-
-
Notifications
You must be signed in to change notification settings - Fork 53
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Fix issues with MIRIAM alignment (#707)
Two issues came up related to recent changes: 1. `miriam:gramene.growthstage` was renamed to `miriam:gro`. This now conflicts with `gro` which is reserved for the Gene Regulation Ontology, so a mismatch was curated and the metaregistry links in the `bioregistry:gramene.growthstage` record was updated 2. `miriam:tair.name` was added, this is equivalent to `bioregistry:araport`. This is the first situation (I think) when Identifiers.org has added a prefix that was a duplicate of something novel in the Bioregistry but didn't have the same prefix. I'm not sure how often this will happen in the future so I'm not sure if this kind of problem needs addressing in the alignment code.
- Loading branch information
Showing
6 changed files
with
22,454 additions
and
22,302 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -2959,9 +2959,22 @@ | |
| "description": "Website with general information about Arabidopsis and functionalities such as a genomic viewer", | ||
| "homepage": "https://www.araport.org/", | ||
| "mappings": { | ||
| "miriam": "tair.name", | ||
| "ncbi": "Araport", | ||
| "uniprot": "DB-0221" | ||
| }, | ||
| "miriam": { | ||
| "deprecated": false, | ||
| "description": "The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The name of a Locus is unique and used by TAIR, TIGR, and MIPS.", | ||
| "homepage": "https://www.arabidopsis.org/index.jsp", | ||
| "id": "00000976", | ||
| "name": "TAIR gene name", | ||
| "namespaceEmbeddedInLui": false, | ||
| "pattern": "^AT.G[0-9]{5}$", | ||
| "prefix": "tair.name", | ||
| "sampleId": "AT5G05330", | ||
| "uri_format": "https://www.arabidopsis.org/servlets/TairObject?type=locus&name=$1" | ||
| }, | ||
| "name": "Arabidopsis Information Portal", | ||
| "ncbi": { | ||
| "example": "AT1G01010", | ||
|
|
@@ -3151,7 +3164,7 @@ | |
| "namespaceEmbeddedInLui": true, | ||
| "pattern": "^(ark\\:)/*[0-9A-Za-z]+(?:/[\\w/.=*+@\\$-]*)?(?:\\?.*)?$", | ||
| "prefix": "ark", | ||
| "sampleId": "/12345/fk1234", | ||
| "sampleId": "/87924/r4154jq8h", | ||
| "uri_format": "http://n2t.net/ark:$1" | ||
| }, | ||
| "n2t": { | ||
|
|
@@ -7892,7 +7905,7 @@ | |
| "id": "00000694", | ||
| "name": "BioStudies database", | ||
| "namespaceEmbeddedInLui": false, | ||
| "pattern": "^S-[A-Z]{4}[A-Z\\d\\-]+$", | ||
| "pattern": "^S-[A-Z]{4}[\\-\\_A-Z\\d]+$", | ||
| "prefix": "biostudies", | ||
| "sampleId": "S-EPMC6266652", | ||
| "uri_format": "https://www.ebi.ac.uk/biostudies/studies/$1" | ||
|
|
@@ -10575,7 +10588,7 @@ | |
| "id": "00000234", | ||
| "name": "Cell Cycle Ontology", | ||
| "namespaceEmbeddedInLui": true, | ||
| "pattern": "^CCO\\:\\w+$", | ||
| "pattern": "^CCO:\\w+$", | ||
| "prefix": "cco", | ||
| "sampleId": "0000003", | ||
| "uri_format": "https://www.ebi.ac.uk/ols/ontologies/cco/terms?obo_id=CCO:$1" | ||
|
|
@@ -13915,6 +13928,23 @@ | |
| ], | ||
| "uri_format": "http://classyfire.wishartlab.com/tax_nodes/C$1" | ||
| }, | ||
| "clb": { | ||
| "mappings": { | ||
| "miriam": "clb" | ||
| }, | ||
| "miriam": { | ||
| "deprecated": false, | ||
| "description": "ChecklistBank is an index and repository for taxonomic and nomenclatural datasets", | ||
| "homepage": "https://www.checklistbank.org", | ||
| "id": "00000964", | ||
| "name": "ChecklistBank", | ||
| "namespaceEmbeddedInLui": false, | ||
| "pattern": "^[0-9]+(LR)?$", | ||
| "prefix": "clb", | ||
| "sampleId": "1010", | ||
| "uri_format": "https://www.checklistbank.org/dataset/$1" | ||
| } | ||
| }, | ||
| "cldb": { | ||
| "biocontext": { | ||
| "is_identifiers": true, | ||
|
|
@@ -16841,6 +16871,32 @@ | |
| "no_own_terms": true, | ||
| "repository": "https://github.com/MIT-LCP/mimic-omop" | ||
| }, | ||
| "col": { | ||
| "mappings": { | ||
| "miriam": "col" | ||
| }, | ||
| "miriam": { | ||
| "deprecated": false, | ||
| "description": "Identifier of a taxon or synonym in the Catalogue of Life", | ||
| "homepage": "https://www.checklistbank.org", | ||
| "id": "00000969", | ||
| "name": "Catalogue of Life", | ||
| "namespaceEmbeddedInLui": false, | ||
