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[bioontology-support] NCIT ontology not working?

manuelso manuelso at stanford.edu
Sat Feb 1 09:55:22 PST 2014


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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> > ------------------------------------------------------------------
> > _______________________________________________
> > bioontology-support mailing list
> > bioontology-support at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> >
> >
> >
> >
> > _______________________________________________
> > bioontology-support mailing list
> > 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
> 
> 
> 
> ------------------------------
> 
> _______________________________________________
> 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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>  
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