'''<br />
|width="90%"| The id of the annotatorResultBean.<br />
|-valign="top"<br />
|width="10%"|'''dictionary'''<br />
|width="90%"| Dictionary contains the metadata (not the content) of the dictionary used for a result. ''dictionaryId'', ''dictionaryName'', and ''dictionaryDate'' identify the dictionary on the server side and give information about its content. Dictionary versioning is strongly linked to the evolution of the ontologies used. Each time ontologies change, the dictionary is updated. All the dictionary information may be useful for comparing results of the Annotator service on time.<br />
|-valign="top"<br />
|width="10%"|'''statistics'''<br />
|width="90%"| Statistics contains information on the number of annotations done for a given context. The ''contextName'' keyword identifies the type of context and ''nbAnnotation'' is the number of annotations of this type.<br />
|-valign="top"<br />
|width="10%"|'''parameters'''<br />
|width="90%"| Parameters summarizes all the parameters specified by the user when requesting the Annotator service. Those parameters are described in previous section.<br />
|-valign="top"<br />
|width="10%"|'''ontologies'''<br />
|width="90%"| To keep the model simple, we provide only the global ontology identifier, ''localOntologyId'' the name (''ontologyName'') and version (''ontologyVersion''). This information come from the original repositories (UMLS/BioPortal) and might help the user to select the right ontology to use. When an ontology is used in the annotation, a result has a set of OntologyUsed which specify 2 other properties: ''nbAnnotation'', the number of annotation that have been made with concepts from this ontology. ''score'', the sum of all the scores of the annotations done with concepts from this ontology (if parameter ''scored=true''). Therefore, score represents the most accurate ontology to annotate the given text.<br />
|-valign="top"<br />
|width="10%"|'''annotations'''<br />
|width="90%"| Annotation is a representation of one annotation. An annotation has a ''score'' which represents the accuracy of the annotation computed by the scoring algorithm (if the scored=true parameter was chosen, otherwise score=-1). An annotation is done with a ''concept'' in a ''context''.<br />
<br />
{| border="2" <!-- The nested table must be on a new line --><br />
|-valign="top"<br />
|width="10%"|'''score'''<br />
|width="90%"| The scoring algorithm gives weight to each annotation according to the annotation context. The final score for an annotation is then calculated as the sum of all the scores of the annotations done with the same concept. Cf Recommender journal paper for more detail for now.<br />
<br />
|-valign="top"<br />
|width="10%"|'''concept'''<br />
|width="90%"| ''Concept'' is a representation of an ontology concept in the Annotator web service ontology model<br />
* ''localConceptId'' - global identifier for the concept in its original repository. <br />
* ''localOntologyId'' - identifier for the ontology in which the concept is defined. <br />
* ''isTopLevel'' - specifies if the concept is a root concept in its ontology. <br />
* ''preferredName'' - label or preferred term for this concept (as assigned by the original repository). <br />
* ''synonyms'' - the set of possible terms that represent the concept but are not preferred. <br />
* ''semanticTypes'' - the set of the semantic types of the concept (assigned by UMLS + T000 and T999). <br />
|-valign="top"<br />
|width="10%"|'''context'''<br />
|width="90%"| ''Context'' specifies if it is a direct or expanded annotation and give precision about the origin of the annotation. ''contextName'' identifies the type of context. The context properties vary with the type of concept. There are 3 possible contexts identified by their contextName:<br />
{| border="2" style="background:#ABCDEF;" <!-- The nested table must be on a new line --><br />
|-valign="top"<br />
|width="10%"|'''MGREP'''<br />
|width="90%"| represents direct annotations done with the Mgrep concept recognizer. A Mgrep context has 3 properties: <br />
* ''termName'' - the expression (preferred name or synonyms) that was matched by Mgrep. <br />
* ''from'' and ''to'' - specify the character index in the given text for the matched expression. Attention, those values are in number of bytes, not characters e.g., ½ is a two-byte character, thus will count for 2 characters.<br />
|-valign="top"<br />
