Ticket #61 (closed enhancement: fixed)

Opened 4 years ago

Last modified 4 years ago

source_mat_id

Reported by: jdeck Owned by: pyilmaz
Priority: minor Component: MIxS general
Version: 4.0 Keywords:
Cc: Sensitive: no

Description

Current source_mat_id field definition is inconsistent with actual use. Here is a new definition for this term which will also obsolete ticket #58 (addition of materialSampleID term).

source_mat_id : A unique identifier assigned to a material sample (as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection provide additional context and suggested syntax for this identifier for data submitted to INSDC databases.

Change History

comment:1 Changed 4 years ago by jdeck

From Ramona Walls:

I am just readiing through this proposal to describe it in the BCO manuscript, and it seems that we have sort of lost the connection to OBI:material sample. I suggest that the revised definition for source_mat_id should make a reference to OBI material sample. Perhaps something like below (my change in italics):

source_mat_id:

A unique identifier assigned to a material sample (as defined by http://purl.obolibrary.org/obo/OBI_0000747, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection provide additional context and suggested syntax for this identifier for data submitted to INSDC databases.

comment:2 Changed 4 years ago by pyilmaz

  • Status changed from new to assigned

comment:3 Changed 4 years ago by jdeck

The source_mat_id term is a property and not a class and is more closely related to the DwC MaterialSampleID term proposed as part of the DwC Standard (http://rs.tdwg.org/dwc/terms/MaterialSampleID). Thus, it is more appropriate to change the "as defined by" from the OBI:MaterialSample URI to the DwC MaterialSampleID URI). The slightly revised definition for source_mat_id follows:

A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/MaterialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection provide additional context and suggested syntax for this identifier for data submitted to INSDC databases.

comment:4 Changed 4 years ago by pyilmaz

  • Status changed from assigned to closed
  • Resolution set to fixed

New definition agreed on 25-10-2013 Developer's call:

A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain “UAM:Herps:14”, referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/21547/R2).

Changes implemented in database

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