| "pattern": "^[23456789BCDFGHJKLMNPQRSTVWXYZ]{1,6}$", | ||
| "prefix": "col", | ||
| "providers": [ | ||
| { | ||
| "code": "col", | ||
| "description": "The Catalogue of Life website providing a view onto the latest release of the COL Checklist.", | ||
| "homepage": "https://www.catalogueoflife.org", | ||
| "name": "Catalogue of Life (COL)", | ||
| "uri_format": "https://www.catalogueoflife.org/data/taxon/$1" | ||
| } | ||
| ], | ||
| "sampleId": "4QHKG", | ||
| "uri_format": "https://www.checklistbank.org/dataset/3LR/taxon/$1" | ||
| } | ||
| }, | ||
| "col.taiwan": { | ||
| "contributor": { | ||
| "email": "[email protected]", | ||
|
|
@@ -38105,7 +38161,7 @@ | |
| "mappings": { | ||
| "biocontext": "GRAMENE.GROWTHSTAGE", | ||
| "bioportal": "GRO-CPGA", | ||
| "miriam": "gramene.growthstage", | ||
| "miriam": "gro", | ||
| "n2t": "gramene.growthstage", | ||
| "obofoundry": "gro", | ||
| "prefixcommons": "gramene.po" | ||
|
|
@@ -38117,8 +38173,8 @@ | |
| "id": "00000508", | ||
| "name": "Gramene Growth Stage Ontology", | ||
| "namespaceEmbeddedInLui": true, | ||
| "pattern": "^GRO\\:\\d+$", | ||
| "prefix": "gramene.growthstage", | ||
| "pattern": "^GRO:\\d+$", | ||
| "prefix": "gro", | ||
| "sampleId": "0007133", | ||
| "uri_format": "http://www.gramene.org/db/ontology/search?id=GRO:$1" | ||
| }, | ||
|
|
@@ -53377,7 +53433,7 @@ | |
| "prefixcommons": "aclame" | ||
| }, | ||
| "miriam": { | ||
| "deprecated": false, | ||
| "deprecated": true, | ||
| "description": "ACLAME is a database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.", | ||
| "homepage": "http://aclame.ulb.ac.be/", | ||
| "id": "00000063", | ||
|
|
@@ -64624,7 +64680,7 @@ | |
| "namespaceEmbeddedInLui": true, | ||
| "pattern": "^HOG:[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", | ||
| "prefix": "oma.hog", | ||
| "sampleId": "HOG:0459895", | ||
| "sampleId": "0459895", | ||
| "uri_format": "https://omabrowser.org/oma/hog/resolve/HOG:$1/" | ||
| }, | ||
| "pattern": "^[0-9]{7}(\\.[0-9a-z.]+)?(_[0-9]+)?$", | ||
|
|
@@ -81363,6 +81419,23 @@ | |
| "name": "Scholia Registry", | ||
| "uri_format": "https://bioregistry.io/metaregistry/scholia/$1" | ||
| }, | ||
| "sciflection": { | ||
| "mappings": { | ||
| "miriam": "sciflection" | ||
| }, | ||
| "miriam": { | ||
| "deprecated": false, | ||
| "description": "Sciflection is a public repository for experiments and associated spectra, usually uploaded from Electronic Lab Notebooks, shared under FAIR conditions", | ||
| "homepage": "https://sciformation.com/sciflection.html", | ||
| "id": "00000973", | ||
| "name": "Sciflection", | ||
| "namespaceEmbeddedInLui": false, | ||
| "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$", | ||
| "prefix": "sciflection", | ||
| "sampleId": "5ede4273-b26c-4ea4-adb7-3ce294ab3397", | ||
| "uri_format": "https://sciflection.com/$1" | ||
| } | ||
| }, | ||
| "scomp": { | ||
| "contributor": { | ||
| "email": "[email protected]", | ||
|
|
@@ -83656,6 +83729,23 @@ | |
| "pattern": "^SKIP\\d+$", | ||
| "uri_format": "https://skip.stemcellinformatics.org/SKIPSearch/cell_line_detail?accession=$1" | ||
| }, | ||
| "skm": { | ||
| "mappings": { | ||
| "miriam": "skm" | ||
| }, | ||
| "miriam": { | ||
| "deprecated": false, | ||
| "description": "Stress Knowledge Map (SKM, available at https://skm.nib.si) is a knowledge graph resulting from the integration of dispersed published information on plant molecular responses to biotic and abiotic stressors. ", | ||
| "homepage": "http://www.nib.si/eng/", | ||
| "id": "00000968", | ||
| "name": "Stress Knowledge Map", | ||
| "namespaceEmbeddedInLui": false, | ||
| "pattern": "^rx[0-9]{5}$", | ||
| "prefix": "skm", | ||
| "sampleId": "rx00408", | ||
| "uri_format": "https://skm.nib.si/api/pss/reactions?reaction_id=$1&return_field=summary" | ||
| } | ||
| }, | ||
| "skos": { | ||
| "aberowl": { | ||
| "description": "This file is imported by vivo-core-1.5.owl. It contains terms relating to concepts from the http://www.w3.org/2004/02/skos/core# namespace of the SKOS (Simple Knowledge Organization System) ontology that are included in the vivo ontology.", | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.