|width="10%"|'''ISA_CLOSURE'''<br />
|width="90%"| represents expanded annotations done with the ''is_a'' transitive closure expansion component. A ISA_CLOSURE context has 2 properties:<br />
* ''childConceptId'' - the concept from which the annotation was derived. <br />
* ''level'' - the distance in the is_a hierarchy between the annotating concept and the concept from which the annotation was derived. <br />
* For example, if a direct annotation with NCI/C0025202 (melanoma) was done, the is_a transitive closure component may expand it to another annotation with NCI/C1302746 (Melanocytic Neoplasm) because the latter is a direct parent (i.e., level 1) concept of the former. The ISA_CLOSURE annotation generated will have the following properties {NCI/C0025202, 1}.<br />
|-valign="top"<br />
|width="10%"|'''MAPPING'''<br />
|width="90%"| represents expanded annotations done with the mapping expansion component. A MAPPING context has 2 properties: <br />
* mappedConceptId identifies the concept from which the annotation was derived. <br />
* mappingType specifies the type of mapping.<br />
|}<br />
|}<br />
|}</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Education&diff=10166Education2010-09-09T05:02:36Z<p>Comm: /* Bio[medical] Informatics */</p>
<hr />
<div>===Publications===<br />
*Please see the main [http://www.bioontology.org/publications.html NCBO Publications Site]<br />
<br />
=== RSS Feeds ===<br />
*Ontology articles in Pubmed in last 60 days [http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0gcn-LTgvdDj0y38wqDUuwq_R5x8QZnS3TX7HIwZ7Jn Feed]<br />
<br />
===Educational Documents, Videos and Slides===<br />
<br />
To see old and new educational materials created and supplied by the NCBO, please visit our main [http://www.bioontology.org/education.html Education Page]<br />
<br />
===Journals of Interest===<br />
====Bio[medical] Informatics====<br />
*[http://www.jamia.org/ Journal of American Medical Informatics Association]<br />
*[http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics]<br />
*[http://bioinformatics.oxfordjournals.org/ Bioinformatics]<br />
*[http://www.biomedcentral.com/bmcbioinformatics/ BMC Bioinformatics]<br />
*[http://bib.oxfordjournals.org/ Briefings in Bioinformatics]<br />
*[http://www.worldscinet.com/jbcb/jbcb.shtml Journal of Bioinformatics and Computational Biology]<br />
*[http://www.elsevier.com/wps/find/journaldescription.cws_home/506040/description?navopenmenu=-2 International Journal of Medical Informatics]<br />
*for more journals, see http://www.hiww.org/jou.html<br />
<br />
====Ontologies====<br />
*[http://www.applied-ontology.org/ Journal of Applied Ontology]<br />
<br />
====Biomedical====<br />
*[http://www.genomebiology.com/ Genome Biology]<br />
*[http://www.nature.com/nbt/index.html Nature Biotechnology]<br />
*[http://www.elsevier.com/wps/find/journaldescription.cws_home/351/description?navopenmenu=-2 Computers in Biology and Medicine]<br />
*[http://www.liebertpub.com/publication.aspx?pub_id=43 Omics: A journal of Integrative Biology]<br />
*[http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description?navopenmenu=-2 Artificial Intelligence in Medicine]<br />
<br />
===Symposia and Meetings===<br />
*[http://iswc2008.semanticweb.org/ ISWC] by [http://www.iswsa.org/ SWSA]<br />
*[http://www.amia.org/meetings/ AMIA]<br />
*[http://www.eswc2008.org/index.html ESWC]<br />
*[http://www.iscb.org/ismb2008/index.php ISMB]<br />
*[http://psb.stanford.edu PSB]<br />
*[http://www2007.org/ WWW Conference]<br />
*[http://www.csd.abdn.ac.uk/kcap07/index.php KCAP/EKAW]<br />
*[http://kr-med.org/2008/index.html KR-MED]<br />
*[http://www.w3.org/2001/sw/hcls/ HCLSIG]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=10130Annotator Web service2010-08-31T16:22:15Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations.<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and continues to rapidly expand. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (formerly referred to as the Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag their data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]] <br />
<br />
*[http://groups.google.com/group/annotator-discuss Annotator GoogleGroup] for discussions on use cases and experiences, e.g. parameters, ontologies, semantic expansion, with the Annotator. <br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Client Examples ===<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]. The sample code includes Perl, Ruby and Java examples. <br />
