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Update all registry files (#32)
Updates all registry release files using linkml-map transforms. Co-authored-by: matentzn <matentzn@users.noreply.github.com>
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Lines changed: 68 additions & 55 deletions

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‎data/mapping-specifications.json‎

Lines changed: 68 additions & 55 deletions
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@@ -246,7 +246,7 @@
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},
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{
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"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_icd10cm.sssom.tsv",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"subject_source": {
@@ -284,7 +284,7 @@
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"id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
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"name": "Biomappings",
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"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.",
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"version": "0.6.1-dev-5d3d419d",
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"version": "0.6.1-dev-ed12b9f4",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/mesh_chebi_biomappings.sssom.tsv",
@@ -440,7 +440,7 @@
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},
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{
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"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"subject_source": {
@@ -480,31 +480,34 @@
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv",
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"license": "https://github.com/mapping-commons/mapping-commons.github.io/blob/main/docs/original_license_applies.md",
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"type": "sssom",
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"status": "fetch_error",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_1.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/monarch",
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"name": "Monarch Mapping Commons",
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"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
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}
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],
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"metadata_completeness_score": 0.0
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"status": "ok",
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"metadata_completeness_score": 0.2727
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv",
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"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.",
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"license": "http://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"status": "fetch_error",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loinc2chebi_2.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/monarch",
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"name": "Monarch Mapping Commons",
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"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
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}
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],
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"metadata_completeness_score": 0.0
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2cl.sssom.tsv",
@@ -524,31 +527,34 @@
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv",
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"license": "http://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"status": "fetch_error",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2go.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/monarch",
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"name": "Monarch Mapping Commons",
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"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
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}
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],
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"metadata_completeness_score": 0.0
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"status": "ok",
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"metadata_completeness_score": 0.2727
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv",
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"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.",
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"license": "http://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"status": "fetch_error",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncbitaxon.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/monarch",
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"name": "Monarch Mapping Commons",
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"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
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}
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],
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"metadata_completeness_score": 0.0
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2ncit.sssom.tsv",
@@ -567,31 +573,35 @@
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv",
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"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.",
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"license": "http://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"status": "fetch_error",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2pr.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/monarch",
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"name": "Monarch Mapping Commons",
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"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
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}
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],
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"metadata_completeness_score": 0.0
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv",
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"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.",
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"license": "http://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"status": "fetch_error",
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"content_url": "http://w3id.org/sssom/commons/monarch/mappings/loincpart2uberon.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/monarch",
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"name": "Monarch Mapping Commons",
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"url": "https://github.com/monarch-initiative/monarch-mapping-commons"
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}
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],
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"metadata_completeness_score": 0.0
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "cpath_obo_omop",
@@ -625,38 +635,6 @@
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "fars_obo_omop",
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"description": "C-Path generated mappings of OBO to OMOP terms: FARS COA",
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"license": "https://creativecommons.org/licenses/by-nc/4.0/",
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"type": "sssom",
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"content_url": "https://w3id.org/cpont/mappings/fars_obo_omop.cpath.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/cpont/mappings",
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"name": "C-Path Mapping Commons",
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"url": "https://gitlab.c-path.org/c-pathontology/mapping-commons"
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}
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],
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "fars_obo_omop_invert",
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"description": "Inversion of the C-Path generated OBO to OMOP mappings: FARS COA",
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"license": "https://creativecommons.org/licenses/by-nc/4.0/",
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"type": "sssom",
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"content_url": "https://w3id.org/cpont/mappings/fars_obo_omop_invert.cpath.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/cpont/mappings",
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"name": "C-Path Mapping Commons",
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"url": "https://gitlab.c-path.org/c-pathontology/mapping-commons"
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}
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],
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"status": "ok",
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"metadata_completeness_score": 0.3409
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},
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{
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"id": "https://doi.org/10.5281/zenodo.7250177",
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"version": "V1.5",
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},
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{
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"id": "http://purl.obolibrary.org/obo/mondo/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-09-01/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"version": "http://purl.obolibrary.org/obo/mondo/releases/2026-10-06/mappings/mondo_hasdbxref_hp.sssom.tsv",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"subject_source": {
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"id": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
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"name": "Biomappings",
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"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.",
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"version": "0.6.1-dev-5d3d419d",
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"version": "0.6.1-dev-ed12b9f4",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"content_url": "https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv",
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"status": "ok",
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"metadata_completeness_score": 0.3182
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},
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{
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"id": "https://github.com/biopragmatics/bioregistry/raw/refs/heads/main/exports/analyses/mapping_checking/mapping_embedding_similarities.tsv",
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"name": "Bioregistry Mapping Similarity Analysis",
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"license": "https://creativecommons.org/publicdomain/zero/1.0/",
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"type": "sssom",
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"content_url": "https://raw.githubusercontent.com/biopragmatics/bioregistry/refs/heads/main/exports/analyses/mapping_checking/mapping_embedding_similarities.sssom.tsv",
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"registries": [
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{
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"id": "https://github.com/biopragmatics/mapping-registry",
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"name": "Biopragmatics Mapping Registry",
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"url": "https://github.com/biopragmatics"
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}
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],
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"status": "ok",
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"metadata_completeness_score": 0.3182
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},
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{
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"id": "https://zenodo.org/records/15504009/files/mappings.sssom.tsv.gz",
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"content_url": "https://zenodo.org/records/15504009/files/mappings.sssom.tsv.gz",
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"status": "ok",
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"metadata_completeness_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/amr-portal.sssom.tsv",
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"description": "Manually curated antimicrobial name-to-ontology mappings from the AMR Portal",
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"license": "https://w3id.org/sssom/license/unspecified",
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"type": "sssom",
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"subject_source": {
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"id": "https://www.ebi.ac.uk/amr/"
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},
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"content_url": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/amr-portal.sssom.tsv",
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"registries": [
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{
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"id": "https://w3id.org/sssom/commons/ebi-text-mappings",
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"name": "EBI Text Mappings",
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"url": "https://github.com/mapping-commons/ebi-text-mappings"
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}
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],
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"status": "ok",
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"metadata_completeness_score": 0.3815
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},
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{
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"id": "https://raw.githubusercontent.com/mapping-commons/ebi-text-mappings/main/mappings/faang.sssom.tsv",
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"description": "FAANG project curated mappings",

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