search

brain-bican / metadata-schemas

A repository for BICAN metadata schemas and their development.
4 stars 3 forks source link

Library Metadata Additions #36

Closed patrick-lloyd-ray closed 5 months ago

patrick-lloyd-ray commented 6 months ago

Per request from Rashmie, the following are requested additions to the library metadata schema:

If @hongna2008 and team approve these, I can add them to the schema and update.

hongna2008 commented 6 months ago

I will check this with Jim.

Thanks,

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.***> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

  • dissociated_cell_sample_preparation_date
  • dissociated_cell_sample_cell_label_barcode
  • enriched_cell_sample_cell_label_barcode
  • enriched_cell_sample_preparation_date
  • histone_modification_marker
  • library_pool_preparation_date
  • flowcell

If @hongna2008 https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHub https://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA . You are receiving this because you were mentioned.Message ID: @.***>

KimberlySmithAllen commented 6 months ago

These fields were part of the final LMM data list and are already in the SeqLib Portal. They need to be approved. Kim

hongna2008 commented 6 months ago

Hi, Patrick and Kim,

These are new data elements to your last version. More information is needed to complete the data elements definition. I am copying this request to Jim and Hua, they may directly response to this request.

Thank you for maintaining this metadata.

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.***> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

  • dissociated_cell_sample_preparation_date
  • dissociated_cell_sample_cell_label_barcode
  • enriched_cell_sample_cell_label_barcode
  • enriched_cell_sample_preparation_date
  • histone_modification_marker
  • library_pool_preparation_date
  • flowcell

If @hongna2008 https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHub https://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA . You are receiving this because you were mentioned.Message ID: @.***>

hongna2008 commented 6 months ago

Hi, Kim,

For the request below,

Per request from Rashmie, the following are requested additions to the library metadata schema:

Is this part of the coordinated effort you and GQ’s team worked on? Are these elements added to your current work with GQ’s team after the final release from the L2M task force? Are these elements in the SeqPortal already? We just want to make sure that these metadata elements are coordinated effort and are not in conflict or redundant with what you guys are currently working on.

Also, alone the line of how we should maintain the library minimal metadata for future update, we propose to let you to be the owner for any future update evaluation and approval, since you are actively continuing this line of work. Would that be ok with you? I think having one owner who has the working knowledge would be appropriate, and we need to have this explicitly decided so that the process of update would be clear.

Thanks,

Jim

-- W. Jim Zheng, Ph.D., Professor Founding Director, Data Science and Informatics Core for Cancer Research Director, Bioinformatics and High-Performance Computing Service Center Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence] 7000 Fannin St | Suite 600 | Houston, Texas, 77030 Phone: (713) 500-3641 | Email: @.**@.> https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm https://sbmi.uth.edu/dsiccr/ https://sbmi.uth.edu/bioinformatics/index.htm

From: Na Hong @.> Date: Thursday, March 14, 2024 at 4:49 PM To: brain-bican/metadata-schemas @.> Cc: Mention @.>, brain-bican/metadata-schemas @.>, @. @.>, @. @.>, Zheng, Wenjin J @.***> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36) External: Increase caution when handling links and attachments.

Hi, Patrick and Kim,

These are new data elements to your last version. More information is needed to complete the data elements definition. I am copying this request to Jim and Hua, they may directly response to this request.

Thank you for maintaining this metadata.

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.**@.>> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

If @hongna2008https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHubhttps://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA. You are receiving this because you were mentioned.Message ID: @.***>

hongna2008 commented 6 months ago

Hi Jim –

Thank you for proposing that I be the owner for evaluating and approving LMM edits. I think this is appropriate and would be happy to take on this role. I agree this will help with clarity in managing this list.

Yes, these elements are part of the coordinated effort with GQ’s team and are already in the SeqPortal. I support their approval.

4 of these elements were part of the final LMM v4.2_230920 (see table below). 2 additional date fields have been added to the Portal. And the final Flowcell field is produced after sequencing, so wasn’t part of the original scope of the LMM (tissue to pool).

