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[bioontology-support] NCIT ontology not working?

Al Shapiro als371 at yahoo.com
Sat Feb 1 14:17:40 PST 2014


Manuel,


Thank you for the quick resolution of this issue...

Al Shapiro



On Saturday, February 1, 2014 9:55 AM, manuelso <manuelso at stanford.edu> wrote:
 
Hi Al,

Thanks for reporting this issue. This issue is resolved now.

Manuel





On Jan 31, 2014, at 5:01 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:

Sorry, my mistake. This is not working. We are looking into it. We did a release yesterday and it seems to have messed things up.
> 
>Ray
> 
>From: Ray Fergerson [mailto:ray.fergerson at stanford.edu>Sent: Friday, January 31, 2014 4:59 PM
>To: Al Shapiro; Mona Salem; bioontology-support at lists.stanford.edu
>Subject: RE: [bioontology-support] NCIT ontology not working?
> 
>Annotation seems to be working. Please post a small snippet of text that should result in annotations.
> 
>Ray
> 
>From: Al Shapiro [mailto:als371 at yahoo.com>Sent: Friday, January 31, 2014 4:50 PM
>To: Ray Fergerson; Mona Salem; bioontology-support at lists.stanford.edu
>Subject: Re: [bioontology-support] NCIT ontology not working?
> 
>Hi Guys,
> 
>I just tried to Manually annotate some text from one of the G6G Abstracts, via the Bioportal Annotator function using NCIT and received:
> 
>No annotations found message...
> 
>I did the same function yesterday, and it all worked A-okay...
> 
>Looks like the NCIT ontology is down or the annotator function is down?
> 
>Correction, I tried the same text, with different Ontologies (GEXO and MO), and received the same No annotations found  message...
> 
>Please advise...
> 
>Thank you,
> 
>Al Shapiro
> 
> 
> 
> 
> 
> 
>On Friday, January 31, 2014 4:30 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
>Mona,
>
>This sample code is setup to access our staging machine. This is almost
>always a bad idea. Suggest you change the REST_URL to our production
>machine (data.bioontology.org) and try it again.
>
>Ray
>
>-----Original Message-----
>From: bioontology-support-bounces at lists.stanford.edu
>[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Mona
>Salem
>Sent: Friday, January 31, 2014 3:39 PM
>To: bioontology-support at lists.stanford.edu
>Subject: [bioontology-support] NCIT ontology not working?
>
>Hi Paul
>I am using your code from github:
>public class AnnotateText {
>
>    static final String REST_URL = "http://stagedata.bioontology.org";
>    static final String API_KEY = "";
>    static final ObjectMapper mapper = new ObjectMapper();
>
>    public static void main(String[] args) throws Exception {
>        String textToAnnotate = URLEncoder.encode("Melanoma is a malignant
>tumor of melanocytes which are found predominantly in skin but also in the
>bowel and the eye.", "ISO-8859-1");
>        
>        // Get just annotations
>        JsonNode annotations = jsonToNode(get(REST_URL +
>"/annotator?text="
>+ textToAnnotate));
>        printAnnotations(annotations);
>        
>        // Annotations with hierarchy
>        annotations = jsonToNode(get(REST_URL +
>"/annotator?max_level=3&text=" + textToAnnotate));
>        printAnnotations(annotations);
>    }
>
>
>I changed the following line, to capture annotations from NCIT ontology
>only.  It did not work:
>JsonNode annotations = jsonToNode(get(REST_URL +
>"/annotator?ontologies=NCIT&text=" + textToAnnotate));  
>
>
>Also, the REST_URL = "http://data.bioontology.org";  right?
>
>Thanks for any follow-up
>Mona Nafoosi
>    
>
>-----Original Message-----
>From: bioontology-support-bounces at lists.stanford.edu
>[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
>bioontology-support-request at lists.stanford.edu
>Sent: Friday, December 20, 2013 11:37 AM
>To: bioontology-support at lists.stanford.edu
>Subject: bioontology-support Digest, Vol 68, Issue 40
>
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>
>Today's Topics:
>
>  1. Re: moving from the old Api to the new Api (Trish Whetzel)
>  2. BioPortal support over the year end holidays (Ray Fergerson)