<br />
=== Prototype releases ===<br />
<br />
* November 2009 - Second prototype including Mmtx: [http://obs.bioontology.org/oba/OBA_v1.2_rest.html] <br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Press Releases ===<br />
* [http://www.genomeweb.com/informatics/stanford-university-and-embl-platforms-aim-give-users-low-pain-handle-ontologies?page=show Stanford University and EMBL Platforms Aim to Give Users a Low-Pain Handle on Ontologies] <br />
* [http://www.genomeweb.com/informatics/jackson-lab-finds-text-mining-software-can-speed-some-database-curation-tasks?page=showJackson Lab Finds Text-Mining Software Can Speed Some Database Curation Tasks]<br />
<br />
=== Papers ===<br />
* [http://www.ncbi.nlm.nih.gov/pubmed/20157492 Integrating text mining into the MGI biocuration workflow.] Dowell KG, McAndrews-Hill MS, Hill DP, Drabkin HJ, Blake JA. Database (Oxford). 2009;2009:bap019. Epub 2009 Nov 21. PMID: 20157492 [PubMed] Free article<br />
* Using the NCBO Web Services for Concept Recognition and Ontology Annotation of Expression Datasets Simon Twigger, Joey Geiger, Jennifer Smith. [http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-559/ SWAT4LS-2009].<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=9957Dissemination Wiki2010-05-25T17:56:28Z<p>Comm: /* NCBO Dissemination */</p>
<hr />
<div>==NCBO Dissemination ==<br />
<br />
'''Past Events'''<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005-2009)]]'''<br />
<br />
'''Events in 2010'''<br />
<br />
*'''[http://www.vph-noe.eu/vph-events/details/100-ontologies-for-the-virtual-physiological-human-workshop Ontologies for the Virtual Physiological Human]''', European Bioinformatics Institute, Hinxton, Cambridge, UK, February 14, 2010 <br />
<br />
*'''[http://abelard.flet.keio.ac.jp/ontology/index.php?InterOntology10 Workshop on Biomedical Ontologies]''', organized as part of InterOntology: Interdisciplinary Ontology Conference, Japanese Center for Ontological Research, Tokyo, Japan, February 27-28, 2010<br />
<br />
*'''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010 Ontology Summit 2010: Creating the Ontologists of the Future]''', NIST, Gaithersburg, MD, March 15-16, 2010. <br />
<br />
*'''[http://fois2010.mie.utoronto.ca/ Formal Ontology in Information Systems]''', Toronto, Canada, May 11-14, 2010.<br />
<br />
*'''[http://www.w3.org/2009/12/rdf-ws/ W3C Workshop – RDF Next Steps]''', Stanford, CA, June 26-17, 2010.<br />
<br />
*'''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_Workshop_-_Medinfo_2010 Workshop on Infectious Disease Ontology]''', Medinfo, Cape Town, South Africa, September 9-15, 2010.<br />
<br />
{| border="1" cellpadding="5" cellspacing="0"<br />
|-<br />
| '''[[ADVANCE NOTICE]]: [http://icbo.buffalo.edu ICBO - 2nd International Conference on Biomedical Ontology], Buffalo, NY, July 29-31, 2011'''<br />
|-<br />
<br />
*For other forthcoming events pertaining to the NCBO's mission, see [http://www.bioontology.org/events.html here]<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/education.html here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations ]]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Dissemination_Wiki&diff=9956Dissemination Wiki2010-05-25T17:51:15Z<p>Comm: /* NCBO Dissemination */</p>
<hr />
<div>==NCBO Dissemination ==<br />
<br />
'''Past Events'''<br />
<br />
*'''[[Meetings and Events | Cumulative List of NCBO Events (2005-2009)]]'''<br />
<br />
'''Events in 2010'''<br />
<br />
*'''[http://www.vph-noe.eu/vph-events/details/100-ontologies-for-the-virtual-physiological-human-workshop Ontologies for the Virtual Physiological Human]''', European Bioinformatics Institute, Hinxton, Cambridge, UK, February 14, 2010 <br />
<br />
*'''[http://abelard.flet.keio.ac.jp/ontology/index.php?InterOntology10 Workshop on Biomedical Ontologies]''', organized as part of InterOntology: Interdisciplinary Ontology Conference, Japanese Center for Ontological Research, Tokyo, Japan, February 27-28, 2010<br />
<br />
*'''[http://ontolog.cim3.net/cgi-bin/wiki.pl?OntologySummit2010 Ontology Summit 2010: Creating the Ontologists of the Future]''', NIST, Gaithersburg, MD, March 15-16, 2010. <br />
<br />
*'''[http://fois2010.mie.utoronto.ca/ Formal Ontology in Information Systems]''', Toronto, Canada, May 11-14, 2010.<br />
<br />
