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[bioontology-support] [BioPortal] Feedback from Melissa Haendel

Melissa Haendel melissa at tislab.org
Mon Jun 24 19:42:06 PDT 2019


Hi John,
Well check on the following ones, just for grins and giggles:

HPO (the popular one we care about)
Mondo (the new not so popular one we care about)

Some examples of surprising results:
"Body in numbers project terminology” and “growth medium ontology” are higher on the list than EFO or Uberon or GO

FoodOn is pretty low down, lower than OGMS (which as far as I know, no one actually uses). FoodOn is quite popular in agriculture and diet domains these days.

I know that “use” is different than “visited” or “searched on Google and found” but I wonder if there is not some combined measure that would actually help understand usage? 

Another example is the Symptom ontology- no one uses this except the Disease ontology developers, but its a common search string. 

Do you see what I mean? Mind you I am not complaining whatsoever, this is just a really hard problem! 
Its more of a philosophical request than an actual one ;-)






> On Jun 24, 2019, at 7:32 PM, John Graybeal <jgraybeal at stanford.edu> wrote:
> 
> Hi Melissa,
> 
> Concrete examples will be helpful for me to appreciate your perspective. (For example, sometimes outdated ontologies actually get heavy usage for particular reasons, depending on the ontology. But the never-used case seems very strange.)
> 
> Yes, I think these rankings are significantly driven by people landing from Google. We have thought about other ways to monitor traffic/value, like downloads, time-on-page, tree view clicks, API calls (weighted for ontology size, since we require people to page through an entire ontology it makes for more calls), and so on.  I think it would be a really interesting exercise to brainstorm all the options with you, and perhaps others to review as well.
> 
> We may have historical statistics, I will see what we can put together. I'd like to get a better idea what causes the variation if we can. Possibly we can change the algorithm to use a longer period of time, but no point if the variability has a long cycle.
> 
> We'll see if anyone else chimes in on the list on this topic, and I'll let you know offline if/when I get more data. 
> 
> I should say, we are likely stretched too thin to make any immediate changes unless they are super-easy. But maybe we can get some data you can use for your purposes. 
> 
> John
> 
> 
> 
>> On Jun 24, 2019, at 7:09 PM, Melissa Haendel <melissa at tislab.org <mailto:melissa at tislab.org>> wrote:
>> 
>> Hi John,
>> 
>> Nice to see you in my inbox.
>> 
>> We are seeing a lot of variability in the rankings. Also there are some outdated or never-used ontologies on the list higher than some we know are more widely used. Is it simply because of people landing there from Google? 
>> 
>> This is an interesting question- how to monitor usage. I wonder what a longer period might look like, and/or by ontologies for which someone actually opens the graph or downloads the file? 
>> 
>> For openly available ontologies, its a nice metric for popularity that we can use in our grants, but not if the ranking changes frequently and by a lot. 
>> 
>> Anyway, there may well be nothing wrong, its just less useful for this purpose then?
>> 
>> Let me know if you want to brainstorm. 
>> 
>> Cheers,
>> Melissa 
>> 
>>> On Jun 23, 2019, at 5:39 PM, John Graybeal <jgraybeal at stanford.edu <mailto:jgraybeal at stanford.edu>> wrote:
>>> 
>>> Hi Melissa,
>>> 
>>> Can you help us with more precise details about your concern?
>>> 
>>> Popularity based on ontology visits is seen on the front page and the ontology browse page (https://bioportal.bioontology.org/ontologies <https://bioportal.bioontology.org/ontologies>). These statistics change monthly based on Google metrics for page visits.
>>> 
>>> The Recommender (https://bioportal.bioontology.org/recommender <https://bioportal.bioontology.org/recommender>) makes recommendations based on a number of factors, one of which is the visit-based popularity. 
>>> 
>>> Are you seeing a lot of variation in the Google visit rankings, and suggesting we should use a longer average of the Google visits metric?  I know there can be significant month-to-month variation in the access statistics for some of these ontologies, as seen on their summary pages.
>>> 
>>> John
>>> 
>>>> On Jun 22, 2019, at 4:29 PM, support at bioontology.org <mailto:support at bioontology.org> wrote:
>>>> 
>>>> Name: Melissa Haendel
>>>> 
>>>> Email: melissa at tislab.org <mailto:melissa at tislab.org>
>>>> Location: https%3A%2F%2Fbioportal.bioontology.org <http://2fbioportal.bioontology.org/>%2Fontologies
>>>> 
>>>> 
>>>> Feedback:
>>>> 
>>>> popularity ranking doesn't seem correct and seems to change daily. I think how it was earlier seemed to work better. A user usually wants to know how frequently a source is accessed, maybe do so over the past year or quarter, so that they don't jump around so much?
>>>> 
>>>> 
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu <mailto:bioontology-support at lists.stanford.edu>
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support <https://mailman.stanford.edu/mailman/listinfo/bioontology-support>
>>> 
>>> ========================
>>> John Graybeal
>>> Technical Program Manager
>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>>> Stanford Center for Biomedical Informatics Research
>>> 650-736-1632
>>> 
>>> 
>> 
> 
> ========================
> John Graybeal
> Technical Program Manager
> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> 650-736-1632
> 
> 

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