Field Name Definition/Description Data Example Identifier/Metadata Data Type Required/Optional for Analysis Required/Optional for Tracking Allow Null Value Required for Alignment SubGroup Dissociated cell source barcode name Name of oligo used in cell plexing. The oligo will tag allow separate dissociated cell samples to be combined downstream in the barcoded cell sample. The oligo name is associated with a sequence in a lookup table. This sequence will be needed to during analysis, after alignment, to associate reads with parent dissociated cell sample. CMO301 Metadata ValueSet Required Optional Allowed No Dissociated cell sample Enriched cell source barcode name Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes] 1,2 - CPU, H3K27ac 3,4 - HYP, H3K27ac 5,6 - HCa, H3K27ac 7,8 - HCp, H3K27ac (#7 has 10% Hela Spike-in) 9,10 - CPU, H3K27me3 11,12 - HYP, H3K27me3 13,14 - HCa, H3K27me3 15,16 - HCp, H3K27me3 Metadata ValueSet Optional Optional Allowed Yes Enriched cell sample Histone modification marker Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. Each of the Histone antibodies captures an essential part of the epigenome. H3K27ac (Abcam,ab4729, Lot: GR3416787-1), H3K27me3 (Abcam,ab4729, Lot: GR3416787-1) Metadata Text Optional Optional Allowed No Enriched cell sample Library construction date Date of library construction 12/9/2021 Metadata Date Optional Optional Allowed No Library

Let me know if you have further questions! Thanks, Kim

From: Zheng, Wenjin J @.> Sent: Friday, March 15, 2024 6:11 AM To: Kimberly Smith @.> Cc: Mention @.>; hua.xu @.>; @.; brain-bican/metadata-schemas @.>; Patrick Ray @.***> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.

Hi, Kim,

For the request below,

Per request from Rashmie, the following are requested additions to the library metadata schema:

Is this part of the coordinated effort you and GQ’s team worked on? Are these elements added to your current work with GQ’s team after the final release from the L2M task force? Are these elements in the SeqPortal already? We just want to make sure that these metadata elements are coordinated effort and are not in conflict or redundant with what you guys are currently working on.

Also, alone the line of how we should maintain the library minimal metadata for future update, we propose to let you to be the owner for any future update evaluation and approval, since you are actively continuing this line of work. Would that be ok with you? I think having one owner who has the working knowledge would be appropriate, and we need to have this explicitly decided so that the process of update would be clear.

Thanks,

Jim

-- W. Jim Zheng, Ph.D., Professor Founding Director, Data Science and Informatics Core for Cancer Research Director, Bioinformatics and High-Performance Computing Service Center Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence] 7000 Fannin St | Suite 600 | Houston, Texas, 77030 Phone: (713) 500-3641 | Email: @.**@.> https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm https://sbmi.uth.edu/dsiccr/ https://sbmi.uth.edu/bioinformatics/index.htm

From: Na Hong @.**@.>> Date: Thursday, March 14, 2024 at 4:49 PM To: brain-bican/metadata-schemas @.**@.>> Cc: Mention @.**@.>>, brain-bican/metadata-schemas @.**@.>>, @.**@.> @.**@.>>, @.**@.> @.**@.>>, Zheng, Wenjin J @.**@.>> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36) External: Increase caution when handling links and attachments.

Hi, Patrick and Kim,

These are new data elements to your last version. More information is needed to complete the data elements definition. I am copying this request to Jim and Hua, they may directly response to this request.

Thank you for maintaining this metadata.

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.**@.>> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

If @hongna2008https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHubhttps://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA. You are receiving this because you were mentioned.Message ID: @.**@.>>

hongna2008 commented 6 months ago

Thanks a lot, Kim. We really appreciate that you agree to take on the role to manage future updates.

Since those four elements are already in the final version we released, I assume that we don’t really need to approve them.