>  3. Re: Internal server error for programmatic    search
>      (Paul R Alexander)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Fri, 20 Dec 2013 11:12:29 -0800
>From: Trish Whetzel <plwhetzel at gmail.com>
>To: Ray Fergerson <ray.fergerson at stanford.edu>
>Cc: Maria Angeles Sanguino Gonzalez <maria.sanguino at atos.net>,
>    "support at bioontology.org" <support at bioontology.org>
>Subject: Re: [bioontology-support] moving from the old Api to the new
>    Api
>Message-ID:
>    
><CAE4f=ng6cgMwpcXBOEYuwzU-m4Wv4XbwS6ivYYKtXaoWbWgD2Q at mail.gmail.com>
>Content-Type: text/plain; charset="windows-1252"
>
>Thanks Ray. I don't need updated mapping data yet, but was looking to see
>if the mappings now more easily include how they were generated, e.g.
>LOOM, BioPortal UI, dbxref, etc. and stumbled upon this issue.
>
>Is the type of process that generated the mapping included in the output
>from this call:
>http://data.bioontology.org/mappings?ontologies=NCIT,FMA
>
>Trish
>
>
>On Fri, Dec 20, 2013 at 10:57 AM, Ray Fergerson
><ray.fergerson at stanford.edu>wrote:
>
>> Trish,
>>
>>
>>
>> We understand the source of this problem. Unfortunately it will take 
>> some time to fix. The count is correct but the mappings are not 
>> reliably returned. As a workaround, suggest you iterate though the 
>> terms in the smaller of the ontologies and ask for mappings between 
>> each term and any term in the other ontology.
>>
>>
>>
>> This workaround is painful and slow but it should work. It is about 
>> all that we can offer until we have addressed the underlying problem.
>>
>>
>>
>> Ray
>>
>>
>>
>> *From:* bioontology-support-bounces at lists.stanford.edu [mailto:
>> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *Paul R 
>> Alexander
>> *Sent:* Friday, December 20, 2013 9:53 AM
>> *To:* Trish Whetzel
>> *Cc:* Maria Angeles Sanguino Gonzalez; support at bioontology.org Support
>> *Subject:* Re: [bioontology-support] moving from the old Api to the 
>> new Api
>>
>>
>>
>> This is a bug. We?ll be looking into it. Thanks for reporting.
>>
>>
>>
>> Paul
>>
>>
>>
>>
>>
>> On Dec 19, 2013, at 3:09 PM, Trish Whetzel <plwhetzel at gmail.com> wrote:
>>
>>
>>
>> Is the call:
>> http://data.bioontology.org/mappings?ontologies=NCIT,FMA&apikey=YourAP
>> IKey intended to return all 1,937 mappings between FMA and NCIt? Only
>> 1 mapping pair is returned.
>>
>> On the BioPortal mappings page, after selecting NCIt the page lists a 
>> count of 1,937 mappings, but when clicking on the link for FMA only 1 
>> mapping pair is displayed.
>>
>> Trish
>>
>>
>>
>>
>>
>> On Thu, Dec 19, 2013 at 10:00 AM, Paul R Alexander < 
>> palexander at stanford.edu> wrote:
>>
>> Nines,
>>
>>
>>
>> We will update the documentation with mappings examples, thank you for 
>> pointing out that there are none.
>>
>>
>>
>> The specific call that would replace the one you were using is this:
>>
>> http://data.bioontology.org/mappings?ontologies=NCIT,FMA
>>
>>
>>
>> Paul
>>
>>
>>
>>
>>
>> On Dec 19, 2013, at 3:22 AM, Maria Angeles Sanguino Gonzalez < 
>> maria.sanguino at atos.net> wrote:
>>
>>
>>
>> Dear Biportal support team,
>>
>>
>>
>> I?ve receive an email suggesting moving any code that accesses the old 
>> API to the new API. I?m particularly interested in the mappings 
>> resources and I was wondering:
>>
>> -          When de new API (http://data.bioontology.org/metadata/Mapping
>concretely)
>> will provide some examples of use.
>>
>> -          And which is the equivalent method to the old method in
>charge
>> of provide mappings (unidirectional o bidirectional) between two 
>> ontologies (an example of the old method)
>>
>> o
>> http://rest.bioontology.org/bioportal/virtual/mappings/ontologies?sour
>> ceontology=1032&targetontology=1053&pagesize=500&pagenum=1&apikey=8b8e
>> 7850-0dbb-43ba-b29d-b5ed5719532c
>>
>>
>>
>> Many thanks for the excellent work and thanks for the suggestion.
>>
>> Regards,
>>
>> Nines
>>
>>
>>
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>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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>> _______________________________________________
