search

infectious-disease-ontology / infectious-disease-ontology-retired

Automatically exported from code.google.com/p/infectious-disease-ontology
1 stars 1 forks source link

ido information still pointed to google project #47

Closed zhengj2007 closed 8 years ago

zhengj2007 commented 8 years ago

The IDO information has not updated. All OWL files still point to google project. Is it possible to update the link on following website: http://www.obofoundry.org/ontology/ido.html http://www.ontobee.org/ontology/IDO

I have problem to view the IDO using the following link today: http://infectious-disease-ontology.googlecode.com/svn/releases/2014-08-01/ido.owl

zhengj2007 commented 8 years ago

Can it be fixed soon?

We cannot load the IDO from the link: http://purl.obolibrary.org/obo/ido.owl which redirect to: http://infectious-disease-ontology.googlecode.com/svn/releases/2014-08-01/ido.owl since the google code shut down.

lgcowell commented 8 years ago

I don’t seem to have edit privileges on the obofoundry site. I will reach out to Chris to see how to proceed. I will reach out to Oliver for ontobee.

The appropriate URL is https://github.com/lgcowell/infectious-disease-ontology.

Thank you for letting us know.

Lindsay — —————————————— Lindsay G. Cowell, PhD Associate Professor Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu 214-648-2289

Administrative Assistant: Mack Dressler Mack.Dressler@UTSouthwestern.edumailto:Mack.Dressler@UTSouthwestern.edu 214-648-2558

From: jie zheng notifications@github.com<mailto:notifications@github.com> Reply-To: lgcowell/infectious-disease-ontology reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, May 11, 2016 at 4:05 PM To: lgcowell/infectious-disease-ontology infectious-disease-ontology@noreply.github.com<mailto:infectious-disease-ontology@noreply.github.com> Subject: [lgcowell/infectious-disease-ontology] ido information still pointed to google project (#47)

The IDO information has not updated. All OWL files still point to google project. Is it possible to update the link on following website: http://www.obofoundry.org/ontology/ido.html http://www.ontobee.org/ontology/IDO

I have problem to view the IDO using the following link today: http://infectious-disease-ontology.googlecode.com/svn/releases/2014-08-01/ido.owl

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHubhttps://github.com/lgcowell/infectious-disease-ontology/issues/47

UT Southwestern

Medical Center

The future of medicine, today.

zhengj2007 commented 8 years ago

@lgcowell you can do it when you have a github account. You can make the changes and commit it in your own branch and create a pull request for your commit. The file you need to update is: https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/ido.yml

zhengj2007 commented 8 years ago

@lgcowell I can help on update the IDO purl redirects and IDO project metadata on the OBO Foundry website. However, I cannot find the release files in the IDO github project. Could you please let me know the links of them? So, I can set the PURL redirects. The EuPathDB project is using IDO and need to load it into the database. It would be nice the issue can be fixed ASAP.

zhengj2007 commented 8 years ago

@lgcowell I downloaded IDO source code from google project and added into my own account today. There is a directory, releases, contains IDO release files. However, I cannot find these files in the IDO github. https://github.com/zhengj2007/infectious-disease-ontology

lgcowell commented 8 years ago

Hi Jie,

Thank you for offering to help. I really appreciate it. It looks like not all the files/directories migrated from Google Code.

I checked in some new files, but I still need to make sure all the newest stuff is in there. I am on my third harddrive since the migration and want to make sure I am looking at the most current local repository. I will let you know when I am sure all the most recent release files are in.

Thanks!

— —————————————— Lindsay G. Cowell, PhD Associate Professor Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu 214-648-2289

Administrative Assistant: Mack Dressler Mack.Dressler@UTSouthwestern.edumailto:Mack.Dressler@UTSouthwestern.edu 214-648-2558

From: jie zheng notifications@github.com Reply-To: lgcowell/infectious-disease-ontology reply@reply.github.com Date: Wednesday, June 22, 2016 at 12:32 PM To: lgcowell/infectious-disease-ontology infectious-disease-ontology@noreply.github.com Cc: LCOWEL Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [lgcowell/infectious-disease-ontology] ido information still pointed to google project (#47)

@lgcowellhttps://github.com/lgcowell I can help on update the IDO purl redirects and IDO project metadata on the OBO Foundry website. However, I cannot find the release files in the IDO github project. Could you please let me know the links of them? So, I can set the PURL redirects. The EuPathDB project is using IDO and need to load it into the database. It would be nice the issue can be fixed ASAP.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/lgcowell/infectious-disease-ontology/issues/47#issuecomment-227818567, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhcLeAYHFgPMjgfe0mhAJY5zBoWaOks5qOXHEgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

lgcowell commented 8 years ago

Yes, it looks like some directories are missing after the google code migration. Trying to fix that now …