*'''[http://www.w3.org/2009/12/rdf-ws/W3C Workshop – RDF Next Steps]''', Stanford, CA, June 26-17, 2010.<br />
<br />
*'''[http://www.bioontology.org/wiki/index.php/Infectious_Disease_Ontology_Workshop_-_Medinfo_2010 Workshop on Infectious Disease Ontology]''', Medinfo, Cape Town, South Africa, September 9-15, 2010.<br />
<br />
{| border="1" cellpadding="5" cellspacing="0"<br />
|-<br />
| '''[[ADVANCE NOTICE]]: [http://icbo.buffalo.edu ICBO - 2nd International Conference on Biomedical Ontology], Buffalo, NY, July 29-31, 2011'''<br />
|-<br />
<br />
*For other forthcoming events pertaining to the NCBO's mission, see [http://www.bioontology.org/events.html here]<br />
<br />
== Educational Documents, Video and Audio Presentations ==<br />
<br />
* Educational materials created and supplied by the NCBO are available [http://www.bioontology.org/education.html here]<br />
<br />
* For video and audio presentations of NCBO dissemination and training events see: [[Ontology Training: Video and Audio Presentations ]]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=9389Annotator Web service2009-10-27T16:54:04Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]<br />
<br />
* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.<br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9388Resource Index2009-10-27T16:51:00Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The NCBO Resource Index is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Resource Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9387Resource Index2009-10-27T16:49:39Z<p>Comm: /* Documentation */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The '''NCBO Resource Index''' is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Resource Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9386Resource Index2009-10-27T16:47:50Z<p>Comm: /* Collaboration & Acknowledgment */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The '''NCBO Resource Index''' is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9385Resource Index2009-10-27T16:46:55Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The '''NCBO Resource Index''' is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Biomedical Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Biomedical Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=9384Annotator Web service2009-10-27T16:37:05Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The '''NCBO Annotator''' (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|NCBO Annotator Web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]<br />
<br />
* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.<br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9383Resource Index2009-10-27T16:34:50Z<p>Comm: /* Collaboration & Acknowledgment */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The '''NCBO Resource Index''' is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Biomedical Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Biomedical Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Biomedical Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Biomedical Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9382Resource Index2009-10-27T16:24:06Z<p>Comm: /* Documentation */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The '''NCBO Resource Index''' is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Biomedical Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Biomedical Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the NCBO Resource Index DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Biomedical Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Biomedical Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Resource_Index&diff=9381Resource Index2009-10-27T16:19:47Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''Indexing biomedical resources with ontology concepts ''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. <br />
<br />
Using the annotation workflow of the [[Annotator_Web_service|Annotator Web Service]] NCBO has built an biomedical resources index in which biomedical data is indexed by ontology concepts. The index allows a user to search for biomedical data based on ontology concepts. The '''NCBO Resource Index''' is directly queriable in the [http://bioportal.bioontology.org BioPortal] ontology repository: when a user browses a given concept, he has access (link) to the list of resource elements that have been annotated with this concept. A user can also search for resources direclty using the 'All resources' tab.<br />
