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] *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
Thu Oct 24 16:40:54 PDT 2013


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

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 





 

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20131024/151ee42b/attachment-0003.html>


More information about the bioontology-support mailing list