pha4ge/contextual_data_qc_tags

Standardized attributes for labelling sequence datasets with known quality control issues

contextual_data_qc_tags's Issues

NTR: add new field "quality control method description"

PHA4GE QC Contextual Data Tag Specification - New Term Request (NTR)

May request multiple terms in a single issue - delete the fields irrelevant to your request.

New Field(s)

Label: quality control method description
Definition/Description: The description of the method used to assess whether a sequence passed a predetermined quality control threshold.
Definition Source: Emma Griffiths
Synonyms or alternative labels:
Additional Comments (not an annotation): Some guidance should be added in any implementation spec that this differs from "quality control method name", which would simply be the name (some kind of simple label) of the method, procedure, pipeline, etc. Whereas this field would be a more lengthy, descriptive representation of the method e.g. in the case of multiple tools, processes, or manual calculations being used to determine data quality.

Picklist Item(s)

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Contributor Attribution: {Optional - ORCiD is preferred}
ORCID 0000-0002-1107-9135

NTR: Test issue template

PHA4GE QC Contextual Data Tag Specification - New Term Request (NTR)

May request multiple terms in a single issue - delete the fields irrelevant to your request.

New Field(s)

Label:
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):

Picklist Item(s)

Associated Field(s):
Parent Term:
Label:
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):

Contributor Attribution: {Optional - ORCiD is preferred}

NTR: new term "Frameshift detected" under qc issues

PHA4GE QC Contextual Data Tag Specification - New Term Request (NTR)

May request multiple terms in a single issue - delete the fields irrelevant to your request.

We're annotating some PHAC datasets for public repo upload and want to use the PHA4GE QC tags but some of the genomes in our datasets have detected frameshifts reducing the overall quality. There doesn't seem to be an appropriate term for frameshifts in the quality control issues field. I had a chat with Emma Griffiths and we think a new term is needed to tag such genomes, details can be viewed below.

New Field(s)

Label:
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):

Picklist Item(s)

Associated Field(s): quality control issues
Parent Term: Not Applicable
Label: Frameshift detected
Definition/Description: The identification of frameshift mutations resulting in reduced overall genome quality.
Definition Source (reference, website): Emma Griffiths
Synonyms or alternative labels: Not Applicable
Additional Comments: Not Applicable

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Contributor Attribution: {Optional - ORCiD is preferred}

Thanks!

NTR: Test Issue

PHA4GE QC Contextual Data Tag Specification - New Term Request (NTR)

May request multiple terms in a single issue - delete the fields irrelevant to your request.

New Field(s)

Label:
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):

Picklist Item(s)

Associated Field(s):
Parent Term:
Label:
Definition/Description:
Definition Source:
Synonyms or alternative labels:
Additional Comments (not an annotation):

Contributor Attribution: {Optional - ORCiD is preferred}