<br />
In the NCBO Resource Index, we have processed the textual metadata of elements from several biomedical resources such as: [http://www.ebi.ac.uk/arrayexpress/ ArrayExpress], [http://clinicaltrials.gov/ Clinical Trials.gov], [http://goldminer.arrs.org GoldMiner], [http://www.ncbi.nlm.nih.gov/geo/ Gene Expression Omnibus (GEO)] and others. The annotations in the index keeps track of the structures of elements that have been annotated i.e., from which part of the element (e.g., title, description) an annotation has been produced. This information is used to score annotations. <br />
<br />
[[Image:NCBO_BRI_workflow.png|thumb|NCBO Biomedical Resource Index workflow]]<br />
<br />
[[Image:OBR_index_creation_resources.png|thumb|NCBO Biomedical Resource Index creation]]<br />
<br />
Please try the [http://bioportal.bioontology.org/resources NCBO Resource Index] in BioPortal.<br />
<br />
=== Contacts ===<br />
<br />
*For questions or feature requests, contact [mailto:support@bioontology.org?subject=NCBO%20Resources%20Index%20support Support] <br />
<br />
=== Documentation ===<br />
<br />
* [[Resource Index REST Web Service User Guide]]<br />
<br />
* [http://rest.bioontology.org/resource_index/resources/list/ Currently available resource list.]<br />
<br />
* Resource index design and underlying data model (see the bottom image on the right) [[Image:OBR_result_model.png|thumb| NCBO Biomedical Resources Index data model]]<br />
<br />
* [[Processing_OBR_Resources]] - Notes on resources being processed - Developers only.<br />
<br />
* [[Populating_OBS_database]] - Notes on the population of the OBS DB used in the annotation workflow - Developers only.<br />
<br />
* [https://bmir-gforge.stanford.edu/gf/project/obs/ Corresponding Gforge project] - Developers only.<br />
<br />
=== References === <br />
<br />
* Clement Jonquet, Mark A. Musen and Nigam H. Shah, '''A System for Ontology-Based Annotation of Biomedical Data''', ''In A. Bairoch, S. Cohen-Boulakia and C. Froidevaux (eds): International Workshop on Data Integration in The Life Sciences 2008, DILS'08,'' Vol. 5109, Lecture Notes in BioInformatics, p.144-152, Springer-Verlag, June 2008, Evry, France. [http://dils2008.lri.fr/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-DILS08_Jonquet_Musen_Shah_published.pdf pdf - 431Kb]<br />
<br />
* Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen, '''Ontology-driven Indexing of Public Datasets for Translational Bioinformatics''', ''BMC Bioinformatics'', Vol. 10, February 2009. [http://www.biomedcentral.com/bmcbioinformatics/ journal's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-BMCBioInformatics08-Shah-Jonquet-Ontolgy-based_Indexing.pdf pdf - 651 Kb]<br />
<br />
<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* February 2009 - New prototype release (v1.2). API: http://obs.bioontology.org/obr/OBR_v1.2_rest.html<br />
<br />
* March 2008 - First prototype (v1 and v1.1) API: http://ncbolabs-dev2.stanford.edu:8080/Ontrez_v1_API/ - not maintained anymore, please do not use.<br />
<br />
* December 2008 - API specification for the new prototype (v1.2) - not maintained anymore, please do not use.<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The annotation workflow used to create the NCBO Biomedical Resource Index uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the NCBO Biomedical Resource Index client in BioPortal (http://bioportal.bioontology.org/all_resources) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=9380Annotator Web service2009-10-27T16:01:25Z<p>Comm: /* Presentation & Demonstration */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The '''NCBO Annotator''' (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]<br />
<br />
* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.<br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=9379Annotator Web service2009-10-27T16:00:55Z<p>Comm: /* Collaboration & Acknowledgment */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]<br />
<br />
* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.<br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developed by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=9378Annotator Web service2009-10-27T16:00:34Z<p>Comm: /* Collaboration & Acknowledgment */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]<br />
<br />
* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.<br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The NCBO Annotator service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the Annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Commhttps://www.bioontology.org//mediawiki/index.php?title=Annotator_Web_service&diff=9377Annotator Web service2009-10-27T15:59:41Z<p>Comm: /* Community */</p>
<hr />
<div>''To automatically process a piece of data text to annotate it with relevant ontology concepts and return the annotations<br />
''<br />
<br />
=== Presentation & Demonstration ===<br />
<br />
The range of publicly available biomedical data is enormous and is expanding fast. This expansion means that researchers now face a hurdle to extracting the data they need from the large numbers of data that are available. Biomedical researchers have turned to ontologies and terminologies to structure and annotate their data with ontology concepts for better search and retrieval. However, this annotation process cannot be easily automated and often requires expert curators. Plus, there is a lack of easy-to-use systems that facilitate the use of ontologies for annotation. The NCBO Annotator (or Open Biomedical Annotator (OBA)) is an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata. The biomedical community can use the annotator service to tag thier data automatically with ontology concepts. These concepts come from the [http://www.nlm.nih.gov/research/umls/ Unified Medical Language System (UMLS) Metathesaurus] and the [http://bioportal.bioontology.org/ National Center for Biomedical Ontology (NCBO) BioPortal] ontologies. Such annotations facilitate translational discoveries by integrating annotated data.<br />
<br />
[[Image:OBA_service_workflow.png|thumb|OBA web service workflow]]<br />
<br />
Please try the [http://bioportal.bioontology.org/annotate NCBO Annotator service in BioPortal].<br />
<br />
=== Contacts ===<br />
<br />
* For questions or feature requests, contact [mailto:support@bioontology.org?subject=Annotator%20help%20request Support]<br />
<br />
=== Documentation & References ===<br />
<br />
* Annotator REST Web Service User Guide [[Annotator_User_Guide | Annotator User Guide]]<br />
<br />
* Annotator REST Web Service client examples [[Annotator_Client_Examples | Annotator Client Examples]]<br />
<br />
* Annotator Design and underlying Data model: [http://obs.bioontology.org/docs/oba/OBA_v1.1_documentation.htm Documentation here]... to be move to the wiki soon.<br />
<br />
* Please refer to: <br />
** Clement Jonquet, Nigam H. Shah, Mark A. Musen, '''The Open Biomedical Annotator''', ''AMIA Summit on Translational Bioinformatics'', p. 56-60, March 2009, San Francisco, CA, USA. [http://summit2009.amia.org/ conference's web site] [http://www.stanford.edu/~jonquet/Publications/Documents/Article-AmiaSTB09_Jonquet_Shah_Musen.pdf pdf - 201Kb]<br />
<br />
=== Versions (prototypes & releases) ===<br />
<br />
* April 2009 - First production release in BioPortal 2.1<br />
<br />
* March 2009 - Prototype user interface has been deployed on the BioPortal staging server.<br />
<br />
* October 2008 - The prototype (v1.1) has bee released for testing and evaluation. The prototype is still available but please don't use it anymore: [http://obs.bioontology.org/oba/OBA_v1.1_rest.html]<br />
<br />
* May 2008 - First prototype (v1.0) - Has been removed from servers.<br />
<br />
=== Community ===<br />
<br />
After eight months of existence the NCBO Annotator counts already eight academic groups including UCSF, University of Indiana and the Jackson Laboratory that use and experiment the service in specific scenarios. Internally, we have used the annotation workflow to index biomedical data resources with ontology concepts (cf. [[Resource_Index]]).<br />
<br />
Learn more about NCBO Annotator users & use cases: [[NCBO Annotator community]]<br />
<br />
=== Collaboration & Acknowledgment ===<br />
<br />
* The OBA service uses Mgrep in the concept recognition step. We acknowledge the assistance of Manhong Dai and Fan Meng from the [http://portal.ncibi.org/gateway/ National Center for Integrative Biomedical Informatics] (NCIBI).<br />
<br />
* The user interface for the annotator client in BioPortal (http://bioportal.bioontology.org/annotate) is designed & developped by NCBO members from [http://www.thechiselgroup.org/ University of Victoria]</div>Comm