Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] contact information about the "Submit a term" functionality in bioportal

Trish Whetzel whetzel at stanford.edu
Mon Oct 18 17:08:24 PDT 2010


Hi Daniel,

I've cc'd the support at bioontology.org mailing list in this reply to help track the discussion.

Best regards,
Trish


On Oct 5, 2010, at 2:17 PM, Daniel Rubin wrote:

> I’ll Trish to this so she can help track it..
>  
> ___________________________________
> <image001.jpg> Daniel L. Rubin, MD, MS                              <image002.jpg>
>             Assistant Professor
>             Department of Radiology | Stanford University
>             Richard M. Lucas Center | 1201 Welch Road, Office P285
>             Stanford, CA 94305-5488
>             Phone: 650-793-9495 | Fax: 650-723-5795
>             Web: http://rubin.web.stanford.edu/
>  
> From: rboden [mailto:rboden at rsna.org] 
> Sent: Tuesday, October 05, 2010 11:19 AM
> To: Paul R Alexander
> Cc: Daniel Rubin
> Subject: Re: contact information about the "Submit a term" functionality in bioportal
>  
> Hello again, I took a stab at putting together a rough web form for submitting notes at the following URL:
> 
> http://radlex.org/suggest_term/
> 
> Upon submitting this, I get the following error:
> No enum const class org.protege.notesapi.notes.NoteType.ProposalForNewEntity
> 
> 
> I'm assuming that I'm not passing in something that it likes for that it likes for the "type" parameter.  I had assumed I should be passing in ProposalForNewEntity based on the following snippet from your documentation:
> 
> * type=ProposalForNewEntity - the type of note to create.
> 
> Perhaps you could shed some light on what I should be passing? Or if I'm doing something wrong with some of the other parameters.
> 
> Thanks!
> 
> 
> On 10/1/2010 1:44 PM, Paul R Alexander wrote:
> Try http://stagerest.bioontology.org/bioportal/notes/44303 orhttp://stage.bioontology.org/ontologies/44303#notes if you want the UI view.
> 
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 
> 
> On 10/1/10 7:54 AM, rboden wrote:
> Thank you, I see that the production link now resolves, but how do I use the staging link?  I tried:http://stage.bioontology.org/bioportal/notes/44303 but it doesn't work for me.  Does the link look different on the staging server?
> 
> 
> 
> On 9/16/2010 1:18 PM, Paul R Alexander wrote:
> The rest service is here:
> http://rest.bioontology.org/bioportal
> 
> So for RadLex the notes would appear here:
> http://rest.bioontology.org/bioportal/notes/44303
> 
> However, RadLex has no notes. NCI Thesaurus does, which you can see here:
> http://rest.bioontology.org/bioportal/notes/42838
> 
> Also, since rest.bioontology.org is our production server, we request that people use our staging server if they want to test the service. On the staging server you can add new notes, delete them, or whatever else you might need to do without affecting the actual service or having test notes appear. The stage address is:
> http://stage.bioontology.org/bioportal
> 
> Let me know if you have any other questions.
> 
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 
> 
> On 9/16/10 11:13 AM, rboden wrote:
> I'm not quite clear on what the URL my HTTP calls should contact should look like.
> 
> I tried: http://bioportal.bioontology.org/notes/44303  But I get back a 404 error.  Am I getting the ontology virtual ID wrong? (I'm just using the number I see in the URL for the standard radlex bioportal page).  Or am I on the wrong domain? or in the wrong subdirectory for the notes service?
> 
> 
> 
> 
> Paul R Alexander wrote:
> Bobby,
> 
> I'm attaching information on using the BioPortal Notes service. Please let me know if I can provide any additional information or answer questions you might have.
> 
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 
> 
> On 9/2/10 1:23 PM, Daniel Rubin wrote:
> Hi Bobby,
> Via this email I'll connect you with Paul.
> DR
>  
> -------------------------------------
> Daniel Rubin, MD, MS
> Assistant Professor, Department of Radiology
> Stanford University
> Richard M. Lucas Center
> 1201 Welch Road, Office P285
> Stanford, CA 94305-5488
> Phone: 650-725-4936  Fax: (650) 723-5795
> http://rubin.web.stanford.edu/
>  
>  
>  
>     
> -----Original Message-----
> From: rboden [mailto:rboden at rsna.org]
> Sent: Thursday, September 02, 2010 9:54 AM
> To: Daniel Rubin
> Subject: contact information about the "Submit a term" functionality in
>       
> bioportal
>     
> I can't seem to get the URL to work in the bioportal that allows us to
> submit a new term.  You'd given me some information on doing it a while
> back, and told me to contact: Paul Alexander if I had any questions, but
> I do not have his contact information.
>       
>     
>  
>  
> Creating Notes in BioPortal
> 
> BioPortal uses ontology notes to describe a variety of user-specified comments and metadata on ontology, including new-term proposals, proposals for changes, comments and questions about classes, and so on.
> 
> BioPortal and REST Principles
> 
> BioPortal utilizes REST principles to create, read, update, and delete resources. The following service documentation uses the HTTP POST method to create notes in the BioPortal system. For more information, please see W3C's documentation on HTTP methods.
> 
> Types of notes in BioPortal
> 
> The following are the types of notes in BioPortal. Please, email us at support at bioontology.org if you have suggestions for other note types (or specific parameters for the notes).
> 
> Basic comments (as they are in BioPortal currently)
> Proposals
> New term proposal
> New relationship proposal
> New attribute value proposal
> Creating a 'Comment' note
> 
> Signature (HTTP POST): ./notes/virtual/{ontology virtual id}?type=Comment&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&email={email_address}
