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[bioontology-support] ChEBI in BioPortal

Michael Dorf mdorf at stanford.edu
Thu Feb 11 11:26:10 PST 2016


Hi Melanie,

This should now be resolved. We've deployed the revised code yesterday, and it appears that the latest version of CHEBI has been pulled and processed overnight.

http://bioportal.bioontology.org/ontologies/CHEBI?p=summary

Let me know if you encounter any further issues.

Thanks,

Misha




On Feb 9, 2016, at 11:35, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Melanie,

This is the location we are pulling CHEBI from: ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo

Please let me know if this needs to change. You can also view/edit ontology pull location by going to:

http://bioportal.bioontology.org/ontologies/CHEBI/submissions/97/edit (you need to be signed in as a user that has Admin rights to the ontology).

Misha


On Feb 9, 2016, at 01:10, Melanie Courtot <mcourtot at ebi.ac.uk<mailto:mcourtot at ebi.ac.uk>> wrote:

Hi Misha,

Thanks for the update. Could you clarify where you pull the ChEBI file from? Janna left and there is some uncertainty as to how the system was set up; it'd be useful to make sure the ChEBI developers are pushing the updates in the right place.

Thanks again,
Melanie

On 09/02/2016 01:08, Michael Dorf wrote:
Hi Melanie,

I've had a chance to investigate this issue and found a problem on our end that prevented new versions of CHEBI to be pulled into BioPortal. I've made changes to our codebase aimed at addressing this issue. Our next code deployment is scheduled for this week, so I expect this issue to be resolved by the end of the week. I'll keep you posted on our progress.

Thanks!

Misha


On Feb 5, 2016, at 08:34, John Graybeal <jbgmeta1 at stanford.edu<mailto:jbgmeta1 at stanford.edu>> wrote:

Hi Melanie, nice to have you in the loop. Misha (copied), our BioPortal person looking into this, was sick for a few days, but his first day back yesterday he started setting up a test rig for this. The usual process is deeply embedded with all the imports, so it isn’t practical to test with that.

(Preliminary note: We found some inconsistency on our end when trying to access the ftp content — programmatic access seemed to work, but 2 different browser accesses failed. I mention this just in case it’s helpful for you to know about it, but you should consider it an informal brief!)

John


On Feb 5, 2016, at 5:55 AM, Melanie Courtot <mcourtot at ebi.ac.uk<mailto:mcourtot at ebi.ac.uk>> wrote:

Hi,

Janna told Gareth I would look into this on their behalf as they were not aware of the technical details. I agree that once we know what happens and how if would be useful to include both of them for future maintenance.

Thanks again for looking into this.

Cheers,
Melanie

On 03/02/2016 01:23, Chris Mungall wrote:
Now it's Gareth:
http://obofoundry.org/ontology/chebi.html
(we actively work to keep these up to date, which is more tractable with our smaller list of ontologies)

However, Janna is still involved in the OBO effort and it's never a bad idea to loop her in (one of the advantages of having discussions like this on the tracker is that it's transparent and others can drop in as needed)

..except in this case, the CHEBI purl is fine and up to date, the problem is entirely on the bioportal side I'm afraid

On 2 Feb 2016, at 16:57, John Graybeal wrote:

By the way, the contact person we show for this ontology is Janna Hastings, at hastings at ebi.ac.uk<mailto:hastings at ebi.ac.uk><mailto:hastings at ebi.ac.uk>. Is that not the right person?  If it is, perhaps we should bring Janna into the thread at this point.

john


On Feb 1, 2016, at 7:12 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu><mailto:jgraybeal at stanford.edu>> wrote:

Hi Chris, hi Melanie,

I got your thread and invitation to your repository, thanks very much. I have in fact replaced Ray Fergerson as the lead of the BioPortal project, and I’m happy to look into this issue.

I’m a little swamped, but by Wednesday (at the latest!) we’ll take a look and figure out what the issue is. I think you’ve provided all the information we need for the moment.

John


On Feb 1, 2016, at 10:12 AM, John Graybeal <jbgraybeal at mindspring.com<mailto:jbgraybeal at mindspring.com><mailto:jbgraybeal at mindspring.com>> wrote:



Begin forwarded message:

From: Melanie Courtot <mcourtot at ebi.ac.uk<mailto:mcourtot at ebi.ac.uk><mailto:mcourtot at ebi.ac.uk>>
Subject: Re: ChEBI in BioPortal
Date: February 1, 2016 at 8:52:54 AM PST
To: Chris Mungall <cjmungall at lbl.gov<mailto:cjmungall at lbl.gov><mailto:cjmungall at lbl.gov>>
Cc: jbgraybeal at mindspring.com<mailto:jbgraybeal at mindspring.com><mailto:jbgraybeal at mindspring.com>

Great, thanks. I thought OBO resources were sharing their PURL with NCBO, which then allowed BioPortal to compute an md5, and reload the file when updated?

In this specific case, the latest ChEBI release seems to have been in January 2016 based on the date in the file at http://purl.obolibrary.org/obo/chebi.owl (though it is not a versionIRI and probably ought to be), while the latest refresh date on NCBO is August 2015.

Cheers,
Melanie

On 01/02/2016 16:46, Chris Mungall wrote:
Invited John to the Community team on https://github.com/OBOFoundry/OBOFoundry.github.io/

On 1 Feb 2016, at 8:45, Chris Mungall wrote:

I had nothing to do with it

I think John is the contact, not Ray

This is a general issue I think. Can be discussed here:
https://github.com/OBOFoundry/OBOFoundry.github.io/issues/80

On 1 Feb 2016, at 8:33, Melanie Courtot wrote:

Hi Chris,

I talked to Gareth and he said you may have been involved with setting up ChEBI on bioportal?
The page at https://bioportal.bioontology.org/ontologies/CHEBI doesn't really tell me where they're getting their file from. If you don't know I'll contact Ray and check with him.

Cheers,
Melanie


-------- Forwarded Message --------
Subject:     ChEBI in BioPortal
Date:     Fri, 29 Jan 2016 17:41:16 +0000
From:     Gareth Owen <gowen at ebi.ac.uk<mailto:gowen at ebi.ac.uk>>
To:     Melanie Courtot <courtot at ebi.ac.uk<mailto:courtot at ebi.ac.uk>>



Hi Melanie,

I was told that you may have something to do with the process by which
the ChEBI ontology gets on to BioPortal (possibly via OBO Foundry). If
so, can you take a look to see whether something has changed somewhere -
the last update of ChEBI on Bioportal seems to have been in August of
last year.

Thanks for any help you can offer!

Gareth



========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski



========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski
========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski





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