For the other three elements, maybe we can count them as the update after the L2M task force scope (as we already wrapped up the L2M Task Force), and add them to what Patrick’s group is managing. That way, we maintain things consistently. Please let me know what you guys think @Kim, @Patrick @.***>

Best,

Jim

-- W. Jim Zheng, Ph.D., Professor Founding Director, Data Science and Informatics Core for Cancer Research Director, Bioinformatics and High-Performance Computing Service Center Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence] 7000 Fannin St | Suite 600 | Houston, Texas, 77030 Phone: (713) 500-3641 | Email: @.**@.> https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm https://sbmi.uth.edu/dsiccr/ https://sbmi.uth.edu/bioinformatics/index.htm

From: Kimberly Smith @.> Date: Friday, March 15, 2024 at 11:17 AM To: Zheng, Wenjin J @.> Cc: Mention @.>, hua.xu @.>, @. @.>, brain-bican/metadata-schemas @.>, Patrick Ray @.>, Lydia Ng @.>, Kimberly Smith @.> Subject: RE: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36) External: Increase caution when handling links and attachments.

Hi Jim –

Thank you for proposing that I be the owner for evaluating and approving LMM edits. I think this is appropriate and would be happy to take on this role. I agree this will help with clarity in managing this list.

Yes, these elements are part of the coordinated effort with GQ’s team and are already in the SeqPortal. I support their approval.

4 of these elements were part of the final LMM v4.2_230920 (see table below). 2 additional date fields have been added to the Portal. And the final Flowcell field is produced after sequencing, so wasn’t part of the original scope of the LMM (tissue to pool).

Field Name Definition/Description Data Example Identifier/Metadata Data Type Required/Optional for Analysis Required/Optional for Tracking Allow Null Value Required for Alignment SubGroup Dissociated cell source barcode name Name of oligo used in cell plexing. The oligo will tag allow separate dissociated cell samples to be combined downstream in the barcoded cell sample. The oligo name is associated with a sequence in a lookup table. This sequence will be needed to during analysis, after alignment, to associate reads with parent dissociated cell sample. CMO301 Metadata ValueSet Required Optional Allowed No Dissociated cell sample Enriched cell source barcode name Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes] 1,2 - CPU, H3K27ac 3,4 - HYP, H3K27ac 5,6 - HCa, H3K27ac 7,8 - HCp, H3K27ac (#7 has 10% Hela Spike-in) 9,10 - CPU, H3K27me3 11,12 - HYP, H3K27me3 13,14 - HCa, H3K27me3 15,16 - HCp, H3K27me3 Metadata ValueSet Optional Optional Allowed Yes Enriched cell sample Histone modification marker Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. Each of the Histone antibodies captures an essential part of the epigenome. H3K27ac (Abcam,ab4729, Lot: GR3416787-1), H3K27me3 (Abcam,ab4729, Lot: GR3416787-1) Metadata Text Optional Optional Allowed No Enriched cell sample Library construction date Date of library construction 12/9/2021 Metadata Date Optional Optional Allowed No Library

Let me know if you have further questions! Thanks, Kim

From: Zheng, Wenjin J @.> Sent: Friday, March 15, 2024 6:11 AM To: Kimberly Smith @.> Cc: Mention @.>; hua.xu @.>; @.; brain-bican/metadata-schemas @.>; Patrick Ray @.***> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.

Hi, Kim,

For the request below,

Per request from Rashmie, the following are requested additions to the library metadata schema:

Is this part of the coordinated effort you and GQ’s team worked on? Are these elements added to your current work with GQ’s team after the final release from the L2M task force? Are these elements in the SeqPortal already? We just want to make sure that these metadata elements are coordinated effort and are not in conflict or redundant with what you guys are currently working on.

Also, alone the line of how we should maintain the library minimal metadata for future update, we propose to let you to be the owner for any future update evaluation and approval, since you are actively continuing this line of work. Would that be ok with you? I think having one owner who has the working knowledge would be appropriate, and we need to have this explicitly decided so that the process of update would be clear.

