Updates to GlycoRDF and GlycoCT

[Kiyoko F. Aoki-Kinoshita]

Hello GLICers,

I hope everyone is staying safe and healthy!

There have been a few update requests recently to the GlycoRDF ontology, managed by Rene at

https://github.com/ReneRanzinger/GlycoRDF.

And I recall hearing from some people who have made their own amendments/modifications to the

ontology, which may not necessarily be reflected in this repository, perhaps because they require

discussion or agreement from the community.  For example, the standard practice for referencing

publications is dcterms:references, but GlycoRDF proposes its own predicate for references.

So I would like to propose to have a discussion about such potential updates to GlycoRDF, which 

could be held either (a) as an online meeting, (b) via email or (c) via some other communication 

forum such as Slack (for which a GLIC workspace already exists) or Discord.  

On another note, the GlycoCT substituent list also needs to be updated.  So I this is another topic

that could be discussed together with GlycoRDF or separately.

Please respond either directly to me or to the list with your preferences or any other comments.  

In order for these standards to hold up, we need to have a consensus from the community. 

I look forward to your feedback!

Best regards,

Kiyoko

------------------------------------------------------
Kiyoko F. Aoki-Kinoshita
Deputy Director, Glycan & Life Systems Integration Center (GaLSIC) and
Professor, Faculty of Science and Engineering, Soka University
kki...@soka.ac.jp
------------------------------------------------------

[Rene Ranzinger]

HI all,

GlycoRDF: I think an online meeting would be better to discuss these changes. Timezones are a problem but depending on who is interested it may be doable. Before the meeting it would be good to build a list of individual changes that people have done/propose (https://docs.google.com/document/d/1NgSgfaDx1Zqy6c-tvYYLZWI--OLp8L-ZmVMNtpJmVmY/edit#). People that are actively working on the ontology (not with but on) can also be made collaborators on the repository. Currently, Kiyoko, Nobu, Thomas, Sena, Saisuke and Yasunori are collaborators but that list needs review anyway.

GlycoCT: Similar proposal. Online, after we collect all change requests (https://docs.google.com/document/d/188-gSN3ppZaqfGZZcV9SDGBusBxbzTOtcly-q7Gl6pw/edit#). Just adding new substituents will not do much good if we do not update the molecular framework, which is mostly used to read and write GlycoCT. Here, it would be good to know who is using the molecular framework jar and who has done modifications to this code. This discussion should also involve the people working on WURCS-to-GlycoCT-and-back code.

Best,
René

________________________________________
From: glycoinformatics...@googlegroups.com <glycoinformatics...@googlegroups.com> on behalf of Kiyoko F. Aoki-Kinoshita <kki...@soka.ac.jp>
Sent: Wednesday, November 17, 2021 7:53 PM
To: glycoinformatics...@googlegroups.com
Subject: [GLIC] Updates to GlycoRDF and GlycoCT

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

kki...@soka.ac.jp<mailto:kki...@soka.ac.jp>
------------------------------------------------------




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[Kiyoko F. Aoki-Kinoshita]

Hi Rene and anyone interested in the discussion,

I’ve set up a Doodle poll to set up the meeting time.

https://doodle.com/poll/8evawpi39fsqz3i3?utm_source=poll&utm_medium=link

Please submit by the end of this week, and I’ll send out a zoom link.  In the meantime, please also add your comments

to Rene’s document about modifications to GlycoRDF:

https://docs.google.com/document/d/1NgSgfaDx1Zqy6c-tvYYLZWI--OLp8L-ZmVMNtpJmVmY/edit#

and to GlycoCT:

https://docs.google.com/document/d/188-gSN3ppZaqfGZZcV9SDGBusBxbzTOtcly-q7Gl6pw/edit#heading=h.b62i7w15bsgd

I look forward to trying to come up with a consensus to end the year!

Best,

Kiyoko

------------------------------------------------------
Kiyoko F. Aoki-Kinoshita
Deputy Director, Glycan & Life Systems Integration Center (GaLSIC) and
Professor, Faculty of Science and Engineering, Soka University
kki...@soka.ac.jp

------------------------------------------------------

On Nov 19, 2021, at 2:04, Rene Ranzinger <re...@ccrc.uga.edu> wrote:

HI all,

GlycoRDF: I think an online meeting would be better to discuss these changes. Timezones are a problem but depending on who is interested it may be doable. Before the meeting it would be good to build a list of individual changes that people have done/propose (https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1NgSgfaDx1Zqy6c-tvYYLZWI--OLp8L-ZmVMNtpJmVmY%2Fedit%23&amp;data=04%7C01%7Ckkiyoko%40soka.ac.jp%7C62fefea3c51b4a54e25508d9aab58cf4%7Ccd32783e2b0346d395863e023dfc388a%7C0%7C1%7C637728519002029506%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=lQ0%2BwMGan5PPluv34ZD3deA5mb5N7ODcwyfd9Ex25fc%3D&amp;reserved=0). People that are actively working on the ontology (not with but on) can also be made collaborators on the repository. Currently, Kiyoko, Nobu, Thomas, Sena, Saisuke and Yasunori are collaborators but that list needs review anyway.

