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Include transferred entries (but marked as obsolete) #187

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cmungall opened this issue Jun 4, 2024 · 0 comments
Open

Include transferred entries (but marked as obsolete) #187

cmungall opened this issue Jun 4, 2024 · 0 comments

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@cmungall
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cmungall commented Jun 4, 2024

In some cases, transferred entries are retained, but not marked as obsolete, and seem to have broken metadata:

https://enzyme.expasy.org/EC/3.4.4.17

Transferred entry: 3.4.21.103
Transferred entry: 3.4.23.20
Transferred entry: 3.4.23.21
Transferred entry: 3.4.23.22,3.4.23.23
Transferred entry: 3.4.23.24
Transferred entry: 3.4.23.25
Transferred entry: 3.4.23.26
Transferred entry: 3.4.23.28
Transferred entry: 3.4.23.29
Transferred entry: 3.4.23.30

curl -L -s https://w3id.org/biopragmatics/resources/eccode/eccode.obo | obo-grep.pl -r 3.4.4.17 --noheader -
[Term]
id: eccode:3.4.4.17
name: 3.4.23.30
is_a: eccode:3.4.4 ! Peptidyl peptide hydrolases

In other cases, the transferred entry is not there at all:

https://enzyme.expasy.org/EC/1.14.13.204

curl -L -s https://w3id.org/biopragmatics/resources/eccode/eccode.obo | obo-grep.pl -r 1.14.13.204 --noheader -
[nothing]

Note that in some cases, transferred entries do not propagate from enzyme-database to expasy until all swissprot annotations are transferred:

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