GEO?

[DataMedFeedback]

Are GEO results being shown? In search I complete it doesn't look like it..

[naturalbeau]

Reply has been sent to user.

Hi, Melissa,

This is from Datamed development team. 
GEO results are included in Datamed. Can you tell us what you search for and take some screenshots about the problem? This will help us to find out the problem.

Thanks Xiaoling

[naturalbeau]

User replied:

For example When I search GEE for the word rabies I get 73 results:

In DataMed there are none showing from GEO. Is it just a subset of GEO?

[naturalbeau]

@jgrethe @yul129

Reply to user as following:

Hi, Melissa,

DataMed includes datasets which are included in GEO dataset browser https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS756. I have put your concern into our github issue and let people in our team handling the data ingestion aware of this issue. Please check the update in the github issue tracker in a later time. https://github.com/biocaddie/prototype_issues/issues/244

Thank you very much for contacting us and letting us know your concern.

Best Xiaoling

[yul129]

This was what i get back when I searched "GDS756". https://datamed.org/search.php?query=GDS756&searchtype=data

Maybe the data was running updates when the user was searching through DataMed.

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From: Xiaoling [notifications@github.com] Sent: Tuesday, February 21, 2017 1:29 PM To: biocaddie/prototype_issues Cc: Yueling Li; Mention Subject: Re: [biocaddie/prototype_issues] GEO? (#244)

@jgrethehttps://github.com/jgrethe @yul129https://github.com/yul129

Reply to user as following:

Hi, Melissa,

DataMed includes datasets which are included in GEO dataset browser https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS756. I have put your concern into our github issue and let people in our team handling the data ingestion aware of this issue. Please check the update in the github issue tracker in a later time.

244https://github.com/biocaddie/prototype_issues/issues/244

Thank you very much for contacting us and letting us know your concern.

Best Xiaoling

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/biocaddie/prototype_issues/issues/244#issuecomment-281486839, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALPhs3ZrO0xOSlLYz2Ue1FtnBO9v4de_ks5re1cigaJpZM4MHztA.

[naturalbeau]

I think the user search "rabies" and get different results from GEO and Datamed. Datamed does not return any result for this search from the geo repository.

[yul129]

Searching "rabies" in GEO dataset browser also gets 0 results.

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From: Xiaoling [notifications@github.com] Sent: Monday, February 27, 2017 11:30 AM To: biocaddie/prototype_issues Cc: Yueling Li; Mention Subject: Re: [biocaddie/prototype_issues] GEO? (#244)

I think the user search "rabies" and get different results from GEO and Datamed. Datamed does not return any result for this search from the geo repository.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/biocaddie/prototype_issues/issues/244#issuecomment-282825764, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ALPhs9wf5Dy1t7DzIoeCugwfCWCryq2Kks5rgyRBgaJpZM4MHztA.

[naturalbeau]

Search from here gets 73 results. https://www.ncbi.nlm.nih.gov/gds/?term=rabies The user expects we return the same results as this one. I think this is because of the granularity problem when we ingest the metadata.

[jgrethe]

It actually returns 0 datasets for that query.

We just added a series index (distinct from the dataset index). We will need to examine the different levels of indexing. As the sample level seems to return the most hits and we don't index down to that level yet...