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geneontology / go-annotation

This repository hosts the tracker for issues pertaining to GO annotations.
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Review annotations to GO:0097311 bacterial biofilm matrix #1964

Closed rachhuntley closed 6 years ago

rachhuntley commented 6 years ago

This term has been renamed from 'biofilm matrix' as it was originally defined for bacteria (see https://github.com/geneontology/go-ontology/pull/15694). Most of the annotations to this term, however, are from fungal species.

Fungal annotations should be moved to the new term GO:0062040 'fungal biofilm matrix'. Any non-fungal or non-bacterial should go to the new parent term GO:0062039 'biofilm matrix'.

Please review the annotations in the spreadsheet https://docs.google.com/spreadsheets/d/1mRunQl71yjU5jHxXL5tdcaX93JSaSq7CJC1B4r47mio/edit#gid=0

I've tagged the following people. Apologies if you are not the correct person, but could you suggest an alternative? @dianeoinglis AspergillusDB @marekskrzypek Candida Genome Database

marekskrzypek commented 6 years ago

Yes, I am the correct person to contact about CGD and AspGD. I don't know anything about AspergillusDB, but I suspect this is meant to be AspGD. Diane is no longer involved.

Thanks, Marek

On May 8, 2018, at 7:29 AM, Rachael Huntley notifications@github.com<mailto:notifications@github.com> wrote:

This term has been renamed from 'biofilm matrix' as it was originally defined for bacteria (see geneontology/go-ontology#15694https://github.com/geneontology/go-ontology/pull/15694). Most of the annotations to this term, however, are from fungal species.

Fungal annotations should be moved to the new term GO:0062040 'fungal biofilm matrix'. Any non-fungal or non-bacterial should go to the new parent term GO:0062039 'biofilm matrix'.

Please review the annotations in the spreadsheet https://docs.google.com/spreadsheets/d/1mRunQl71yjU5jHxXL5tdcaX93JSaSq7CJC1B4r47mio/edit#gid=0

I've tagged the following people. Apologies if you are not the correct person, but could you suggest an alternative? @dianeoinglishttps://github.com/dianeoinglis AspergillusDB @marekskrzypekhttps://github.com/marekskrzypek Candida Genome Database

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/geneontology/go-annotation/issues/1964, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVeuT0RnW_H7DhPPJDWhPzGKBKErSVlnks5twYGJgaJpZM4T2eZr.

Marek S. Skrzypek, Ph.D. Senior Biocuration Scientist, Candida Genome Database Saccharomyces Genome Databases Department of Genetics Stanford University School of Medicine Stanford, CA 94305 marek.skrzypek@stanford.edumailto:marek.skrzypek@stanford.edu ORCID: 0000-0001-6749-615X http://www.candidagenome.org/ http://www.yeastgenome.org/

rachhuntley commented 6 years ago

Hi Marek @marekskrzypek, Thanks for this. AspergillusDB is my mistake, I do mean AspGD.

Would you also mind taking a look at this ticket https://github.com/geneontology/go-ontology/issues/15299 to give your opinion on terms for fungal vs. bacterial biofilm matrix?

We would value your expertise. Thanks, Rachael.

marekskrzypek commented 6 years ago

Hi Rachel,

Absolutely! I'll take a look later today.

Thanks, Marek

On May 9, 2018, at 10:32 AM, Rachael Huntley notifications@github.com<mailto:notifications@github.com> wrote:

Hi Marek @marekskrzypekhttps://github.com/marekskrzypek, Thanks for this. AspergillusDB is my mistake, I do mean AspGD.

Would you also mind taking a look at this ticket geneontology/go-ontology#15299https://github.com/geneontology/go-ontology/issues/15299 to give your opinion on terms for fungal vs. bacterial biofilm matrix?

We would value your expertise. Thanks, Rachael.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/geneontology/go-annotation/issues/1964#issuecomment-387759390, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVeuT9xjqdq1DBBCJcv2bfgHCIoxg0hKks5twv4VgaJpZM4T2eZr.

marekskrzypek commented 6 years ago

OK, I just glanced through a few papers... I think I can live with the current definitions for GO:0062039 and GO:0062040. Unless some greater biofilm expert says otherwise, I'll fix them as soon as CGD/AspGD refresh their GO terms (should be in a couple of days )

rachhuntley commented 6 years ago

Great, thanks for looking Marek.

rachhuntley commented 6 years ago

All Candida annotations have now been moved to fungal biofilm matrix. Thanks Marek.