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[bioontology-support] *Second Request* - The annotations in the output report for the Annotator do Not always match the Annotations in the JSON file...

Ray Fergerson ray.fergerson at stanford.edu
Fri Nov 1 13:23:03 PDT 2013


The documentation essentially is an example:



http://data.bioontology.org/documentation#nav_batch



This call gets back prefLabel, Synonym, and semantic type. You can eliminate 
the last two (toward the end of the example) to just get prefLabel.



Ray



From: Al Shapiro [mailto:als371 at yahoo.com]
Sent: Thursday, October 24, 2013 5:34 PM
To: Ray Fergerson; bioontology-support at lists.stanford.edu; 
support at bioontology.org
Cc: Mona Salem
Subject: Re: *Second Request* - The annotations in the output report for the 
Annotator do Not always match the Annotations in the JSON file...



Ray,



When you have some time, can you send me an example of the batch call 
passing all classes, so that I can then get access to all the preferred 
names, because it is the "preferred names" that I consider to be the 
multiple annotations that I am looking for, for my project....



In other words, how does one do this process!



Thank you for your quick response because I know you guys are swamped with 
support e-mails...



Al Shapiro











On Thursday, October 24, 2013 4:40 PM, Ray Fergerson 
<ray.fergerson at stanford.edu> wrote:

Sorry about the delay. I think that I understand the question. I think that 
the service and the file are working correctly. I believe that the problem 
is that it is difficult to see the connection between what it displayed in 
the table and the contents of the json file. Perhaps this will help:



The first column in the table is the preferred name of the matched class. 
This name does not necessarily appear anywhere in the json output. We make 
another call to get the preferred name for all matched classes (a batch call 
passing all classes and getting back all preferred names). The “annotations 
text” in the result may or may not be the same as the preferred name. For 
example if the match was on a synonym then it will not be the same. Likewise 
if the match was a hierarchy or mapping match then it will not be the same.



Ray



From: Al Shapiro [mailto:als371 at yahoo.com]
Sent: Thursday, October 24, 2013 12:20 PM
To: Ray Fergerson; bioontology-support at lists.stanford.edu; 
support at bioontology.org
Cc: Al; Mona Salem
Subject: *Second Request* - The annotations in the output report for the 
Annotator do Not always match the Annotations in the JSON file...



Ray and support personnel,



I know you guys are busy but I would appreciate some feedback on the 
following BioPortal Annotator problem that I have outlined below the 
following:



a) Acknowledgement that it is or it is Not a problem;



b) If it is Not a problem, how can I locate (via the JSON output file) the 
matching annotations that display in the Annotation report;



c) If it is deemed a problem, approximately how long will it take for you 
guys to fix it.



Thanks again - see details about this problem below,



Al Shapiro



On Monday, October 21, 2013 5:17 PM, Al Shapiro <als371 at yahoo.com> wrote:

Hi there again,



The annotations in the output report for the Annotator do Not always match 
the Annotations in the JSON file...



The annotations from the output report in column 1 do Not always match the 
"annotations text" in the JSON file...



Note: Over 60% of the Annotations on the displayed report do Not match what 
is in the JSON file...



entry 1) column 1 of the report = NCI CTEP SDC Melanoma Sub-Category 
Terminology;

and the first "annotations text" entry in the JSON file  =  "MELANOMA"



entry 2) column 1 of the report = Melanoma Pathway;

and the second "annotations text" entry in the JSON file  =  "MELANOMA"



entry 3) column  1 of the report = Melanoma;

and the third "annotations text" entry in the JSON file  =  "MELANOMA"



entry 4) column  1 of the report = Mouse Melanoma;

and the fourth "annotations text" entry in the JSON file  =  "MELANOMA"



entry 5) column  1 of the report = Malignant Neoplasm;

and the fifth "annotations text" entry in the JSON file  =  "MALIGNANT 
TUMOR"



entry 6) column  1 of the report = Malignant Paraganglioma;

and the sixth "annotations text" entry in the JSON file  =  "MALIGNANT"



entry 7) column  1 of the report = Anaplastic Oligodendroglioma;

and the seventh "annotations text" entry in the JSON file  =  "MALIGNANT"



entry 8) column  1 of the report = MALIGNANT;

and the eighth "annotations text" entry in the JSON file  =  "MALIGNANT"



entry 9) column  1 of the report = Neoplasm;

and the ninth "annotations text" entry in the JSON file  =  "Tumor"



entry 10) column  1 of the report = Tumor Mass;

and the tenth "annotations text" entry in the JSON file  =  "Tumor"



entry 11) column  1 of the report = Melanocyte;

and the eleventh "annotations text" entry in the JSON file  =  "MELANOCYTES"



entry 12) column  1 of the report = Murine Melanocytes;

and the twelfth "annotations text" entry in the JSON file  =  "MELANOCYTES"



entry 13) column  1 of the report = Present;

and the thirteenth "annotations text" entry in the JSON file  =  "FOUND"



entry 14) column  1 of the report = Skin;

and the fourteenth "annotations text" entry in the JSON file  =  "SKIN"



entry 15) column  1 of the report = Murine Skin;

and the fifteenth "annotations text" entry in the JSON file  =  "SKIN"



entry 16) column  1 of the report = Mouse Skin;

and the sixteenth "annotations text" entry in the JSON file  =  "SKIN"



entry 17) column  1 of the report = Murine Intestines;

and the seventeenth "annotations text" entry in the JSON file  =  "BOWEL"



entry 18) column  1 of the report = Intestine;

and the eighteenth "annotations text" entry in the JSON file  =  "BOWEL"



entry 19) column  1 of the report = Murine Eye;

and the nineteenth "annotations text" entry in the JSON file  =  "EYE"



entry 20) column  1 of the report = Eye;

and the twentieth "annotations text" entry in the JSON file  =  "EYE"



entry 21) column  1 of the report = Mouse Eye;

and the twenty first "annotations text" entry in the JSON file  =  "EYE"



Do the following to reproduce the above results:



1) Go to the  BioPortal Manual Annotator page;

2) Click on "insert sample text"; [Melanoma is a malignant tumor of 
melanocytes which are found predominantly in skin but also in the bowel and 
the eye.]

3) In the "Select Ontologies" box enter the National Cancer Institute 
Thesaurus (NCIT) ontology;

4) Click on "Get Annotations" button;

5) After the Annotations report displays on the screen, Click on Format 
Results As:     JSON link;

6) Examine results from both outputs.



Note: My company is developing an application system that needs to Annotate 
the Text contained in the biological software product abstracts located at 
The G6G Directory of Omics and Intelligent Software web-site: 
http://g6g-softwaredirectory.com/



Any insight would be greatly appreciated,



Thank you,



Al Shapiro







































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