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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...

Al Shapiro als371 at yahoo.com
Thu Oct 24 12:20:23 PDT 2013


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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