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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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>------------------------------
>
>Message: 2
>Date: Fri, 20 Dec 2013 11:25:10 -0800 (PST)
>From: Ray Fergerson <ray.fergerson at stanford.edu>
>To: <support at bioontology.org>
>Subject: [bioontology-support] BioPortal support over the year end
>    holidays
>Message-ID: <30df73bc.00002df4.0000001c at BMIR-WIN8L-RF1.stanford.edu>
>Content-Type: text/plain; charset="us-ascii"
>
>Every year Stanford has a shutdown of all facilities at the end of the
>year.
>This year the shutdown is from Dec 21 until Jan 6.
>
>
>
>We will of course keep BioPortal running over the holidays. There will be
>little other support available through this mailing list in this period.
>We will only address problems that result in a system failure. We will
>respond to all other bug reports and feature requests when we return the
>week of Jan 6.
>
>
>
>We wish you all a happy holiday season and look forward to working with
>you again in the new year.
>
>
>
>Ray 
>
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>------------------------------
>
>Message: 3
>Date: Fri, 20 Dec 2013 11:36:36 -0800
>From: Paul R Alexander <palexander at stanford.edu>
>To: Maxwell Neal <mneal at u.washington.edu>
>Cc: "support at bioontology.org Support" <support at bioontology.org>
>Subject: Re: [bioontology-support] Internal server error for
>    programmatic    search
>Message-ID: <E42A2924-D7D4-416C-8672-C297E06BE507 at stanford.edu>
>Content-Type: text/plain; charset=windows-1252
>
>You will need to pass along your API Key using the ?apikey=YOUR_APIKEY?
>parameter when you do the request from code. It gets stored in a browser
>cookie and so you may be able to access from your browser just fine.
>
>Here is some sample java code for doing search (The API key here gets set
>in a header, but passing the apikey query string parameter works as well):
>https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/Classes
>Se
>arch.java
>
>Paul
>
>
>On Dec 19, 2013, at 12:16 PM, Maxwell Neal <mneal at u.washington.edu> wrote:
>
>> Hi all,
>> 
>> I am in the process of adapting some existing Java code that I use to
>programmatically search ontologies in BioPortal.  When I try to open a
>connection to the following BioPortal REST URL, I get an HTTP 500 error.
>> 
>> http://data.bioontology.org/search?q=brainstem&ontologies=FMA&format=x
>> ml&exact_match=0
>> 
>> When I paste the same URL into my browser, I do get a successful 
>> search
>result.
>> 
>> Is this really an error on the BioPortal side, as the HTTP code 
>> indicates? (I've included a snippet of my code below, in case it's
>> useful.)
>> 
>> Many thanks,
>> 
>> M
>> 
>> 
>> String text = "brainstem";
>> String bioportalID = "FMA";
>> SAXBuilder builder = new SAXBuilder(); Document doc = null; text = 
>> text.replace(" ", "+"); URL url = new URL(
>>     "http://data.bioontology.org/search?q="
>>         + text + "&ontologies="
>>         + bioportalID + "&format=xml" + "&exact_match=" +
>exactmatch);                
>>             
>> System.out.println(url);
>> URLConnection yc = url.openConnection(); yc.setReadTimeout(60000); // 
>> Timeout after a minute BufferedReader in = new BufferedReader(new 
>> InputStreamReader(yc.getInputStream()));
>> 
>> 
>> 
>> 
>> ---------------------------------
>> Maxwell Neal
>> 
>> Post-doctoral researcher
>> Department of Bioengineering
>> University of Washington
>> mneal at uw.edu
>> ---------------------------------
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>
>------------------------------
>
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>bioontology-support mailing list
>bioontology-support at lists.stanford.edu
>https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
>End of bioontology-support Digest, Vol 68, Issue 40
>
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