From 7ebf4d655bde627a5fadc239dece9b606d753936 Mon Sep 17 00:00:00 2001 From: matentzn Date: Thu, 15 Oct 2026 20:35:52 +0000 Subject: [PATCH] Update registry files --- data/mapping-specifications.json | 123 +++++++++++++++++-------------- 1 file changed, 68 insertions(+), 55 deletions(-) diff --git a/data/mapping-specifications.json b/data/mapping-specifications.json index 9c06d1d..77eede5 100644 --- a/data/mapping-specifications.json +++ b/data/mapping-specifications.json @@ -246,7 +246,7 @@ }, { "id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_icd10cm.sssom.tsv", - "version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_icd10cm.sssom.tsv", + "version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_icd10cm.sssom.tsv", "license": "https://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", "subject_source": { @@ -284,7 +284,7 @@ "id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv", "name": "Biomappings", "description": "Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings.", - "version": "0.6.1-dev-5d3d419d", + "version": "0.6.1-dev-ed12b9f4", "license": "https://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", "content_url": "http://w3id.org/sssom/commons/monarch/mappings/mesh_chebi_biomappings.sssom.tsv", @@ -440,7 +440,7 @@ }, { "id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv", - "version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_hp.sssom.tsv", + "version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_hp.sssom.tsv", "license": "https://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", "subject_source": { @@ -480,9 +480,9 @@ }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv", - "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv", + "license": "https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md", "type": "sssom", - "status": "fetch_error", + "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv", "registries": [ { "id": "https://w3id.org/sssom/commons/monarch", @@ -490,13 +490,15 @@ "url": "https://github.com/monarch-initiative/monarch-mapping-commons" } ], - "metadata_completeness_score": 0.0 + "status": "ok", + "metadata_completeness_score": 0.2727 }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv", - "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv", + "description": "LOINC part to ChEBI mappings. Parts carrying a '^' qualifier denote a measurement context (timing, specimen order, posture, challenge protocol) applied to the same underlying entity; these are asserted as skos:broadMatch, since the LOINC part is narrower than the ontology concept. Unqualified parts use skos:exactMatch. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.", + "license": "http://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", - "status": "fetch_error", + "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv", "registries": [ { "id": "https://w3id.org/sssom/commons/monarch", @@ -504,7 +506,8 @@ "url": "https://github.com/monarch-initiative/monarch-mapping-commons" } ], - "metadata_completeness_score": 0.0 + "status": "ok", + "metadata_completeness_score": 0.3409 }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2cl.sssom.tsv", @@ -524,9 +527,9 @@ }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv", - "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv", + "license": "http://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", - "status": "fetch_error", + "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv", "registries": [ { "id": "https://w3id.org/sssom/commons/monarch", @@ -534,13 +537,15 @@ "url": "https://github.com/monarch-initiative/monarch-mapping-commons" } ], - "metadata_completeness_score": 0.0 + "status": "ok", + "metadata_completeness_score": 0.2727 }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv", - "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv", + "description": "LOINC part to NCBI Taxon mappings. Parts carrying a '^' qualifier denote a measurement context (timing, specimen order, posture, challenge protocol) applied to the same underlying entity; these are asserted as skos:broadMatch, since the LOINC part is narrower than the ontology concept. Unqualified parts use skos:exactMatch. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.", + "license": "http://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", - "status": "fetch_error", + "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv", "registries": [ { "id": "https://w3id.org/sssom/commons/monarch", @@ -548,7 +553,8 @@ "url": "https://github.com/monarch-initiative/monarch-mapping-commons" } ], - "metadata_completeness_score": 0.0 + "status": "ok", + "metadata_completeness_score": 0.3409 }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncit.sssom.tsv", @@ -567,9 +573,10 @@ }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv", - "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv", + "description": "LOINC part to Protein Ontology mappings. Parts carrying a '^' qualifier denote a measurement context (timing, specimen order, posture, challenge protocol) applied to the same underlying entity; these are asserted as skos:broadMatch, since the LOINC part is narrower than the ontology concept. Unqualified parts use skos:exactMatch. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.", + "license": "http://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", - "status": "fetch_error", + "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv", "registries": [ { "id": "https://w3id.org/sssom/commons/monarch", @@ -577,13 +584,15 @@ "url": "https://github.com/monarch-initiative/monarch-mapping-commons" } ], - "metadata_completeness_score": 0.0 + "status": "ok", + "metadata_completeness_score": 0.3409 }, { "id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv", - "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv", + "description": "This mapping set contains mappings between LOINC parts and Uberon anatomical entities. The predicate revision on qualified parts was applied programmatically; the underlying subject-object mappings are the original manual curation.", + "license": "http://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", - "status": "fetch_error", + "content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv", "registries": [ { "id": "https://w3id.org/sssom/commons/monarch", @@ -591,7 +600,8 @@ "url": "https://github.com/monarch-initiative/monarch-mapping-commons" } ], - "metadata_completeness_score": 0.0 + "status": "ok", + "metadata_completeness_score": 0.3409 }, { "id": "cpath_obo_omop", @@ -625,38 +635,6 @@ "status": "ok", "metadata_completeness_score": 0.3409 }, - { - "id": "fars_obo_omop", - "description": "C-Path generated mappings of OBO to OMOP terms: FARS COA", - "license": "https://creativecommons.org/licenses/by-nc/4.0/", - "type": "sssom", - "content_url": "https://w3id.org/cpont/mappings/fars_obo_omop.cpath.sssom.tsv", - "registries": [ - { - "id": "https://w3id.org/cpont/mappings", - "name": "C-Path Mapping Commons", - "url": "https://gitlab.c-path.org/c-pathontology/mapping-commons" - } - ], - "status": "ok", - "metadata_completeness_score": 0.3409 - }, - { - "id": "fars_obo_omop_invert", - "description": "Inversion of the C-Path generated OBO to OMOP mappings: FARS COA", - "license": "https://creativecommons.org/licenses/by-nc/4.0/", - "type": "sssom", - "content_url": "https://w3id.org/cpont/mappings/fars_obo_omop_invert.cpath.sssom.tsv", - "registries": [ - { - "id": "https://w3id.org/cpont/mappings", - "name": "C-Path Mapping Commons", - "url": "https://gitlab.c-path.org/c-pathontology/mapping-commons" - } - ], - "status": "ok", - "metadata_completeness_score": 0.3409 - }, { "id": "https://doi.org/10.5281/zenodo.7250177", "version": "V1.5", @@ -707,7 +685,7 @@ }, { "id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv", - "version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_hp.sssom.tsv", + "version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_hp.sssom.tsv", "license": "https://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", "subject_source": { @@ -728,7 +706,7 @@ "id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv", "name": "Biomappings", "description": "Biomappings is a repository of community curated and predicted equivalences and related mappings between named biological entities that are not available from primary sources. It's also a place where anyone can contribute curations of predicted mappings or their own novel mappings.", - "version": "0.6.1-dev-5d3d419d", + "version": "0.6.1-dev-ed12b9f4", "license": "https://creativecommons.org/publicdomain/zero/1.0/", "type": "sssom", "content_url": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv", @@ -758,6 +736,22 @@ "status": "ok", "metadata_completeness_score": 0.3182 }, + { + "id": "https://github.com/biopragmatics/bioregistry/raw/refs/heads/main/exports/analyses/mapping_checking/mapping_embedding_similarities.tsv", + "name": "Bioregistry Mapping Similarity Analysis", + "license": "https://creativecommons.org/publicdomain/zero/1.0/", + "type": "sssom", + "content_url": "https://raw.githubusercontent.com/biopragmatics/bioregistry/refs/heads/main/exports/analyses/mapping_checking/mapping_embedding_similarities.sssom.tsv", + "registries": [ + { + "id": "https://github.com/biopragmatics/mapping-registry", + "name": "Biopragmatics Mapping Registry", + "url": "https://github.com/biopragmatics" + } + ], + "status": "ok", + "metadata_completeness_score": 0.3182 + }, { "id": "https://zenodo.org/records/15504009/files/mappings.sssom.tsv.gz", "content_url": "https://zenodo.org/records/15504009/files/mappings.sssom.tsv.gz", @@ -1298,6 +1292,25 @@ "status": "ok", "metadata_completeness_score": 0.3815 }, + { + "id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/amr-portal.sssom.tsv", + "description": "Manually curated antimicrobial name-to-ontology mappings from the AMR Portal", + "license": "https://w3id.org/sssom/license/unspecified", + "type": "sssom", + "subject_source": { + "id": "https://www.ebi.ac.uk/amr/" + }, + "content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/amr-portal.sssom.tsv", + "registries": [ + { + "id": "https://w3id.org/sssom/commons/ebi-text-mappings", + "name": "EBI Text Mappings", + "url": "https://github.com/mapping-commons/ebi-text-mappings" + } + ], + "status": "ok", + "metadata_completeness_score": 0.3815 + }, { "id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/faang.sssom.tsv", "description": "FAANG project curated mappings",