— —————————————— Lindsay G. Cowell, PhD Associate Professor Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu 214-648-2289

Administrative Assistant: Mack Dressler Mack.Dressler@UTSouthwestern.edumailto:Mack.Dressler@UTSouthwestern.edu 214-648-2558

From: jie zheng notifications@github.com Reply-To: lgcowell/infectious-disease-ontology reply@reply.github.com Date: Wednesday, June 22, 2016 at 12:53 PM To: lgcowell/infectious-disease-ontology infectious-disease-ontology@noreply.github.com Cc: LCOWEL Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [lgcowell/infectious-disease-ontology] ido information still pointed to google project (#47)

@lgcowellhttps://github.com/lgcowell I downloaded IDO source code from google project and added into my own account today. There is a directory, releases, contains IDO release files. However, I cannot find these files in the IDO github. https://github.com/zhengj2007/infectious-disease-ontology

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/lgcowell/infectious-disease-ontology/issues/47#issuecomment-227824407, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhdBbBNkdbvJ_-p-adYsa1rnuVtx3ks5qOXaPgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

lgcowell commented 8 years ago

The files you need should be in https://github.com/lgcowell/infectious-disease-ontology/tree/master/releases/2014-08-01

I am going to try and update the ido.yml etc now.

Thanks,

Lindsay

— —————————————— Lindsay G. Cowell, PhD Associate Professor Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu 214-648-2289

Administrative Assistant: Mack Dressler Mack.Dressler@UTSouthwestern.edumailto:Mack.Dressler@UTSouthwestern.edu 214-648-2558

From: jie zheng notifications@github.com Reply-To: lgcowell/infectious-disease-ontology reply@reply.github.com Date: Wednesday, June 22, 2016 at 12:53 PM To: lgcowell/infectious-disease-ontology infectious-disease-ontology@noreply.github.com Cc: LCOWEL Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [lgcowell/infectious-disease-ontology] ido information still pointed to google project (#47)

@lgcowellhttps://github.com/lgcowell I downloaded IDO source code from google project and added into my own account today. There is a directory, releases, contains IDO release files. However, I cannot find these files in the IDO github. https://github.com/zhengj2007/infectious-disease-ontology

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/lgcowell/infectious-disease-ontology/issues/47#issuecomment-227824407, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhdBbBNkdbvJ_-p-adYsa1rnuVtx3ks5qOXaPgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

zhengj2007 commented 8 years ago

@lgcowell Thanks for your quick response. Please let me know if anything I can help.

lgcowell commented 8 years ago

Might you have time for a short phone call this afternoon?

Thanks!

Sent from my iPhone

On Jun 23, 2016, at 8:40 PM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

@lgcowellhttps://github.com/lgcowell Thanks for your quick response. Please let me know if anything I can help.

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/lgcowell/infectious-disease-ontology/issues/47#issuecomment-228234863, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhZz4WEch6gLOZ-wvaVEvBqVCiEBIks5qOzWdgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

zhengj2007 commented 8 years ago

@lgcowell

I made following changes on IDO development version:

Following changes on release 2010-12-02

Following changes on release 2014-08-01

I think PURL redirect to a merged release file is much easy to maintain especially when location of the project repository is changed.

The editing commit history can be found on the page: https://github.com/infectious-disease-ontology/infectious-disease-ontology/commits/jz

Lindsay, could you please review the development version IDO under jz branch: https://github.com/infectious-disease-ontology/infectious-disease-ontology/tree/jz/trunk/src/ontology/ido-core

If you think it is OK, I will merge the changes I made to master branch and make a new release.

Thanks!

Jie

ps: I have updated IDO PURL links by editing ido.yml. James has committed the changes I made. However, it won't fix the issue of loading latest IDO release (2014-08-01) since the PURLs were not set for the imported IDO files.

lgcowell commented 8 years ago

These look great! Thank you!!