Thanks,

Jim

-- W. Jim Zheng, Ph.D., Professor Founding Director, Data Science and Informatics Core for Cancer Research Director, Bioinformatics and High-Performance Computing Service Center Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence] 7000 Fannin St | Suite 600 | Houston, Texas, 77030 Phone: (713) 500-3641 | Email: @.**@.> https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm https://sbmi.uth.edu/dsiccr/ https://sbmi.uth.edu/bioinformatics/index.htm

From: Na Hong @.**@.>> Date: Thursday, March 14, 2024 at 4:49 PM To: brain-bican/metadata-schemas @.**@.>> Cc: Mention @.**@.>>, brain-bican/metadata-schemas @.**@.>>, @.**@.> @.**@.>>, @.**@.> @.**@.>>, Zheng, Wenjin J @.**@.>> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36) External: Increase caution when handling links and attachments.

Hi, Patrick and Kim,

These are new data elements to your last version. More information is needed to complete the data elements definition. I am copying this request to Jim and Hua, they may directly response to this request.

Thank you for maintaining this metadata.

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.**@.>> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

If @hongna2008https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHubhttps://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA. You are receiving this because you were mentioned.Message ID: @.**@.>>

hongna2008 commented 6 months ago

I'm happy to add these to the metadata standard. I think I have all that I need to update it from here.

I may ask for help with 'flowcell' to make sure that it conforms with shared understanding of the concept. But I'll do that on GitHub (and tag you, Kim).

Best,

Patrick

Patrick L. Ray, Ph.D.

Ontologist

Allen Institute for Brain Science

T: 206.516.6431

M: 206.548.7099

E: @.**@.>

brainscience.alleninstitute.org brain-map.orghttps://brain-map.org/

From: Zheng, Wenjin J @.> Sent: Friday, March 15, 2024 12:33 PM To: Kimberly Smith @.>; Patrick Ray @.> Cc: Mention @.>; hua.xu @.>; @. @.>; brain-bican/metadata-schemas @.>; Lydia Ng @.>; Kimberly Smith @.> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.

Thanks a lot, Kim. We really appreciate that you agree to take on the role to manage future updates.

Since those four elements are already in the final version we released, I assume that we don’t really need to approve them.

For the other three elements, maybe we can count them as the update after the L2M task force scope (as we already wrapped up the L2M Task Force), and add them to what Patrick’s group is managing. That way, we maintain things consistently. Please let me know what you guys think @Kim, @Patrick @.***>

Best,

Jim

--

W. Jim Zheng, Ph.D., Professor

Founding Director, Data Science and Informatics Core for Cancer Research

Director, Bioinformatics and High-Performance Computing Service Center

Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence]

7000 Fannin St | Suite 600 | Houston, Texas, 77030

Phone: (713) 500-3641 | Email: @.**@.>

https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm

https://sbmi.uth.edu/dsiccr/

https://sbmi.uth.edu/bioinformatics/index.htm

From: Kimberly Smith @.> Date: Friday, March 15, 2024 at 11:17 AM To: Zheng, Wenjin J @.> Cc: Mention @.>, hua.xu @.>, @. @.>, brain-bican/metadata-schemas @.>, Patrick Ray @.>, Lydia Ng @.>, Kimberly Smith @.> Subject: RE: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

External: Increase caution when handling links and attachments.

Hi Jim –

Thank you for proposing that I be the owner for evaluating and approving LMM edits. I think this is appropriate and would be happy to take on this role. I agree this will help with clarity in managing this list.

Yes, these elements are part of the coordinated effort with GQ’s team and are already in the SeqPortal.

I support their approval.

4 of these elements were part of the final LMM v4.2_230920 (see table below).

2 additional date fields have been added to the Portal.

And the final Flowcell field is produced after sequencing, so wasn’t part of the original scope of the LMM (tissue to pool).

