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This pull request addresses the following issue: #1404 The following changes are implemented: - Rename `eccode` prefix to `ec` - `preferred_prefix` is set to `EC` - Maintain `eccode` as a synonym - Update any instances of `provides: eccode` to `provides: ec` A few additional files that referenced `eccode` are updated to reflect this change as well. --------- Co-authored-by: Ben Gyori <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -11108,7 +11108,7 @@ | |
| ], | ||
| "uri_format": "http://www.brenda-enzymes.org/php/result_flat.php4?ecno=$1" | ||
| }, | ||
| "provides": "eccode", | ||
| "provides": "ec", | ||
| "publications": [ | ||
| { | ||
| "doi": "10.1016/j.jbiotec.2017.04.020", | ||
|
|
@@ -30923,97 +30923,7 @@ | |
| }, | ||
| "pattern": "^E(S|D)i\\d+-\\w$" | ||
| }, | ||
| "ecacc": { | ||
| "cellosaurus": { | ||
| "category": "Cell line collections (Providers)", | ||
| "homepage": "https://www.culturecollections.org.uk/about-us/ecacc/", | ||
| "name": "European Collection of Cell Cultures", | ||
| "prefix": "ECACC", | ||
| "uri_format": "https://www.culturecollections.org.uk/products/celllines/detail.jsp?refId=$1" | ||
| }, | ||
| "contributor": { | ||
| "email": "[email protected]", | ||
| "github": "cthoyt", | ||
| "name": "Charles Tapley Hoyt", | ||
| "orcid": "0000-0003-4423-4370" | ||
| }, | ||
| "description": "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).", | ||
| "example": "90062901", | ||
| "homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx", | ||
| "mappings": { | ||
| "cellosaurus": "ECACC" | ||
| }, | ||
| "name": "European Collection of Authenticated Cell Culture", | ||
| "pattern": "^\\d+$", | ||
| "uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1" | ||
| }, | ||
| "ecao": { | ||
| "aberowl": { | ||
| "description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).", | ||
| "download_owl": "http://aber-owl.net/media/ontologies/ECAO/4/ecao.owl", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ECAO" | ||
| }, | ||
| "bioportal": { | ||
| "contact": { | ||
| "email": "[email protected]", | ||
| "name": "Charles Ettensohn" | ||
| }, | ||
| "description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ECAO" | ||
| }, | ||
| "example": "0107180", | ||
| "mappings": { | ||
| "aberowl": "ECAO", | ||
| "bioportal": "ECAO", | ||
| "obofoundry": "ecao", | ||
| "ols": "ecao", | ||
| "ontobee": "ECAO" | ||
| }, | ||
| "obofoundry": { | ||
| "contact": "[email protected]", | ||
| "contact.github": "ettensohn", | ||
| "contact.label": "Charles Ettensohn", | ||
| "contact.orcid": "0000-0002-3625-0955", | ||
| "depends_on": [ | ||
| "cl", | ||
| "ro", | ||
| "uberon" | ||
| ], | ||
| "deprecated": false, | ||
| "description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).", | ||
| "domain": "anatomy and development", | ||
| "download.obo": "http://purl.obolibrary.org/obo/ecao.obo", | ||
| "download.owl": "http://purl.obolibrary.org/obo/ecao.owl", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "license": "CC BY 3.0", | ||
| "license.url": "http://creativecommons.org/licenses/by/3.0/", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "preferredPrefix": "ECAO", | ||
| "prefix": "ecao", | ||
| "repository": "https://github.com/echinoderm-ontology/ecao_ontology" | ||
| }, | ||
| "ols": { | ||
| "description": "None", | ||
| "download_owl": "http://purl.obolibrary.org/obo/ecao.owl", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "name": "Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ecao", | ||
| "version": "2024-08-22", | ||
| "version.iri": "http://purl.obolibrary.org/obo/ecao/releases/2024-08-22/ecao.owl" | ||
| }, | ||
| "ontobee": { | ||
| "library": "Library", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ECAO" | ||
| }, | ||
| "pattern": "^\\d{7}$", | ||
| "uri_format": "http://purl.obolibrary.org/obo/ECAO_$1" | ||
| }, | ||
| "eccode": { | ||
| "ec": { | ||
| "bartoc": { | ||
| "description": "By the late 1950's it had become evident that the nomenclature of enzymology, in the absence of any guiding authority, in a period when the number of known enzymes was increasing rapidly, was getting out of hand. The naming of enzymes by individual workers had proved far from satisfactory in practice. In many cases the same enzymes became known by several different names, while conversely the same name was sometimes given to different enzymes. Many of the names conveyed little or no idea of the nature of the reactions catalysed, and similar names were sometimes given to enzymes of quite different types. To meet this situation, various attempts to bring order into the general nomenclature of enzymes, or into that of particular groups of enzymes, were made by individuals or small groups of specialists, but none of the resulting nomenclatures met with general approval. (...) The Enzyme List in the sixth edition (1992) contains 3540 entries, of which 178 record enzymes which are now transferred elsewhere in the list, and 166 have been deleted completely. Thus the number of enzymes actually listed is 3196, an increase of 29% on the 1984 edition.", | ||
