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TITLE: FAIR Maturity Indicator MI-R1.3-324358ad68-IV-PROTEIN_IDENT_CONFIDENCE

Authors:

Ammar Ammar, ORCID:0000-0002-8399-8990

Publication Date: 2021-03-17

Last Edit: 2021-05-03

Accepted: pending

Maturity Indicator Identifier: MI-R1.3-324358ad68-IV-PROTEIN_IDENT_CONFIDENCE

This maturity indicator falls under the FAIR principle R1.3: (meta)data meet domain-relevant community standards

The ID of this MI is composed of the following segments (separated by hyphen):

  1. Acronym for "Maturity Indicator"
  2. The FAIR principle this maturity indicator belongs to
  3. The first 10 characters truncated from the SHA-256 hash of the primary reference DOI of this maturity indicator.
  4. A short name to distinguish the maturity indicator definition file

This MI is to indicate if "protein identification confidence" information is reported by the nano toxicity study data or not.

Maturity Indicator Name: The protein identification confidence information is reported by the nano toxicity study

This maturity indicator is extracted from the following paper Title: Best practice in reporting corona studies: minimum information about Nanomaterial Biocorona Experiments (MINBE) DOI: https://doi.org/10.1016/j.nantod.2019.06.004

To which principle does it apply?

R1.3

What is being measured?

If the protein identification confidence information is reported by the nano toxicity study data or not.

Why should we measure it?

Protein identification confidence inforamtion is important to report for corona characterization and to maximize the ability cross-comparison with other reported studies. Information to report: â?¢ % Coverage: The percentage of the protein sequence covered. â?¢ Number of peptides: Total number of peptides detected for each protein, ideally 2 or more peptides. â?¢ Number of unique peptides: Number of peptide sequences that are unique to the identified protein. â?¢ Missed cleavages: Number of missed cleavages in the protein or peptide sequence. â?¢ Protein probabilities and scores: Calculated probabilities or scores to give a sense of confidence in a protein identification.

What must be provided for the measurement?

If the value is measured and reported in the data, the following field(s) should appear in JSON-LD metadata:

Field Name Alternative terms
protein identification confidence protein_identification_confidence,
protein-identification-confidence

How is the measurement executed?

The "protein identification confidence" should be provided in a machine-readable format (JSON-LD) which can be queried using open universal protocol like HTTP.

What is/are considered valid result(s)?

The presence of the field "protein identification confidence" in the JSON-LD metadata means the measurement is reported which is the valid result.

For which digital resource(s) is this relevant? (or 'all')

For nano toxicity related datasets.

Examples of good practices (that would score well on this assessment)

{
 	"@context": {
 		"bs": "https://bioschemas.org/",
 		"schema": "https://schema.org/",
 		"citation": "schema:citation",
 		"name": "schema:name",
 		"url": "schema:url",
 		"variableMeasured": "schema:variableMeasured",
 		"unitText": "schema:unitText"
 	},
 	"@type": "schema:Dataset",
 	"name": "Dataset title",
 	"@id": "Dataset DOI",
 	"url": "Dataset URL",
 	"citation": "Dataset Citation/Publication",
 	"variableMeasured": [
 		{
 			"@type": "schema:PropertyValue",
 			"name": "protein identification confidence"
 		}
 	]
 }

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