Field Name

Definition/Description

Data Example

Identifier/Metadata

Data Type

Required/Optional for Analysis

Required/Optional for Tracking

Allow Null Value

Required for Alignment

SubGroup

Dissociated cell source barcode name

Name of oligo used in cell plexing. The oligo will tag allow separate dissociated cell samples to be combined downstream in the barcoded cell sample. The oligo name is associated with a sequence in a lookup table. This sequence will be needed to during analysis, after alignment, to associate reads with parent dissociated cell sample.

CMO301

Metadata

ValueSet

Required

Optional

Allowed

No

Dissociated cell sample

Enriched cell source barcode name

Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes]

1,2 - CPU, H3K27ac 3,4 - HYP, H3K27ac 5,6 - HCa, H3K27ac 7,8 - HCp, H3K27ac (#7 has 10% Hela Spike-in) 9,10 - CPU, H3K27me3 11,12 - HYP, H3K27me3 13,14 - HCa, H3K27me3 15,16 - HCp, H3K27me3

Metadata

ValueSet

Optional

Optional

Allowed

Yes

Enriched cell sample

Histone modification marker

Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. Each of the Histone antibodies captures an essential part of the epigenome.

H3K27ac (Abcam,ab4729, Lot: GR3416787-1), H3K27me3 (Abcam,ab4729, Lot: GR3416787-1)

Metadata

Text

Optional

Optional

Allowed

No

Enriched cell sample

Library construction date

Date of library construction

12/9/2021

Metadata

Date

Optional

Optional

Allowed

No

Library

Let me know if you have further questions!

Thanks,

Kim

From: Zheng, Wenjin J @.> Sent: Friday, March 15, 2024 6:11 AM To: Kimberly Smith @.> Cc: Mention @.>; hua.xu @.>; @.; brain-bican/metadata-schemas @.>; Patrick Ray @.***> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.

Hi, Kim,

For the request below,

Per request from Rashmie, the following are requested additions to the library metadata schema:

Is this part of the coordinated effort you and GQ’s team worked on? Are these elements added to your current work with GQ’s team after the final release from the L2M task force? Are these elements in the SeqPortal already? We just want to make sure that these metadata elements are coordinated effort and are not in conflict or redundant with what you guys are currently working on.

Also, alone the line of how we should maintain the library minimal metadata for future update, we propose to let you to be the owner for any future update evaluation and approval, since you are actively continuing this line of work. Would that be ok with you? I think having one owner who has the working knowledge would be appropriate, and we need to have this explicitly decided so that the process of update would be clear.

Thanks,

Jim

--

W. Jim Zheng, Ph.D., Professor

Founding Director, Data Science and Informatics Core for Cancer Research

Director, Bioinformatics and High-Performance Computing Service Center

Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence]

7000 Fannin St | Suite 600 | Houston, Texas, 77030

Phone: (713) 500-3641 | Email: @.**@.>

https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm

https://sbmi.uth.edu/dsiccr/

https://sbmi.uth.edu/bioinformatics/index.htm

From: Na Hong @.**@.>> Date: Thursday, March 14, 2024 at 4:49 PM To: brain-bican/metadata-schemas @.**@.>> Cc: Mention @.**@.>>, brain-bican/metadata-schemas @.**@.>>, @.**@.> @.**@.>>, @.**@.> @.**@.>>, Zheng, Wenjin J @.**@.>> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

External: Increase caution when handling links and attachments.

Hi, Patrick and Kim,

These are new data elements to your last version. More information is needed to complete the data elements definition. I am copying this request to Jim and Hua, they may directly response to this request.

Thank you for maintaining this metadata.

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.**@.>> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

If @hongna2008https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHubhttps://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA. You are receiving this because you were mentioned.Message ID: @.**@.>>

hongna2008 commented 6 months ago

Hi, Patrick and Kim,

Great, thanks a lot.

Please do not hesitate to contact us if we can be of any help with future update.