— —————————————— Lindsay G. Cowell, PhD Associate Professor Division of Biomedical Informatics Department of Clinical Sciences University of Texas Southwestern Medical Center Lindsay.Cowell@utsouthwestern.edumailto:Lindsay.Cowell@utsouthwestern.edu 214-648-2289

Administrative Assistant: Mack Dressler Mack.Dressler@UTSouthwestern.edumailto:Mack.Dressler@UTSouthwestern.edu 214-648-2558

From: jie zheng notifications@github.com Reply-To: infectious-disease-ontology/infectious-disease-ontology reply@reply.github.com Date: Friday, July 1, 2016 at 10:25 AM To: infectious-disease-ontology/infectious-disease-ontology infectious-disease-ontology@noreply.github.com Cc: LCOWEL Lindsay.Cowell@UTSouthwestern.edu, Mention mention@noreply.github.com Subject: Re: [infectious-disease-ontology/infectious-disease-ontology] ido information still pointed to google project (#47)

@lgcowellhttps://github.com/lgcowell

I made following changes on IDO development version:

Following changes on release 2010-12-02

Following changes on release 2014-08-01

I think PURL redirect to a merged release file is much easy to maintain especially when location of the project repository is changed.

The editing commit history can be found on the page: https://github.com/infectious-disease-ontology/infectious-disease-ontology/commits/jz

Lindsay, could you please review the development version IDO under jz branch: https://github.com/infectious-disease-ontology/infectious-disease-ontology/tree/jz/trunk/src/ontology/ido-core

If you think it is OK, I will merge the changes I made to master branch and make a new release.

Thanks!

Jie

ps: I have updated IDO PURL links by editing ido.yml. James has committed the changes I made. However, it won't fix the issue of loading latest IDO release (2014-08-01) since the PURLs were not set for the imported IDO files.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/infectious-disease-ontology/infectious-disease-ontology/issues/47#issuecomment-229975763, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhWRGSl1xG_dNjMKMeKcvJXJqy3ZDks5qRTFvgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

zhengj2007 commented 8 years ago

@lgcowell Shall i merge the changes and make a release of IDO?

lgcowell commented 8 years ago

That would be wonderful! Thank you again for all your help!

Sent from my iPhone

On Jul 3, 2016, at 10:21 PM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

@lgcowellhttps://github.com/lgcowell Shall i merge the changes and make a release of IDO?

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/infectious-disease-ontology/infectious-disease-ontology/issues/47#issuecomment-230192509, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhSJHdooaGSSBIm5_fWoJniiMDpLpks5qSG4SgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

zhengj2007 commented 8 years ago

Sure. I will work on it. Jie

On 7/3/16 10:39 PM, lgcowell wrote:

That would be wonderful! Thank you again for all your help!

Sent from my iPhone

On Jul 3, 2016, at 10:21 PM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

@lgcowellhttps://github.com/lgcowell Shall i merge the changes and make a release of IDO?

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/infectious-disease-ontology/infectious-disease-ontology/issues/47#issuecomment-230192509, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhSJHdooaGSSBIm5_fWoJniiMDpLpks5qSG4SgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/infectious-disease-ontology/infectious-disease-ontology/issues/47#issuecomment-230194075, or mute the thread https://github.com/notifications/unsubscribe/AF9bRHkyu1BpZOuKVakxrPHvbs5TbCcuks5qSHJSgaJpZM4IcfgJ.

zhengj2007 commented 8 years ago

@lgcowell I have created a new release and merged the changes I made to master branch. I will update the PURLs redirection. When everything works, I will let you know.

lgcowell commented 8 years ago

That's fantastic. Thanks!

Sent from my iPhone

On Jul 5, 2016, at 1:47 PM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

@lgcowellhttps://github.com/lgcowell I have created a new release and merged the changes I made to master branch. I will update the PURLs redirection. When everything works, I will let you know.

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/infectious-disease-ontology/infectious-disease-ontology/issues/47#issuecomment-230550579, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhV1Y36HTuJy7zt1qaCsABJ4Vxzz9ks5qSpjCgaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.

zhengj2007 commented 8 years ago

@lgcowell IDO purls have been updated. We are done :)

lgcowell commented 8 years ago

Yay!!

Sent from my iPhone

On Jul 6, 2016, at 10:15 PM, jie zheng notifications@github.com<mailto:notifications@github.com> wrote:

@lgcowellhttps://github.com/lgcowell IDO purls have been updated. We are done :)

You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/infectious-disease-ontology/infectious-disease-ontology/issues/47#issuecomment-230961286, or mute the threadhttps://github.com/notifications/unsubscribe/AF4uhUWMer3Yugkka1fZz27wcO-dxBu4ks5qTGE3gaJpZM4IcfgJ.

UT Southwestern

Medical Center

The future of medicine, today.