Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update ECCODE pattern to allow optional dashes #1396

Merged
merged 4 commits into from
Feb 3, 2025
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 18 additions & 3 deletions src/bioregistry/data/bioregistry.json
Original file line number Diff line number Diff line change
Expand Up @@ -31023,12 +31023,14 @@
"biocontext": {
"prefix": "EC-CODE"
},
"comment": "The Nomenclature Committee website does not yet contain an official policy regarding the use of dashes in the hierarchical categorization of enzymes, so the Bioregistry's regular expression is permissive and accepts both EC identifiers with dashes (e.g. <code>2.3.-.-</code>) and without dashes (e.g., <code>2.3</code>). This means you may have to do post-processing of EC identifiers in data integration scenarios.",
"contact": {
"email": "[email protected]",
"github": "kaxelsen",
"name": "Kristian Axelsen",
"orcid": "0000-0003-3889-2879"
},
"description": "The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories.\n\nThe Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).\n\nThere are few notable resources providing access to the Enzyme Nomenclature:\n\n<table class=\"table table-striped\"><thead><tr><th>Website</td><th>Homepage</td><th>Notes</td></tr></thead><tbody><tr><td>ExplorEnz</td><td>https://www.enzyme-database.org</td><td>This is the resources officially recommended by IUBMB</td></tr><tr><td>IUBMB (via by Queen Mary)</td><td>https://iubmb.qmul.ac.uk/enzyme</td><td>This is a web-based version of the <a href=\"https://archive.org/details/enzymenomenclatu0000inte_d6c2\">1992 publication</a>.</td></tr><tr><td>IntEnz</td><td>https://www.ebi.ac.uk/intenz</td><td></td></tr><tr><td>ExPaSy</td><td>https://enzyme.expasy.org</td><td></td></tr></tbody></table>",
"edam": {
"description": "An Enzyme Commission (EC) number of an enzyme.",
"name": "EC number",
Expand All @@ -31043,12 +31045,18 @@
"2.3.n1",
"2.3.1.",
"2.3.1.n",
"2.3.4.1."
"2.3.4.1.",
"2.-.-",
"2.-",
"2.3.4.1.-"
],
"example_extras": [
"2",
"2.3",
"2.3.1",
"2.-.-.-",
"2.3.-.-",
"2.3.1.-",
"2.3.1.n12",
"3.1.26.n2",
"3.4.24.B15"
Expand Down Expand Up @@ -31153,7 +31161,14 @@
"prefix": "ec-code",
"uri_format": "https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=$1"
},
"name": "Enzyme Commission Code",
"name": "Enzyme Nomenclature",
"owners": [
{
"name": "International Union of Biochemistry and Molecular Biology",
"partnered": false,
"ror": "00910ay07"
}
],
"pathguide": {
"abbreviation": "IntEnz",
"homepage": "http://www.ebi.ac.uk/intenz/index.html",
Expand All @@ -31163,7 +31178,7 @@
"name": "Integrated relational Enzyme database",
"prefix": "106"
},
"pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.[nB]\\d{1,3})?$",
"pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.[nB]\\d{1,3}|\\.-\\.-\\.-|\\.\\d{1,3}\\.-\\.-|\\.\\d{1,3}\\.\\d{1,3}\\.-)?$",
"prefixcommons": {
"description": "IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.",
"example": "17854",
Expand Down