Best,

Jim

-- W. Jim Zheng, Ph.D., Professor Founding Director, Data Science and Informatics Core for Cancer Research Director, Bioinformatics and High-Performance Computing Service Center Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence] 7000 Fannin St | Suite 600 | Houston, Texas, 77030 Phone: (713) 500-3641 | Email: @.**@.> https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm https://sbmi.uth.edu/dsiccr/ https://sbmi.uth.edu/bioinformatics/index.htm

From: Patrick Ray @.> Date: Friday, March 15, 2024 at 2:39 PM To: Zheng, Wenjin J @.>, Kimberly Smith @.> Cc: Mention @.>, hua.xu @.>, @. @.>, brain-bican/metadata-schemas @.>, Lydia Ng @.***> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36) External: Increase caution when handling links and attachments.

I'm happy to add these to the metadata standard. I think I have all that I need to update it from here.

I may ask for help with 'flowcell' to make sure that it conforms with shared understanding of the concept. But I'll do that on GitHub (and tag you, Kim).

Best,

Patrick

Patrick L. Ray, Ph.D.

Ontologist

Allen Institute for Brain Science

T: 206.516.6431

M: 206.548.7099

E: @.**@.>

brainscience.alleninstitute.org brain-map.orghttps://brain-map.org/

From: Zheng, Wenjin J @.> Sent: Friday, March 15, 2024 12:33 PM To: Kimberly Smith @.>; Patrick Ray @.> Cc: Mention @.>; hua.xu @.>; @. @.>; brain-bican/metadata-schemas @.>; Lydia Ng @.>; Kimberly Smith @.> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.

Thanks a lot, Kim. We really appreciate that you agree to take on the role to manage future updates.

Since those four elements are already in the final version we released, I assume that we don’t really need to approve them.

For the other three elements, maybe we can count them as the update after the L2M task force scope (as we already wrapped up the L2M Task Force), and add them to what Patrick’s group is managing. That way, we maintain things consistently. Please let me know what you guys think @Kim, @Patrick @.***>

Best,

Jim

--

W. Jim Zheng, Ph.D., Professor

Founding Director, Data Science and Informatics Core for Cancer Research

Director, Bioinformatics and High-Performance Computing Service Center

Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence]

7000 Fannin St | Suite 600 | Houston, Texas, 77030

Phone: (713) 500-3641 | Email: @.**@.>

https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm

https://sbmi.uth.edu/dsiccr/

https://sbmi.uth.edu/bioinformatics/index.htm

From: Kimberly Smith @.> Date: Friday, March 15, 2024 at 11:17 AM To: Zheng, Wenjin J @.> Cc: Mention @.>, hua.xu @.>, @. @.>, brain-bican/metadata-schemas @.>, Patrick Ray @.>, Lydia Ng @.>, Kimberly Smith @.> Subject: RE: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

External: Increase caution when handling links and attachments.

Hi Jim –

Thank you for proposing that I be the owner for evaluating and approving LMM edits. I think this is appropriate and would be happy to take on this role. I agree this will help with clarity in managing this list.

Yes, these elements are part of the coordinated effort with GQ’s team and are already in the SeqPortal.

I support their approval.

4 of these elements were part of the final LMM v4.2_230920 (see table below).

2 additional date fields have been added to the Portal.

And the final Flowcell field is produced after sequencing, so wasn’t part of the original scope of the LMM (tissue to pool).

Field Name

Definition/Description

Data Example

Identifier/Metadata

Data Type

Required/Optional for Analysis

Required/Optional for Tracking

Allow Null Value

Required for Alignment

SubGroup

Dissociated cell source barcode name

Name of oligo used in cell plexing. The oligo will tag allow separate dissociated cell samples to be combined downstream in the barcoded cell sample. The oligo name is associated with a sequence in a lookup table. This sequence will be needed to during analysis, after alignment, to associate reads with parent dissociated cell sample.