GlycoCT: Similar proposal. Online, after we collect all change requests (https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F188-gSN3ppZaqfGZZcV9SDGBusBxbzTOtcly-q7Gl6pw%2Fedit%23&amp;data=04%7C01%7Ckkiyoko%40soka.ac.jp%7C62fefea3c51b4a54e25508d9aab58cf4%7Ccd32783e2b0346d395863e023dfc388a%7C0%7C1%7C637728519002029506%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=xaMsae%2FQbT%2FQrcO4QChyaK6YKVS6FGfyHSVgGqHL1m0%3D&amp;reserved=0). Just adding new substituents will not do much good if we do not update the molecular framework, which is mostly used to read and write GlycoCT. Here, it would be good to know who is using the molecular framework jar and who has done modifications to this code. This discussion should also involve the people working on WURCS-to-GlycoCT-and-back code.

Best,
 René

________________________________________
From: glycoinformatics...@googlegroups.com <glycoinformatics...@googlegroups.com> on behalf of Kiyoko F. Aoki-Kinoshita <kki...@soka.ac.jp>
Sent: Wednesday, November 17, 2021 7:53 PM
To: glycoinformatics...@googlegroups.com
Subject: [GLIC] Updates to GlycoRDF and GlycoCT

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello GLICers,

I hope everyone is staying safe and healthy!

There have been a few update requests recently to the GlycoRDF ontology, managed by Rene at

https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FReneRanzinger%2FGlycoRDF&amp;data=04%7C01%7Ckkiyoko%40soka.ac.jp%7C62fefea3c51b4a54e25508d9aab58cf4%7Ccd32783e2b0346d395863e023dfc388a%7C0%7C1%7C637728519002029506%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=ee%2FCbNKNFYVv3RdFD4oSMPArbyzvkQlbTNtWZgmy014%3D&amp;reserved=0.

And I recall hearing from some people who have made their own amendments/modifications to the
ontology, which may not necessarily be reflected in this repository, perhaps because they require
discussion or agreement from the community.  For example, the standard practice for referencing
publications is dcterms:references, but GlycoRDF proposes its own predicate for references.
So I would like to propose to have a discussion about such potential updates to GlycoRDF, which
could be held either (a) as an online meeting, (b) via email or (c) via some other communication
forum such as Slack (for which a GLIC workspace already exists) or Discord.

On another note, the GlycoCT substituent list also needs to be updated.  So I this is another topic
that could be discussed together with GlycoRDF or separately.

Please respond either directly to me or to the list with your preferences or any other comments.
In order for these standards to hold up, we need to have a consensus from the community.
I look forward to your feedback!

Best regards,
Kiyoko

------------------------------------------------------
Kiyoko F. Aoki-Kinoshita
Deputy Director, Glycan & Life Systems Integration Center (GaLSIC) and
Professor, Faculty of Science and Engineering, Soka University
kki...@soka.ac.jp<mailto:kki...@soka.ac.jp>
------------------------------------------------------




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[Kiyoko F. Aoki-Kinoshita]

Hi all,

Based on those who responded to the Doodle poll, I’d like to set the GLIC meeting for Dec. 20, 9pm Japan time.

Here’s the zoom link:

Topic: GLIC online meeting
Time: Dec 20, 2021 09:00 PM Osaka, Sapporo, Tokyo

Join Zoom Meeting
https://us02web.zoom.us/j/81018493618?pwd=eUIxMDZKdnN0WHllSXNuR2ZTNjRHZz09

Meeting ID: 810 1849 3618
Passcode: 440440

Please add your comments to the documents that Rene set up.

Looking forward to the discussion!