> Alt Signature (HTTP POST): ./notes/{ontology version id}?type=Comment&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&email={email_address}
> Description: creates a new note of the type 'Comment'
> Arguments (* - required):
> * type=Comment - the type of note to create.
> * appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.
> * appliestotype={Class|Individual|Property|Note} - The type of the thing that the note is associated with.
> * subject={subject} - The subject for the comment.
> * content={content} - The content of the comment.
> * author={authorid} - The author's BioPortal user id.
> Creating a 'New Term Proposal' note
> 
> Signature (HTTP POST): ./notes/virtual/{ontology virtual id} ?type=ProposalForNewEntity&appliesto={appliestoid}&appliestotype=Ontology&subject={subject}&reasonforchange={reasonforchange}&author={author}&newtermdefinition={definition}&newtermid={termid}&newtermparent={termparent}&newtermpreferredname={preferredname}&email={email_address}
> Alt Signature (HTTP POST): ./notes/{ontology version id} ?type=ProposalForNewEntity&appliesto={appliestoid}&appliestotype=Ontology&subject={subject}&reasonforchange={reasonforchange}&author={author}&newtermdefinition={definition}&newtermid={termid}&newtermparent={termparent}&newtermpreferredname={preferredname}&email={email_address}
> Description: creates a new note of the type 'New Term Proposal'
> Arguments (* - required):
> * type=ProposalForNewEntity - the type of note to create.
> * appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URLs must be URL-encoded.
> * appliestotype=Ontology - The type of the thing that the note is associated with.
> * subject={subject} - The subject for the comment.
> * author={authorid} - The author's (or application's) BioPortal user id.
> * reasonforchange={reason for change} - An explanation for why the proposal is being made.
> contactinfo={contact information} - Contact information for the entity making the request.
> * termdefinition={definition} - Definition for the new term.
> * termparent={termparent} - ID for the parent of the new term.
> * termpreferredname={preferredname} - Preferred name for the new term.
> termsynonyms={synonym1,synonym2,synonym3} - Synonyms for the new term. Can be a single entry or comma-separated list.
> Obsolete Arugments:
> * termid={termid} - Proposed or generated id for the new term.
> This has been removed to allow for automatic generation of URI ids for use with proposed terms. This will allow you to refer to a term immediately after creating a new term proposal.
> Creating a 'Change Relationship/Hierarchy' note
> 
> Signature (HTTP POST): ./notes/virtual/{ontology virtual id}?type=ProposalForChangeHierarchy&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newtermdefinition={definition}&newtermid={termid}&newtermparent={parent}&newtermpreferredname={preferredname}&newtermsynonyms={listofsynonyms}&email={email_address}
> Alt Signature (HTTP POST): ./notes/{ontology version id}?type=ProposalForChangeHierarchy&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newtermdefinition={definition}&newtermid={termid}&newtermparent={parent}&newtermpreferredname={preferredname}&newtermsynonyms={listofsynonyms}&email={email_address}
> Description: creates a new note of the type 'Comment'
> Arguments (* - required):
> * type=ProposalForChangeHierarchy - the type of note to create.
> * appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.
> * appliestotype=Ontology - The type of the thing that the note is associated with.
> * subject={subject} - The subject for the comment.
> * author={authorid} - The author's BioPortal user id.
> * reasonforchange={reason for change} - An explanation for why the proposal is being made.
> contactinfo={contact information} - Contact information for the entity making the request.
> * relationshiptype={relationshiptype} - The type of relationship that should be created (is_a, part_of, has_part, etc)
> * relationshiptarget={relationshiptarget} - The term to create the relationship with.
> oldrelationshiptarget={oldrelationshiptarget} - The term that the relationship is being changed from (if different than relationshiptarget).
> Creating a 'Change Property Value' note
> 
> Signature (HTTP POST): ./notes/virtual/{ontology virtual id}?type=ProposalForPropertyValueChange&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newpropertyvalue={newvalue}&oldpropertyvalue={oldvalue}&propertyid={propertyid}&email={email_address}
> Alt Signature (HTTP POST): ./notes/{ontology version id}?type=ProposalForPropertyValueChange&appliesto={appliestoid}&appliestotype={appliestotype}&subject={subject}&content={content}&author={author}&newpropertyvalue={newvalue}&oldpropertyvalue={oldvalue}&propertyid={propertyid}&email={email_address}
> Description: creates a new note of the type 'Change Property Value'
> Arguments (* - required):
> * type=ProposalForPropertyValueChange - the type of note to create.
> * appliesto={appliestoid} - The id of the thing to associate the note with. This can be a class (term), individual, property, or another note. For classes, individuals, and properties, the specified id must exist in the target ontology. URIs must be URL-encoded.
> * appliestotype=Ontology - The type of the thing that the note is associated with.
> * subject={subject} - The subject for the comment.
> * author={authorid} - The author's BioPortal user id.
> * reasonforchange={reason for change} - An explanation for why the proposal is being made.
> contactinfo={contact information} - Contact information for the entity making the request.
> * newpropertyvalue={newpropertyvalue} - The new value for the property.
> * oldpropertyvalue={oldpropertyvalue} - The old value for the property.
> * propertyid={propertyid}= The ID of the property to change.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20101018/0bcd9bf9/attachment.html>


More information about the bioontology-support mailing list