CMO301

Metadata

ValueSet

Required

Optional

Allowed

No

Dissociated cell sample

Enriched cell source barcode name

Name of molecular barcode used to individual Enriched Cell Source to allow for pooling of Enriched Cell Sources before 10x load (Barcoding Cell step) [aka 1st round barcodes]

1,2 - CPU, H3K27ac 3,4 - HYP, H3K27ac 5,6 - HCa, H3K27ac 7,8 - HCp, H3K27ac (#7 has 10% Hela Spike-in) 9,10 - CPU, H3K27me3 11,12 - HYP, H3K27me3 13,14 - HCa, H3K27me3 15,16 - HCp, H3K27me3

Metadata

ValueSet

Optional

Optional

Allowed

Yes

Enriched cell sample

Histone modification marker

Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used in conjunction with an Enriched Cell Source Barcode in order to combine multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome method. Each of the Histone antibodies captures an essential part of the epigenome.

H3K27ac (Abcam,ab4729, Lot: GR3416787-1), H3K27me3 (Abcam,ab4729, Lot: GR3416787-1)

Metadata

Text

Optional

Optional

Allowed

No

Enriched cell sample

Library construction date

Date of library construction

12/9/2021

Metadata

Date

Optional

Optional

Allowed

No

Library

Let me know if you have further questions!

Thanks,

Kim

From: Zheng, Wenjin J @.> Sent: Friday, March 15, 2024 6:11 AM To: Kimberly Smith @.> Cc: Mention @.>; hua.xu @.>; @.; brain-bican/metadata-schemas @.>; Patrick Ray @.***> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

CAUTION: This email originated from outside the Allen Institute. Please do not click links or open attachments unless you've validated the sender and know the content is safe.

Hi, Kim,

For the request below,

Per request from Rashmie, the following are requested additions to the library metadata schema:

Is this part of the coordinated effort you and GQ’s team worked on? Are these elements added to your current work with GQ’s team after the final release from the L2M task force? Are these elements in the SeqPortal already? We just want to make sure that these metadata elements are coordinated effort and are not in conflict or redundant with what you guys are currently working on.

Also, alone the line of how we should maintain the library minimal metadata for future update, we propose to let you to be the owner for any future update evaluation and approval, since you are actively continuing this line of work. Would that be ok with you? I think having one owner who has the working knowledge would be appropriate, and we need to have this explicitly decided so that the process of update would be clear.

Thanks,

Jim

--

W. Jim Zheng, Ph.D., Professor

Founding Director, Data Science and Informatics Core for Cancer Research

Director, Bioinformatics and High-Performance Computing Service Center

Associate Director, Translational Excellence and Application in Medicine – Artificial Intelligence

[Text Description automatically generated with medium confidence]

7000 Fannin St | Suite 600 | Houston, Texas, 77030

Phone: (713) 500-3641 | Email: @.**@.>

https://sbmi.uth.edu/faculty-and-staff/jim-zheng.htm

https://sbmi.uth.edu/dsiccr/

https://sbmi.uth.edu/bioinformatics/index.htm

From: Na Hong @.**@.>> Date: Thursday, March 14, 2024 at 4:49 PM To: brain-bican/metadata-schemas @.**@.>> Cc: Mention @.**@.>>, brain-bican/metadata-schemas @.**@.>>, @.**@.> @.**@.>>, @.**@.> @.**@.>>, Zheng, Wenjin J @.**@.>> Subject: Re: [brain-bican/metadata-schemas] Library Metadata Additions (Issue #36)

External: Increase caution when handling links and attachments.

Hi, Patrick and Kim,

These are new data elements to your last version. More information is needed to complete the data elements definition. I am copying this request to Jim and Hua, they may directly response to this request.

Thank you for maintaining this metadata.

Na

On Thu, Mar 14, 2024 at 16:13 Patrick Lloyd Ray @.**@.>> wrote:

Per request from Rashmie, the following are requested additions to the library metadata schema:

If @hongna2008https://github.com/hongna2008 and team approve these, I can add them to the schema and update.

— Reply to this email directly, view it on GitHubhttps://github.com/brain-bican/metadata-schemas/issues/36, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AEAG5Q5BKURNFFOONYGTFZTYYIAGNAVCNFSM6AAAAABEWY2EFGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE4DOMJYHE2TQOA. You are receiving this because you were mentioned.Message ID: @.**@.>>