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[bioontology-support] Annotation GET results

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Apr 30 09:02:40 PDT 2020


Hi Ching-Hua,

You could use an API call like the following to examine the latest submission of a given ontology:

http://data.bioontology.org/ontologies/ICD10/latest_submission?include=all

In the JSON results, there should be a “submissionStatus” name/value pair with an array of statuses, e.g.:


[cid:AAB79AAB-3DE6-4EC3-9430-1DDF539B5A07 at stanford.edu]


If any of the processing steps failed, there would be status values with an “ERROR” string, e.g.:


[cid:098F4D4C-6B11-4CCA-81C8-11AFFE790663 at stanford.edu]


Alternatively, you could issue API calls to get the root classes of an ontology, or all of the classes for an ontology. If the ontology failed to process correctly, you would likely see failures or empty sets when trying to access the ontology content:

http://data.bioontology.org/ontologies/ICD10/classes/roots
http://data.bioontology.org/ontologies/ICD10/classes

Finally, you could look at the log file for a given ontology to see if there were any error during processing. Information about log file location is here:

https://www.bioontology.org/wiki/Virtual_Appliance_FAQ#Is_there_a_log_file_for_parsing.3F

We also have some public documentation of the REST API that you may find helpful:

http://data.bioontology.org/documentation

Kind regards,
Jennifer



On Apr 30, 2020, at 7:59 AM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

Thanks, Jennifer!

My apologies, the text I was actually annotating is:

text_to_annotate = "Relationship among genotype, biochemical phenotype, and cognitive performance in females with phenylalanine hydroxylase deficiency: report from the Maternal Phenylketonuria Collaborative Study. OBJECTIVE  To examine the relationship of phenylalanine hydroxylase ( PAH ) genotypes to biochemical phenotype and cognitive development in maternal phenylketonuria ( PKU ) . METHODOLOGY  PAH gene mutations were examined in 222 hyperphenylalaninemic females enrolled in the Maternal PKU Collaborative Study ( MPKUCS ) . A total of 84 different mutations were detected , and complete genotype was obtained in 199 individuals . Based on previous knowledge about mutation-phenotype associations , 78 of the mutations could be assigned to one of four classes of severity ( severe PKU , moderate PKU , mild PKU , and mild hyperphenylalaninemia [ MHP ] ) . Then , 189 MPKUCS subjects were grouped according to the various combinations of mutation classifications . The sample sizes were large enough for statistical testing in four groups with at least one mutation that completely abolishes enzyme activity . These patients are considered functionally hemizygous . RESULTS  The biochemical phenotype predicted from the genotype in functionally hemizygous patients was related significantly to the assigned phenylalanine level . Cognitive performance ( IQ ) was also significantly related to genotype . The IQ of PAH-deficient mothers with a severe PKU mutation in combination with a MHP mutation or a mild PKU mutation was 99 and 96 , respectively , whereas the IQ of PKU mothers with two severe PKU mutations or with one severe and one moderate PKU mutation was 83 and 84 , respectively . Of the patients with PKU , 92 % had been treated during childhood . Those who were untreated or treated late had lower than average IQ scores for their group of mutation combinations . Females with moderate or mild PKU who were treated early and treated for > 6 years showed IQ scores 10 points above average for their group . CONCLUSIONS  The reproductive outcome in maternal phenylketonuria is dependent on prenatal metabolic control and postnatal environmental circumstances . Both factors depend on the intellectual resources of the mother with PKU . The significant relationship among genotype , biochemical phenotype , and cognitive performance observed in the present study is of importance for the development of an optimal strategy for future treatment of females with PKU who plan pregnancy"


Is there a way to check the status of submitted ontologies without using the UI? (My appliance is not very responsive when I try to access it using the UI. However, when I make API calls it seems to be quite responsive. Maybe the reason I am getting empty results for some ontologies is that the request is timing out....)

Should I be examining the ontology submission status? I'm not very familiar with the API yet, if you are able to provide an example API call that can return the status would be much appreciated!

Best,

Ching-Hua Chen

Computational Health Behavior & Decision Science
IBM, T.J. Watson Research Center
1101 Kitchawan Road, Yorktown Heights, NY 10598

chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>
(914) 945-2061 (o); (845) 519-7582 (m)

"Important things tend to be hard. Stay focused on why you started down a particular path in the first place." - Shirley Ann Jackson


----- Original message -----
From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
To: Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>>
Cc: "bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>" <bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>>
Subject: [EXTERNAL] Re: [bioontology-support] Annotation GET results
Date: Wed, Apr 29, 2020 7:25 PM

Hello Ching-Hua,


On Apr 29, 2020, at 3:37 PM, Ching-Hua Chen <chinghua at us.ibm.com<mailto:chinghua at us.ibm.com>> wrote:

I am running the sample code "annotate_txt.py" and experiencing results that I can't understand.

I modified the API call to the following, in order to specifically use the ICD10 ontology:

get_json(REST_URL + "/annotator?ontologies=ICD10&text=" + urllib.parse.quote(text_to_annotate))

When I reference the public bioportal, I get non-zero results for the text_to_annotate provided.


I’m not able to reproduce this on our end. I issued that REST call and public BioPortal returns empty results if you constrain to the ICD10 ontology. This is the specific call that I used:

http://data.bioontology.org/annotator?ontologies=ICD10&text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.

… and I see an empty result set:

<Image.67099FF0-67F6-41E3-80D6-B12A2DAA72E6 at stanford.edu.png>



However, when I change the URL to reference my local Virtual Appliance, the annotation results are empty, even though ICD10 is listed as one of the ontologies on my virtual appliance.

This discrepancy only occurs for some ontologies, and not others, that are on my virtual appliance. Any suggestions on why this might be happening?


If you’re not seeing expected Annotator results from a particular ontology, one thing to check is whether that ontology has been fully and successfully processed in your appliance instance. In other words, look at the ontology metadata page and see if there are any error statuses for the last submission of the ontology. You should see a list of statuses for the last submission that include “Parsed, Indexed, Metrics, Annotator”:

<Image.9FCDB055-8868-46ED-B34B-F08CDE085D2F at stanford.edu.png>


Alternatively, if you have administrative privileges for your appliance instance, you can log in and look at the Admin -> Ontology Administration tab, which will indicate if there are any ontology processing issues.

Kind regards,
Jennifer




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