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What are the automatic changes conducted by the tool during WIPO ST.25 import?

ST.25 numeric identifierTransformation performed by the tool

160

Discard element 160 (number of SEQ ID numbers)

170

Discard element 170 (Software used)

210

Element 210: set sequence identifier (SEQ ID)

n.a.

Set sequence name.

211

Set sequence length to value of <211>

212

Replace molecule type (i) 'ADN' with 'DNA', (ii) 'ARN' with 'RNA'

212

Replace molecule type 'PRT' with 'AA'

213

Replace ‘Artificial Sequence’ and specified equivalents with ‘synthetic construct’

213

Replace FR and DE translations of ‘Artificial Sequence’ and specified equivalents (‘Séquence artificielle’,  ‘Künstliche Sequenz’) with ‘synthetic construct’

213

Replace ‘Unknown’ and specified equivalents (see UC12, step 5) with ‘unidentified’

213

Replace FR and DE translations of ‘Unknown’ and specified equivalents (‘inconnu’, ‘unbekannt’) with ‘unidentified’

221

Replace obsolete feature key with recommended key (Scenario 8, ST.26, Annex VII)

221

Replace custom feature key with recommended key (Scenario 12, ST.26, Annex VII)

221

Replace VARSPLIC key with VAR_SEQ (Scenario 13, ST.26, Annex VII)

221

Skip transformation of feature key if 1) molecule type is PRT and 2) feature key is NOT valid ST.26 and 3) the tool can’t determine whether the location is a single position or a range of positions

222

Clean feature location value provided (i.e., remove parentheses, replace invalid separator, reduce redundant ranges)

222 (negative value)

If negative numbering in PRT sequence, the feature location need to be corrected (see Scenario 16, ST.26, Annex VII).

222 (missing)

Provide a warning that feature location is missing in import report OR does it provide a feature location of 1..sequence length 

223

Import value of 223 after replacing the obsolete feature key with recommended key (Scenario 8, ST.26, Annex VII)

223

Import value of 223 after replacing custom feature key with recommended key (Scenario 12, ST.26, Annex VII).

223

Import 223 after replacing VARSPLIC key with VAR_SEQ (Scenario 13, ST.26, Annex VII).

300-313

Discard publication information provided

400

Replace ‘u’ with ‘t’ in RNA sequence.

400

Replace ‘u’ with ‘t’ in DNA sequence.

400

Replace amino acid symbols in 3-letter code with 1-letter code.

400

Provide a warning that the annotation of 'Xaa' symbols must be reviewed in the import report

400

Set skipped indicator to ‘yes’ for those with a 400 value of '000'

n.a.

Create mandatory source/SOURCE feature for each sequence that: 1) is NOT intentionally skipped and 2) does NOT already have a source feature.

n.a.

Set value of qualifier /mol_type for ‘synthetic construct’ and protein sequences

n.a.

Notify the user to set the value of qualifier /mol_type.

n.a.

Notify the user to set/review the value of the mandatory qualifier

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