Best,

Kiyoko

------------------------------------------------------
Kiyoko F. Aoki-Kinoshita
Deputy Director, Glycan & Life Systems Integration Center (GaLSIC) and
Professor, Faculty of Science and Engineering, Soka University
kki...@soka.ac.jp

------------------------------------------------------



> On Nov 19, 2021, at 2:04, Rene Ranzinger <re...@ccrc.uga.edu> wrote:
>

> HI all,
>
> GlycoRDF: I think an online meeting would be better to discuss these changes. Timezones are a problem but depending on who is interested it may be doable. Before the meeting it would be good to build a list of individual changes that people have done/propose (https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1NgSgfaDx1Zqy6c-tvYYLZWI--OLp8L-ZmVMNtpJmVmY%2Fedit%23&amp;data=04%7C01%7Ckkiyoko%40soka.ac.jp%7C62fefea3c51b4a54e25508d9aab58cf4%7Ccd32783e2b0346d395863e023dfc388a%7C0%7C1%7C637728519002029506%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=lQ0%2BwMGan5PPluv34ZD3deA5mb5N7ODcwyfd9Ex25fc%3D&amp;reserved=0). People that are actively working on the ontology (not with but on) can also be made collaborators on the repository. Currently, Kiyoko, Nobu, Thomas, Sena, Saisuke and Yasunori are collaborators but that list needs review anyway.
>
> GlycoCT: Similar proposal. Online, after we collect all change requests (https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F188-gSN3ppZaqfGZZcV9SDGBusBxbzTOtcly-q7Gl6pw%2Fedit%23&amp;data=04%7C01%7Ckkiyoko%40soka.ac.jp%7C62fefea3c51b4a54e25508d9aab58cf4%7Ccd32783e2b0346d395863e023dfc388a%7C0%7C1%7C637728519002029506%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=xaMsae%2FQbT%2FQrcO4QChyaK6YKVS6FGfyHSVgGqHL1m0%3D&amp;reserved=0). Just adding new substituents will not do much good if we do not update the molecular framework, which is mostly used to read and write GlycoCT. Here, it would be good to know who is using the molecular framework jar and who has done modifications to this code. This discussion should also involve the people working on WURCS-to-GlycoCT-and-back code.

>
> Best,
> René
>
> ________________________________________
> From: glycoinformatics...@googlegroups.com <glycoinformatics...@googlegroups.com> on behalf of Kiyoko F. Aoki-Kinoshita <kki...@soka.ac.jp>
> Sent: Wednesday, November 17, 2021 7:53 PM
> To: glycoinformatics...@googlegroups.com
> Subject: [GLIC] Updates to GlycoRDF and GlycoCT
>
> [EXTERNAL SENDER - PROCEED CAUTIOUSLY]
>
> Hello GLICers,
>
> I hope everyone is staying safe and healthy!
>
> There have been a few update requests recently to the GlycoRDF ontology, managed by Rene at

> https://jpn01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FReneRanzinger%2FGlycoRDF&amp;data=04%7C01%7Ckkiyoko%40soka.ac.jp%7C62fefea3c51b4a54e25508d9aab58cf4%7Ccd32783e2b0346d395863e023dfc388a%7C0%7C1%7C637728519002029506%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&amp;sdata=ee%2FCbNKNFYVv3RdFD4oSMPArbyzvkQlbTNtWZgmy014%3D&amp;reserved=0.

>
> And I recall hearing from some people who have made their own amendments/modifications to the
> ontology, which may not necessarily be reflected in this repository, perhaps because they require
> discussion or agreement from the community. For example, the standard practice for referencing
> publications is dcterms:references, but GlycoRDF proposes its own predicate for references.
> So I would like to propose to have a discussion about such potential updates to GlycoRDF, which
> could be held either (a) as an online meeting, (b) via email or (c) via some other communication
> forum such as Slack (for which a GLIC workspace already exists) or Discord.
>
> On another note, the GlycoCT substituent list also needs to be updated. So I this is another topic
> that could be discussed together with GlycoRDF or separately.
>
> Please respond either directly to me or to the list with your preferences or any other comments.
> In order for these standards to hold up, we need to have a consensus from the community.
> I look forward to your feedback!
>
> Best regards,
> Kiyoko
>
> ------------------------------------------------------
> Kiyoko F. Aoki-Kinoshita
> Deputy Director, Glycan & Life Systems Integration Center (GaLSIC) and
> Professor, Faculty of Science and Engineering, Soka University
> kki...@soka.ac.jp<mailto:kki...@soka.ac.jp>
> ------------------------------------------------------
>
>
>
>
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> You received this message because you are subscribed to the Google Groups "Glycoinformatics Consortium GLIC" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to glycoinformatics-conso...@googlegroups.com<mailto:glycoinformatics-conso...@googlegroups.com>.

[Thomas Lütteke]

Hi all,

I apologize for not attending today's meeting. Some colleagues start their x-mas break tomorrow, so today we had an extended "last-day-of-the-year" lunch break, and I forgot to leave for the zoom meeting. Please let me know if there is any important result of today's meeting that I should know.

Best regards
Thomas