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[bioontology-support] REST API for Mappings

Manuel Salvadores Olaizola manuelso at stanford.edu
Thu Dec 11 11:40:03 PST 2014


Hi Erik,

The counts in the statistics endpoints get processed once a month. It is actually quite a expensive process and it is possible to have discrepancies between the actual data that you download and the mapping counts. Consider the mapping counts as approximations.

What seems to be a bug is the fact that you downloaded all GO mappings and you did not get any references to GRO. I am created and issue tracker to address this problem. I will get back to you with more comments on this soon.

Thank you very much for reporting this issue.

Manuel


----- Original Message -----
From: "Erik Fäßler" <erik.faessler at uni-jena.de>
To: support at bioontology.org
Sent: Saturday, December 6, 2014 8:50:46 AM
Subject: [bioontology-support] REST API for Mappings

Dear Bioontology-Team, 

I am downloading mappings for GO via the REST api (parameters: pagesize=500&no_context=true&no_links=true). I was expecting mappings into GRO, however my download doesn’t show any. I have got 107000 mappings, most due to “SAME_URI”. I did a ‘grep’ for “GRO” in the mapping data and didn’t find anything. 
I also noticed that my downloaded data does not contain a single LOOM mapping. Viewed from this angle, it’s no wonder I don’t get mappings to GRO since those mappings should all be found by LOOM. 

I did also download the mappings for GRO directory with the same algorithm I used before. Here, I did get 83 LOOM mappings to GO. There should be 94 as I can see from the BioPortal homepage and also from the REST mappings stats call. 

Could you please have a look and tell me what I did wrong perhaps? 

A few other issues I came across: 
1) I tested the mapping download without any parameters; here I got 81 mappings from GRO to GO. When I then used my original parameters again (as shown at the beginning of my mail) the server suddenly responded " <h1>Not Found</h1>” although it had worked moments before. 
2) I wanted to use the mapping stats REST endpoint to validate that my download went alright by comparing the expected number of mappings in the stats response with the actual number of downloaded mappings. According to a call to http://data.bioontology.org/mappings/statistics/ontologies , GO should have 106669 mappings (but I got 107000 as I meantioned before) and GRO should have 5026 mappings but I got 5500. Is this is an intended discrepancy? 

I really hope I’m not just doing all the calls plain wrong and I apologize for any inconvenience my questions might cause. 

Best, 

Erik 

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