| "homepage": "https://www.abbexa.com/enzyme-commission-number", | ||
|
|
@@ -31180,6 +31090,7 @@ | |
| "prefix": "106" | ||
| }, | ||
| "pattern": "^\\d{1,2}(((\\.\\d{1,3}){1,3})|(\\.\\d+){2}\\.[nB]\\d{1,3}|\\.-\\.-\\.-|\\.\\d{1,3}\\.-\\.-|\\.\\d{1,3}\\.\\d{1,3}\\.-)?$", | ||
| "preferred_prefix": "EC", | ||
| "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", | ||
|
|
@@ -31228,6 +31139,7 @@ | |
| "ECCODE", | ||
| "EC_CODE", | ||
| "ec-code", | ||
| "eccode", | ||
| "intenz" | ||
| ], | ||
| "togoid": { | ||
|
|
@@ -31281,6 +31193,96 @@ | |
| "uri_format": "http://enzyme.expasy.org/EC/$1" | ||
| } | ||
| }, | ||
| "ecacc": { | ||
| "cellosaurus": { | ||
| "category": "Cell line collections (Providers)", | ||
| "homepage": "https://www.culturecollections.org.uk/about-us/ecacc/", | ||
| "name": "European Collection of Cell Cultures", | ||
| "prefix": "ECACC", | ||
| "uri_format": "https://www.culturecollections.org.uk/products/celllines/detail.jsp?refId=$1" | ||
| }, | ||
| "contributor": { | ||
| "email": "[email protected]", | ||
| "github": "cthoyt", | ||
| "name": "Charles Tapley Hoyt", | ||
| "orcid": "0000-0003-4423-4370" | ||
| }, | ||
| "description": "The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of Public Health England. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs).", | ||
| "example": "90062901", | ||
| "homepage": "https://www.phe-culturecollections.org.uk/collections/ecacc.aspx", | ||
| "mappings": { | ||
| "cellosaurus": "ECACC" | ||
| }, | ||
| "name": "European Collection of Authenticated Cell Culture", | ||
| "pattern": "^\\d+$", | ||
| "uri_format": "https://www.phe-culturecollections.org.uk/products/celllines/generalcell/detail.jsp?collection=ecacc_gc&refId=$1" | ||
| }, | ||
| "ecao": { | ||
| "aberowl": { | ||
| "description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).", | ||
| "download_owl": "http://aber-owl.net/media/ontologies/ECAO/4/ecao.owl", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ECAO" | ||
| }, | ||
| "bioportal": { | ||
| "contact": { | ||
| "email": "[email protected]", | ||
| "name": "Charles Ettensohn" | ||
| }, | ||
| "description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ECAO" | ||
| }, | ||
| "example": "0107180", | ||
| "mappings": { | ||
| "aberowl": "ECAO", | ||
| "bioportal": "ECAO", | ||
| "obofoundry": "ecao", | ||
| "ols": "ecao", | ||
| "ontobee": "ECAO" | ||
| }, | ||
| "obofoundry": { | ||
| "contact": "[email protected]", | ||
| "contact.github": "ettensohn", | ||
| "contact.label": "Charles Ettensohn", | ||
| "contact.orcid": "0000-0002-3625-0955", | ||
| "depends_on": [ | ||
| "cl", | ||
| "ro", | ||
| "uberon" | ||
| ], | ||
| "deprecated": false, | ||
| "description": "An ontology for the development and anatomy of the different species of the phylum Echinodermata (NCBITaxon:7586).", | ||
| "domain": "anatomy and development", | ||
| "download.obo": "http://purl.obolibrary.org/obo/ecao.obo", | ||
| "download.owl": "http://purl.obolibrary.org/obo/ecao.owl", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "license": "CC BY 3.0", | ||
| "license.url": "http://creativecommons.org/licenses/by/3.0/", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "preferredPrefix": "ECAO", | ||
| "prefix": "ecao", | ||
| "repository": "https://github.com/echinoderm-ontology/ecao_ontology" | ||
| }, | ||
| "ols": { | ||
| "description": "None", | ||
| "download_owl": "http://purl.obolibrary.org/obo/ecao.owl", | ||
| "homepage": "https://github.com/echinoderm-ontology/ecao_ontology", | ||
| "name": "Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ecao", | ||
| "version": "2024-08-22", | ||
| "version.iri": "http://purl.obolibrary.org/obo/ecao/releases/2024-08-22/ecao.owl" | ||
| }, | ||
| "ontobee": { | ||
| "library": "Library", | ||
| "name": "The Echinoderm Anatomy and Development Ontology", | ||
| "prefix": "ECAO" | ||
| }, | ||
| "pattern": "^\\d{7}$", | ||
| "uri_format": "http://purl.obolibrary.org/obo/ECAO_$1" | ||
| }, | ||
| "ecg": { | ||
| "aberowl": { | ||
| "description": "The Electrocardiography (ECG) Ontology is a Driving Biological Project of the NCBO. The ECG Ontology will contain terms for describing electrocardiograms, their capture method(s) and their waveforms.", | ||
|
|
@@ -62046,7 +62048,7 @@ | |
| }, | ||
| "name": "KEGG Enzyme", | ||
| "part_of": "kegg", | ||
| "provides": "eccode" | ||
| "provides": "ec" | ||
| }, | ||
| "kegg.genes": { | ||
| "biocontext": { | ||
|
|
@@ -103286,7 +103288,7 @@ | |
| ], | ||
| "uri_format": "http://sabiork.h-its.org/index2.jsp?EC=$1" | ||
| }, | ||
| "provides": "eccode", | ||
| "provides": "ec", | ||
| "publications": [ | ||
| { | ||
| "pubmed": "17822389", | ||
|
|
||
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