SEA-PHAGES | Filling in the Product field

Link to this post \| posted 21 Mar, 2017 16:08
fbaliraine	We are finalizing our annotations but want to be sure of one thing before submission to the QC team. According to Fig 12.2 (attached) in the Resource Guide, the space under “product” is just having the feature number i.e. gp5. I mean, if say we had a “Hypothetical protein” or a known product like “lysin A”, do we still not put this information under product (and thus not replace the “gp5” in this example? Is it the QC team to fill in the product name? 435Kb

Link to this post | posted 21 Mar, 2017 16:08

We are finalizing our annotations but want to be sure of one thing before submission to the QC team. According to Fig 12.2 (attached) in the Resource Guide, the space under “product” is just having the feature number i.e. gp5. I mean, if say we had a “Hypothetical protein” or a known product like “lysin A”, do we still not put this information under product (and thus not replace the “gp5” in this example? Is it the QC team to fill in the product name?

Link to this post \| posted 22 Mar, 2017 18:49
cdshaffer	The important thing with respect to "hypothetical protein" or known function is to be sure to have the correct entries in the notes of your "minimalistic" file when you have a "reportable" function and have the notes field empty when you do not. The "minimalistic" file is described in the section that follows Fig 12.2. Someone from the SMART QC team can correct me it I am wrong, but for the fully noted final file I do not believe you need to add any entries to the product field. Just follow the protocol as described in section "9.3.3 Renumbering & formatting annotated features" to auto fill the product field.

Link to this post | posted 22 Mar, 2017 18:49

cdshaffer

The important thing with respect to "hypothetical protein" or known function is to be sure to have the correct entries in the notes of your "minimalistic" file when you have a "reportable" function and have the notes field empty when you do not. The "minimalistic" file is described in the section that follows Fig 12.2.

Someone from the SMART QC team can correct me it I am wrong, but for the fully noted final file I do not believe you need to add any entries to the product field. Just follow the protocol as described in section "9.3.3 Renumbering & formatting annotated features" to auto fill the product field.

Link to this post \| posted 23 Mar, 2017 23:50
debbie	I am going to add to Chris' correct statement. The "functional annotation" does eventually get put in the product field - by SMART. But you are asked to place functions in the notes. There are buttons in DNA Mater that move the contents of the Notes, Functions, and Products fields. We ask for it in the Notes so that as we overwrite the final file, it will format correctly. So your thinking is logical, our protocol is simply a logistics request to minimize the amount of re-formatting done at QC.

Link to this post | posted 23 Mar, 2017 23:50

debbie

I am going to add to Chris' correct statement. The "functional annotation" does eventually get put in the product field - by SMART. But you are asked to place functions in the notes. There are buttons in DNA Mater that move the contents of the Notes, Functions, and Products fields. We ask for it in the Notes so that as we overwrite the final file, it will format correctly. So your thinking is logical, our protocol is simply a logistics request to minimize the amount of re-formatting done at QC.

Link to this post \| posted 23 Mar, 2018 20:12
kaylafast	I've read the previous responses in this post, but still feel conflicted about the correct formatting for the complete notes and minimalistic files. I've been following the instructions in the online SEA-PHAGES Bioinformatics Guide under the tab "Documenting Your Annotation" and the cover sheet requirements. For the Complete Notes File: Attached is a screenshot of what my files looks like now. I have copied official functions to the function field because of the following line in the online guide, 'All functions are from the official SEA-PHAGES list and are written in the “Function field”. Functions do not have a hard return after them.' Is the "Function Field" the field/box in DNA Master or the "F" slot in the notes? For the Minimal File: Here I followed the instructions in the online guide section called "Final .dnam5 file: Minimal version". Following these steps filled the product field and leaves the function field and notes empty. I'd appreciate help pointing out if there is anything that I should change. 513Kb

Link to this post | posted 23 Mar, 2018 20:12

kaylafast

I've read the previous responses in this post, but still feel conflicted about the correct formatting for the complete notes and minimalistic files. I've been following the instructions in the online SEA-PHAGES Bioinformatics Guide under the tab "Documenting Your Annotation" and the cover sheet requirements.

For the Complete Notes File:
Attached is a screenshot of what my files looks like now. I have copied official functions to the function field because of the following line in the online guide, 'All functions are from the official SEA-PHAGES list and are written in the “Function field”. Functions do not have a hard return after them.' Is the "Function Field" the field/box in DNA Master or the "F" slot in the notes?

For the Minimal File:
Here I followed the instructions in the online guide section called "Final .dnam5 file: Minimal version". Following these steps filled the product field and leaves the function field and notes empty.

I'd appreciate help pointing out if there is anything that I should change.

Link to this post \| posted 24 Mar, 2018 18:19
dbolliva	In answer to your first question, the function field is indeed the field/box in DNA Master. Placing the function in this box is to make creation of the minimal file possible and straightforward. In essence the function is listed in two places, following the F in the notes box and in the function box. If you put functions directly into the product field, it will mess up the process of automatically adding Hypothetical Protein for all of the genes with no function as you create the minimal file. Your screenshot of the minimal file also looks right to me. It seems empty after the complete notes, but it makes the submission process easier. The new online version of the manual seems to have submitters do more than the older paper version of the bioinformatics manual. Edited 24 Mar, 2018 18:26

Link to this post | posted 24 Mar, 2018 18:19

dbolliva

In answer to your first question, the function field is indeed the field/box in DNA Master. Placing the function in this box is to make creation of the minimal file possible and straightforward. In essence the function is listed in two places, following the F in the notes box and in the function box. If you put functions directly into the product field, it will mess up the process of automatically adding Hypothetical Protein for all of the genes with no function as you create the minimal file.

Your screenshot of the minimal file also looks right to me. It seems empty after the complete notes, but it makes the submission process easier. The new online version of the manual seems to have submitters do more than the older paper version of the bioinformatics manual.

Edited 24 Mar, 2018 18:26

Link to this post \| posted 16 Dec, 2020 22:02
DrCatalase	Is it okay to have "hypothetical protein" in the function field of your your complete notes file? Thank you.

Link to this post \| posted 17 Dec, 2020 02:48
debbie	Dr. Catalase, Yes. Please use the validation function in DNA Master to do this when you renumber the genes. It is always best to let DNA Master auto-fill any field that you can debbie

Link to this post \| posted 17 Dec, 2020 15:12
DrCatalase	debbie Dr. Catalase, Yes. Please use the validation function in DNA Master to do this when you renumber the genes. It is always best to let DNA Master auto-fill any field that you can debbie Thank you.

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Filling in the Product field